-- dump date 20120504_135121 -- class Genbank::misc_feature -- table misc_feature_note -- id note 340100000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 340100000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 340100000003 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 340100000004 Walker A motif; other site 340100000005 ATP binding site [chemical binding]; other site 340100000006 Walker B motif; other site 340100000007 arginine finger; other site 340100000008 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 340100000009 DnaA box-binding interface [nucleotide binding]; other site 340100000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 340100000011 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 340100000012 putative DNA binding surface [nucleotide binding]; other site 340100000013 dimer interface [polypeptide binding]; other site 340100000014 beta-clamp/clamp loader binding surface; other site 340100000015 beta-clamp/translesion DNA polymerase binding surface; other site 340100000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 340100000017 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 340100000018 ATP binding site [chemical binding]; other site 340100000019 Mg2+ binding site [ion binding]; other site 340100000020 G-X-G motif; other site 340100000021 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 340100000022 anchoring element; other site 340100000023 dimer interface [polypeptide binding]; other site 340100000024 ATP binding site [chemical binding]; other site 340100000025 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 340100000026 active site 340100000027 putative metal-binding site [ion binding]; other site 340100000028 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 340100000029 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100000030 HipA N-terminal domain; Region: Couple_hipA; cl11853 340100000031 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100000032 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100000033 Isochorismatase family; Region: Isochorismatase; pfam00857 340100000034 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 340100000035 catalytic triad [active] 340100000036 dimer interface [polypeptide binding]; other site 340100000037 conserved cis-peptide bond; other site 340100000038 Pirin-related protein [General function prediction only]; Region: COG1741 340100000039 Cupin domain; Region: Cupin_2; cl09118 340100000040 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 340100000041 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100000042 Helix-turn-helix domains; Region: HTH; cl00088 340100000043 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 340100000044 putative effector binding pocket; other site 340100000045 putative dimerization interface [polypeptide binding]; other site 340100000046 AAA domain; Region: AAA_26; pfam13500 340100000047 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100000048 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 340100000049 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 340100000050 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100000051 catalytic residue [active] 340100000052 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 340100000053 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 340100000054 inhibitor-cofactor binding pocket; inhibition site 340100000055 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000056 catalytic residue [active] 340100000057 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 340100000058 active site 340100000059 Acylphosphatase; Region: Acylphosphatase; cl00551 340100000060 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 340100000061 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340100000062 phosphate binding site [ion binding]; other site 340100000063 GAF domain; Region: GAF; cl15785 340100000064 LytTr DNA-binding domain; Region: LytTR; cl04498 340100000065 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100000066 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 340100000067 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100000068 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 340100000069 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100000070 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 340100000071 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 340100000072 putative ligand binding site [chemical binding]; other site 340100000073 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 340100000074 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000075 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 340100000076 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 340100000077 NADH(P)-binding; Region: NAD_binding_10; pfam13460 340100000078 NAD binding site [chemical binding]; other site 340100000079 putative active site [active] 340100000080 substrate binding site [chemical binding]; other site 340100000081 TIR domain; Region: TIR_2; cl15770 340100000082 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 340100000083 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 340100000084 SET domain; Region: SET; cl02566 340100000085 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100000086 Helix-turn-helix domains; Region: HTH; cl00088 340100000087 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 340100000088 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100000089 PYR/PP interface [polypeptide binding]; other site 340100000090 dimer interface [polypeptide binding]; other site 340100000091 TPP binding site [chemical binding]; other site 340100000092 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100000093 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 340100000094 TPP-binding site [chemical binding]; other site 340100000095 dimer interface [polypeptide binding]; other site 340100000096 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100000097 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100000098 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000099 NMT1-like family; Region: NMT1_2; cl15260 340100000100 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100000101 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 340100000102 substrate binding site [chemical binding]; other site 340100000103 oxyanion hole (OAH) forming residues; other site 340100000104 trimer interface [polypeptide binding]; other site 340100000105 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000106 Helix-turn-helix domains; Region: HTH; cl00088 340100000107 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100000108 dimerization interface [polypeptide binding]; other site 340100000109 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100000110 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 340100000111 NAD(P) binding site [chemical binding]; other site 340100000112 catalytic residues [active] 340100000113 catalytic residues [active] 340100000114 gluconate 5-dehydrogenase; Provisional; Region: PRK06124 340100000115 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000116 NAD(P) binding site [chemical binding]; other site 340100000117 active site 340100000118 DNA topoisomerase III; Validated; Region: PRK08173 340100000119 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 340100000120 active site 340100000121 putative interdomain interaction site [polypeptide binding]; other site 340100000122 putative metal-binding site [ion binding]; other site 340100000123 putative nucleotide binding site [chemical binding]; other site 340100000124 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 340100000125 domain I; other site 340100000126 DNA binding groove [nucleotide binding] 340100000127 phosphate binding site [ion binding]; other site 340100000128 domain II; other site 340100000129 domain III; other site 340100000130 nucleotide binding site [chemical binding]; other site 340100000131 catalytic site [active] 340100000132 domain IV; other site 340100000133 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 340100000134 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 340100000135 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 340100000136 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 340100000137 GDYXXLXY protein; Region: GDYXXLXY; cl02066 340100000138 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100000139 S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic...; Region: S15_NS1_EPRS_RNA-bind; cl00349 340100000140 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100000141 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100000142 active site 340100000143 HIGH motif; other site 340100000144 nucleotide binding site [chemical binding]; other site 340100000145 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100000146 active site 340100000147 KMSKS motif; other site 340100000148 Protein of unknown function (DUF494); Region: DUF494; cl01103 340100000149 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100000150 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 340100000151 NMT1-like family; Region: NMT1_2; cl15260 340100000152 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 340100000153 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 340100000154 dimer interface [polypeptide binding]; other site 340100000155 active site 340100000156 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100000157 substrate binding site [chemical binding]; other site 340100000158 catalytic residue [active] 340100000159 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 340100000160 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 340100000161 inhibitor-cofactor binding pocket; inhibition site 340100000162 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000163 catalytic residue [active] 340100000164 acyl-CoA synthetase; Validated; Region: PRK08162 340100000165 AMP-binding enzyme; Region: AMP-binding; cl15778 340100000166 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100000167 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 340100000168 Phosphotransferase enzyme family; Region: APH; pfam01636 340100000169 putative active site [active] 340100000170 putative substrate binding site [chemical binding]; other site 340100000171 ATP binding site [chemical binding]; other site 340100000172 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100000173 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100000174 active site 340100000175 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000176 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100000177 NAD(P) binding site [chemical binding]; other site 340100000178 active site 340100000179 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100000180 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000181 NMT1-like family; Region: NMT1_2; cl15260 340100000182 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000183 CoA-ligase; Region: Ligase_CoA; cl02894 340100000184 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100000185 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000186 NMT1-like family; Region: NMT1_2; cl15260 340100000187 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100000188 thiolase; Provisional; Region: PRK06158 340100000189 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100000190 active site 340100000191 Helix-turn-helix domains; Region: HTH; cl00088 340100000192 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100000193 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100000194 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 340100000195 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100000196 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100000197 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 340100000198 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 340100000199 carboxyltransferase (CT) interaction site; other site 340100000200 biotinylation site [posttranslational modification]; other site 340100000201 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 340100000202 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340100000203 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340100000204 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 340100000205 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 340100000206 dimer interface [polypeptide binding]; other site 340100000207 active site 340100000208 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 340100000209 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 340100000210 isovaleryl-CoA dehydrogenase; Region: PLN02519 340100000211 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 340100000212 substrate binding site [chemical binding]; other site 340100000213 FAD binding site [chemical binding]; other site 340100000214 catalytic base [active] 340100000215 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100000216 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100000217 metal binding site [ion binding]; metal-binding site 340100000218 putative dimer interface [polypeptide binding]; other site 340100000219 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000220 NMT1-like family; Region: NMT1_2; cl15260 340100000221 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 340100000222 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 340100000223 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 340100000224 DNA binding residues [nucleotide binding] 340100000225 putative dimer interface [polypeptide binding]; other site 340100000226 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100000227 LysE type translocator; Region: LysE; cl00565 340100000228 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 340100000229 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 340100000230 homodimer interface [polypeptide binding]; other site 340100000231 substrate-cofactor binding pocket; other site 340100000232 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000233 catalytic residue [active] 340100000234 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 340100000235 catalytic residues [active] 340100000236 hinge region; other site 340100000237 alpha helical domain; other site 340100000238 Sporulation related domain; Region: SPOR; cl10051 340100000239 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 340100000240 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 340100000241 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 340100000242 active site 340100000243 HIGH motif; other site 340100000244 KMSK motif region; other site 340100000245 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 340100000246 tRNA binding surface [nucleotide binding]; other site 340100000247 anticodon binding site; other site 340100000248 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 340100000249 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 340100000250 dimer interface [polypeptide binding]; other site 340100000251 conserved gate region; other site 340100000252 putative PBP binding loops; other site 340100000253 ABC-ATPase subunit interface; other site 340100000254 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 340100000255 dimer interface [polypeptide binding]; other site 340100000256 conserved gate region; other site 340100000257 putative PBP binding loops; other site 340100000258 ABC-ATPase subunit interface; other site 340100000259 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100000260 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100000261 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 340100000262 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 340100000263 Walker A/P-loop; other site 340100000264 ATP binding site [chemical binding]; other site 340100000265 Q-loop/lid; other site 340100000266 ABC transporter signature motif; other site 340100000267 Walker B; other site 340100000268 D-loop; other site 340100000269 H-loop/switch region; other site 340100000270 TOBE domain; Region: TOBE_2; cl01440 340100000271 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 340100000272 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100000273 active site 340100000274 metal binding site [ion binding]; metal-binding site 340100000275 hexamer interface [polypeptide binding]; other site 340100000276 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 340100000277 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100000278 Walker A/P-loop; other site 340100000279 ATP binding site [chemical binding]; other site 340100000280 Q-loop/lid; other site 340100000281 ABC transporter signature motif; other site 340100000282 Walker B; other site 340100000283 D-loop; other site 340100000284 H-loop/switch region; other site 340100000285 TOBE domain; Region: TOBE_2; cl01440 340100000286 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 340100000287 dimer interface [polypeptide binding]; other site 340100000288 conserved gate region; other site 340100000289 putative PBP binding loops; other site 340100000290 ABC-ATPase subunit interface; other site 340100000291 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100000292 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 340100000293 dimer interface [polypeptide binding]; other site 340100000294 conserved gate region; other site 340100000295 putative PBP binding loops; other site 340100000296 ABC-ATPase subunit interface; other site 340100000297 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100000298 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 340100000299 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100000300 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100000301 DNA binding site [nucleotide binding] 340100000302 domain linker motif; other site 340100000303 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100000304 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100000305 Amidase; Region: Amidase; cl11426 340100000306 2-isopropylmalate synthase; Validated; Region: PRK03739 340100000307 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 340100000308 active site 340100000309 catalytic residues [active] 340100000310 metal binding site [ion binding]; metal-binding site 340100000311 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 340100000312 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 340100000313 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 340100000314 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 340100000315 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 340100000316 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 340100000317 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 340100000318 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 340100000319 heme binding site [chemical binding]; other site 340100000320 ferroxidase pore; other site 340100000321 ferroxidase diiron center [ion binding]; other site 340100000322 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 340100000323 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 340100000324 G1 box; other site 340100000325 putative GEF interaction site [polypeptide binding]; other site 340100000326 GTP/Mg2+ binding site [chemical binding]; other site 340100000327 Switch I region; other site 340100000328 G2 box; other site 340100000329 G3 box; other site 340100000330 Switch II region; other site 340100000331 G4 box; other site 340100000332 G5 box; other site 340100000333 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 340100000334 LysE type translocator; Region: LysE; cl00565 340100000335 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 340100000336 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 340100000337 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100000338 ATP binding site [chemical binding]; other site 340100000339 Mg++ binding site [ion binding]; other site 340100000340 motif III; other site 340100000341 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 340100000342 nucleotide binding region [chemical binding]; other site 340100000343 LemA family; Region: LemA; cl00742 340100000344 Repair protein; Region: Repair_PSII; cl01535 340100000345 sensor protein PhoQ; Provisional; Region: PRK10815 340100000346 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 340100000347 ATP binding site [chemical binding]; other site 340100000348 Mg2+ binding site [ion binding]; other site 340100000349 G-X-G motif; other site 340100000350 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100000351 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100000352 active site 340100000353 phosphorylation site [posttranslational modification] 340100000354 intermolecular recognition site; other site 340100000355 dimerization interface [polypeptide binding]; other site 340100000356 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 340100000357 DNA binding site [nucleotide binding] 340100000358 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 340100000359 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 340100000360 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 340100000361 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 340100000362 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 340100000363 FAD binding pocket [chemical binding]; other site 340100000364 FAD binding motif [chemical binding]; other site 340100000365 phosphate binding motif [ion binding]; other site 340100000366 beta-alpha-beta structure motif; other site 340100000367 NAD binding pocket [chemical binding]; other site 340100000368 dihydroorotase; Provisional; Region: PRK09237 340100000369 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 340100000370 Amidohydrolase; Region: Amidohydro_4; pfam13147 340100000371 active site 340100000372 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100000373 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100000374 Walker A/P-loop; other site 340100000375 ATP binding site [chemical binding]; other site 340100000376 Q-loop/lid; other site 340100000377 ABC transporter signature motif; other site 340100000378 Walker B; other site 340100000379 D-loop; other site 340100000380 H-loop/switch region; other site 340100000381 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100000382 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100000383 Walker A/P-loop; other site 340100000384 ATP binding site [chemical binding]; other site 340100000385 Q-loop/lid; other site 340100000386 ABC transporter signature motif; other site 340100000387 Walker B; other site 340100000388 D-loop; other site 340100000389 H-loop/switch region; other site 340100000390 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 340100000391 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340100000392 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 340100000393 dimer interface [polypeptide binding]; other site 340100000394 conserved gate region; other site 340100000395 putative PBP binding loops; other site 340100000396 ABC-ATPase subunit interface; other site 340100000397 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100000398 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 340100000399 dimer interface [polypeptide binding]; other site 340100000400 conserved gate region; other site 340100000401 putative PBP binding loops; other site 340100000402 ABC-ATPase subunit interface; other site 340100000403 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 340100000404 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100000405 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100000406 S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic...; Region: S15_NS1_EPRS_RNA-bind; cl00349 340100000407 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100000408 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100000409 G1 box; other site 340100000410 GTP/Mg2+ binding site [chemical binding]; other site 340100000411 G2 box; other site 340100000412 Switch I region; other site 340100000413 G3 box; other site 340100000414 Switch II region; other site 340100000415 G4 box; other site 340100000416 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 340100000417 G5 box; other site 340100000418 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 340100000419 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 340100000420 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100000421 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100000422 EamA-like transporter family; Region: EamA; cl01037 340100000423 Fimbrial protein; Region: Fimbrial; cl01416 340100000424 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 340100000425 PapC N-terminal domain; Region: PapC_N; pfam13954 340100000426 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100000427 PapC C-terminal domain; Region: PapC_C; pfam13953 340100000428 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 340100000429 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 340100000430 Fimbrial protein; Region: Fimbrial; cl01416 340100000431 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 340100000432 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 340100000433 tetramer interface [polypeptide binding]; other site 340100000434 active site 340100000435 Mg2+/Mn2+ binding site [ion binding]; other site 340100000436 NMT1-like family; Region: NMT1_2; cl15260 340100000437 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100000438 Stringent starvation protein B; Region: SspB; cl01120 340100000439 stringent starvation protein A; Provisional; Region: sspA; PRK09481 340100000440 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 340100000441 C-terminal domain interface [polypeptide binding]; other site 340100000442 putative GSH binding site (G-site) [chemical binding]; other site 340100000443 dimer interface [polypeptide binding]; other site 340100000444 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 340100000445 dimer interface [polypeptide binding]; other site 340100000446 N-terminal domain interface [polypeptide binding]; other site 340100000447 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 340100000448 cytochrome b; Provisional; Region: CYTB; MTH00145 340100000449 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 340100000450 Qi binding site; other site 340100000451 intrachain domain interface; other site 340100000452 interchain domain interface [polypeptide binding]; other site 340100000453 heme bH binding site [chemical binding]; other site 340100000454 heme bL binding site [chemical binding]; other site 340100000455 Qo binding site; other site 340100000456 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cl00193 340100000457 interchain domain interface [polypeptide binding]; other site 340100000458 intrachain domain interface; other site 340100000459 Qi binding site; other site 340100000460 Qo binding site; other site 340100000461 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 340100000462 [2Fe-2S] cluster binding site [ion binding]; other site 340100000463 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 340100000464 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 340100000465 Uncharacterized conserved protein [Function unknown]; Region: COG0327 340100000466 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 340100000467 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 340100000468 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 340100000469 protein binding site [polypeptide binding]; other site 340100000470 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 340100000471 non-specific DNA binding site [nucleotide binding]; other site 340100000472 salt bridge; other site 340100000473 sequence-specific DNA binding site [nucleotide binding]; other site 340100000474 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 340100000475 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 340100000476 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 340100000477 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 340100000478 nucleotide binding site/active site [active] 340100000479 HIT family signature motif; other site 340100000480 catalytic residue [active] 340100000481 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 340100000482 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 340100000483 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 340100000484 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 340100000485 substrate binding site [chemical binding]; other site 340100000486 glutamase interaction surface [polypeptide binding]; other site 340100000487 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 340100000488 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 340100000489 catalytic residues [active] 340100000490 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 340100000491 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 340100000492 putative active site [active] 340100000493 oxyanion strand; other site 340100000494 catalytic triad [active] 340100000495 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 340100000496 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 340100000497 putative active site pocket [active] 340100000498 4-fold oligomerization interface [polypeptide binding]; other site 340100000499 metal binding residues [ion binding]; metal-binding site 340100000500 3-fold/trimer interface [polypeptide binding]; other site 340100000501 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 340100000502 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 340100000503 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000504 homodimer interface [polypeptide binding]; other site 340100000505 catalytic residue [active] 340100000506 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 340100000507 histidinol dehydrogenase; Region: hisD; TIGR00069 340100000508 NAD binding site [chemical binding]; other site 340100000509 dimerization interface [polypeptide binding]; other site 340100000510 product binding site; other site 340100000511 substrate binding site [chemical binding]; other site 340100000512 zinc binding site [ion binding]; other site 340100000513 catalytic residues [active] 340100000514 ATP phosphoribosyltransferase; Region: HisG; cl15266 340100000515 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 340100000516 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 340100000517 hinge; other site 340100000518 active site 340100000519 BolA-like protein; Region: BolA; cl00386 340100000520 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100000521 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 340100000522 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 340100000523 Walker A/P-loop; other site 340100000524 ATP binding site [chemical binding]; other site 340100000525 Q-loop/lid; other site 340100000526 ABC transporter signature motif; other site 340100000527 Walker B; other site 340100000528 D-loop; other site 340100000529 H-loop/switch region; other site 340100000530 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 340100000531 VacJ like lipoprotein; Region: VacJ; cl01073 340100000532 mce related protein; Region: MCE; pfam02470 340100000533 Permease; Region: Permease; cl00510 340100000534 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 340100000535 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 340100000536 Walker A/P-loop; other site 340100000537 ATP binding site [chemical binding]; other site 340100000538 Q-loop/lid; other site 340100000539 ABC transporter signature motif; other site 340100000540 Walker B; other site 340100000541 D-loop; other site 340100000542 H-loop/switch region; other site 340100000543 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 340100000544 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000545 Helix-turn-helix domains; Region: HTH; cl00088 340100000546 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 340100000547 putative dimerization interface [polypeptide binding]; other site 340100000548 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340100000549 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 340100000550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000551 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 340100000552 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 340100000553 active site 340100000554 dimer interface [polypeptide binding]; other site 340100000555 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 340100000556 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 340100000557 active site 340100000558 FMN binding site [chemical binding]; other site 340100000559 substrate binding site [chemical binding]; other site 340100000560 3Fe-4S cluster binding site [ion binding]; other site 340100000561 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 340100000562 domain interface; other site 340100000563 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 340100000564 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 340100000565 substrate binding site [chemical binding]; other site 340100000566 catalytic Zn binding site [ion binding]; other site 340100000567 NAD binding site [chemical binding]; other site 340100000568 structural Zn binding site [ion binding]; other site 340100000569 dimer interface [polypeptide binding]; other site 340100000570 Predicted esterase [General function prediction only]; Region: COG0627 340100000571 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100000572 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 340100000573 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 340100000574 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100000575 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 340100000576 DNA binding residues [nucleotide binding] 340100000577 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 340100000578 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100000579 active site 340100000580 metal binding site [ion binding]; metal-binding site 340100000581 hexamer interface [polypeptide binding]; other site 340100000582 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 340100000583 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 340100000584 ligand binding site [chemical binding]; other site 340100000585 flexible hinge region; other site 340100000586 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100000587 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100000588 DNA binding site [nucleotide binding] 340100000589 domain linker motif; other site 340100000590 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 340100000591 putative ligand binding site [chemical binding]; other site 340100000592 putative dimerization interface [polypeptide binding]; other site 340100000593 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100000594 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100000595 DctM-like transporters; Region: DctM; pfam06808 340100000596 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100000597 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100000598 Dehydratase family; Region: ILVD_EDD; cl00340 340100000599 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 340100000600 nudix motif; other site 340100000601 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100000602 Cytochrome c; Region: Cytochrom_C; cl11414 340100000603 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100000604 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 340100000605 Subunit I/III interface [polypeptide binding]; other site 340100000606 D-pathway; other site 340100000607 Subunit I/VIIc interface [polypeptide binding]; other site 340100000608 Subunit I/IV interface [polypeptide binding]; other site 340100000609 Subunit I/II interface [polypeptide binding]; other site 340100000610 Low-spin heme (heme a) binding site [chemical binding]; other site 340100000611 Subunit I/VIIa interface [polypeptide binding]; other site 340100000612 Subunit I/VIa interface [polypeptide binding]; other site 340100000613 Dimer interface; other site 340100000614 Putative water exit pathway; other site 340100000615 Binuclear center (heme a3/CuB) [ion binding]; other site 340100000616 K-pathway; other site 340100000617 Subunit I/Vb interface [polypeptide binding]; other site 340100000618 Putative proton exit pathway; other site 340100000619 Subunit I/VIb interface; other site 340100000620 Subunit I/VIc interface [polypeptide binding]; other site 340100000621 Electron transfer pathway; other site 340100000622 Subunit I/VIIIb interface [polypeptide binding]; other site 340100000623 Subunit I/VIIb interface [polypeptide binding]; other site 340100000624 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 340100000625 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 340100000626 Subunit III/VIIa interface [polypeptide binding]; other site 340100000627 Phospholipid binding site [chemical binding]; other site 340100000628 Subunit I/III interface [polypeptide binding]; other site 340100000629 Subunit III/VIb interface [polypeptide binding]; other site 340100000630 Subunit III/VIa interface; other site 340100000631 Subunit III/Vb interface [polypeptide binding]; other site 340100000632 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 340100000633 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 340100000634 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100000635 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 340100000636 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 340100000637 UbiA prenyltransferase family; Region: UbiA; cl00337 340100000638 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 340100000639 Cu(I) binding site [ion binding]; other site 340100000640 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 340100000641 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 340100000642 Substrate binding site; other site 340100000643 Mg++ binding site; other site 340100000644 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 340100000645 active site 340100000646 substrate binding site [chemical binding]; other site 340100000647 CoA binding site [chemical binding]; other site 340100000648 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 340100000649 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100000650 putative substrate translocation pore; other site 340100000651 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 340100000652 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000653 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340100000654 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000655 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100000656 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 340100000657 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100000658 Helix-turn-helix domains; Region: HTH; cl00088 340100000659 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 340100000660 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 340100000661 glutaminase active site [active] 340100000662 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 340100000663 dimer interface [polypeptide binding]; other site 340100000664 active site 340100000665 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 340100000666 dimer interface [polypeptide binding]; other site 340100000667 active site 340100000668 Protein of unknown function (DUF2837); Region: DUF2837; pfam10997 340100000669 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 340100000670 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 340100000671 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 340100000672 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340100000673 rod shape-determining protein MreB; Provisional; Region: PRK13927 340100000674 Cell division protein FtsA; Region: FtsA; cl11496 340100000675 autotransport protein MisL; Provisional; Region: PRK15313 340100000676 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 340100000677 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340100000678 Helix-turn-helix domains; Region: HTH; cl00088 340100000679 putative transposase OrfB; Reviewed; Region: PHA02517 340100000680 HTH-like domain; Region: HTH_21; pfam13276 340100000681 Integrase core domain; Region: rve; cl01316 340100000682 Integrase core domain; Region: rve_3; cl15866 340100000683 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100000684 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 340100000685 DNA binding site [nucleotide binding] 340100000686 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340100000687 DNA-binding interface [nucleotide binding]; DNA binding site 340100000688 HTH-like domain; Region: HTH_21; pfam13276 340100000689 Integrase core domain; Region: rve; cl01316 340100000690 Integrase core domain; Region: rve_3; cl15866 340100000691 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 340100000692 non-specific DNA binding site [nucleotide binding]; other site 340100000693 salt bridge; other site 340100000694 sequence-specific DNA binding site [nucleotide binding]; other site 340100000695 Helix-turn-helix domains; Region: HTH; cl00088 340100000696 HTH-like domain; Region: HTH_21; pfam13276 340100000697 Integrase core domain; Region: rve; cl01316 340100000698 Integrase core domain; Region: rve_3; cl15866 340100000699 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 340100000700 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 340100000701 ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 340100000702 Walker B; other site 340100000703 D-loop; other site 340100000704 H-loop/switch region; other site 340100000705 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 340100000706 putative active site [active] 340100000707 putative metal-binding site [ion binding]; other site 340100000708 putative transposase OrfB; Reviewed; Region: PHA02517 340100000709 HTH-like domain; Region: HTH_21; pfam13276 340100000710 Integrase core domain; Region: rve; cl01316 340100000711 Integrase core domain; Region: rve_3; cl15866 340100000712 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340100000713 DNA-binding interface [nucleotide binding]; DNA binding site 340100000714 Helix-turn-helix domains; Region: HTH; cl00088 340100000715 putative transposase OrfB; Reviewed; Region: PHA02517 340100000716 HTH-like domain; Region: HTH_21; pfam13276 340100000717 Integrase core domain; Region: rve; cl01316 340100000718 Integrase core domain; Region: rve_3; cl15866 340100000719 Helix-turn-helix domains; Region: HTH; cl00088 340100000720 Integrase core domain; Region: rve; cl01316 340100000721 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100000722 Integrase core domain; Region: rve_3; cl15866 340100000723 Helix-turn-helix domains; Region: HTH; cl00088 340100000724 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 340100000725 iron-dicitrate transporter ATP-binding subunit; Provisional; Region: fecE; PRK11231 340100000726 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100000727 HTH-like domain; Region: HTH_21; pfam13276 340100000728 Helix-turn-helix domains; Region: HTH; cl00088 340100000729 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 340100000730 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 340100000731 ATP binding site [chemical binding]; other site 340100000732 putative Mg++ binding site [ion binding]; other site 340100000733 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 340100000734 nucleotide binding region [chemical binding]; other site 340100000735 ATP-binding site [chemical binding]; other site 340100000736 Restriction endonuclease; Region: Mrr_cat; cl00516 340100000737 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 340100000738 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 340100000739 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 340100000740 ligand binding site [chemical binding]; other site 340100000741 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 340100000742 Integrase core domain; Region: rve_3; cl15866 340100000743 Integrase core domain; Region: rve; cl01316 340100000744 Helix-turn-helix domains; Region: HTH; cl00088 340100000745 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 340100000746 non-specific DNA binding site [nucleotide binding]; other site 340100000747 salt bridge; other site 340100000748 sequence-specific DNA binding site [nucleotide binding]; other site 340100000749 HipA N-terminal domain; Region: Couple_hipA; cl11853 340100000750 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100000751 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100000752 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 340100000753 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340100000754 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000755 Vi polysaccharide biosynthesis protein TviD; Provisional; Region: PRK15180 340100000756 Vi polysaccharide biosynthesis protein TviD; Provisional; Region: PRK15180 340100000757 Vi polysaccharide biosynthesis protein TviE; Provisional; Region: PRK15179 340100000758 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 340100000759 Vi polysaccharide export protein VexA; Provisional; Region: PRK15175 340100000760 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 340100000761 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100000762 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100000763 Q-loop/lid; other site 340100000764 ABC transporter signature motif; other site 340100000765 Walker B; other site 340100000766 D-loop; other site 340100000767 H-loop/switch region; other site 340100000768 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 340100000769 Vi polysaccharide export protein VexE; Provisional; Region: PRK15174 340100000770 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 340100000771 TPR motif; other site 340100000772 binding surface 340100000773 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100000774 putative acyl-acceptor binding pocket; other site 340100000775 Pectate lyase; Region: Pec_lyase_C; cl01593 340100000776 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100000777 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000778 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100000779 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100000780 DNA-binding site [nucleotide binding]; DNA binding site 340100000781 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 340100000782 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000783 homodimer interface [polypeptide binding]; other site 340100000784 catalytic residue [active] 340100000785 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340100000786 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 340100000787 putative substrate translocation pore; other site 340100000788 Helix-turn-helix domains; Region: HTH; cl00088 340100000789 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100000790 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000791 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 340100000792 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 340100000793 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 340100000794 FMN-binding pocket [chemical binding]; other site 340100000795 flavin binding motif; other site 340100000796 phosphate binding motif [ion binding]; other site 340100000797 beta-alpha-beta structure motif; other site 340100000798 NAD binding pocket [chemical binding]; other site 340100000799 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 340100000800 catalytic loop [active] 340100000801 iron binding site [ion binding]; other site 340100000802 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 340100000803 NMT1-like family; Region: NMT1_2; cl15260 340100000804 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 340100000805 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 340100000806 hydrophobic ligand binding site; other site 340100000807 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000808 NMT1-like family; Region: NMT1_2; cl15260 340100000809 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 340100000810 active site 340100000811 Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_beta; cd03464 340100000812 multimer interface [polypeptide binding]; other site 340100000813 heterodimer interface [polypeptide binding]; other site 340100000814 protocatechuate 3,4-dioxygenase, beta subunit; Region: protocat_beta; TIGR02422 340100000815 active site 340100000816 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100000817 Helix-turn-helix domains; Region: HTH; cl00088 340100000818 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100000819 dimerization interface [polypeptide binding]; other site 340100000820 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100000821 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 340100000822 tetramer interface [polypeptide binding]; other site 340100000823 NMT1-like family; Region: NMT1_2; cl15260 340100000824 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000825 Helix-turn-helix domains; Region: HTH; cl00088 340100000826 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100000827 dimerization interface [polypeptide binding]; other site 340100000828 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 340100000829 Histidine kinase; Region: His_kinase; pfam06580 340100000830 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100000831 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100000832 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 340100000833 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 340100000834 NADP binding site [chemical binding]; other site 340100000835 dimer interface [polypeptide binding]; other site 340100000836 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100000837 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100000838 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100000839 Helix-turn-helix domains; Region: HTH; cl00088 340100000840 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100000841 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100000842 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100000843 active site 340100000844 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000845 NMT1-like family; Region: NMT1_2; cl15260 340100000846 Nitronate monooxygenase; Region: NMO; pfam03060 340100000847 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100000848 FMN binding site [chemical binding]; other site 340100000849 substrate binding site [chemical binding]; other site 340100000850 putative catalytic residue [active] 340100000851 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100000852 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 340100000853 substrate binding site [chemical binding]; other site 340100000854 oxyanion hole (OAH) forming residues; other site 340100000855 trimer interface [polypeptide binding]; other site 340100000856 RES domain; Region: RES; cl02411 340100000857 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100000858 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 340100000859 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 340100000860 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 340100000861 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 340100000862 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 340100000863 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 340100000864 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100000865 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 340100000866 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 340100000867 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 340100000868 active site 340100000869 homotetramer interface [polypeptide binding]; other site 340100000870 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100000871 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 340100000872 putative ligand binding site [chemical binding]; other site 340100000873 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100000874 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340100000875 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 340100000876 phosphate binding site [ion binding]; other site 340100000877 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000878 Helix-turn-helix domains; Region: HTH; cl00088 340100000879 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 340100000880 dimerization interface [polypeptide binding]; other site 340100000881 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100000882 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100000883 MlrC C-terminus; Region: MlrC_C; pfam07171 340100000884 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_16; cd08502 340100000885 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100000886 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100000887 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 340100000888 dimer interface [polypeptide binding]; other site 340100000889 conserved gate region; other site 340100000890 putative PBP binding loops; other site 340100000891 ABC-ATPase subunit interface; other site 340100000892 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100000893 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 340100000894 dimer interface [polypeptide binding]; other site 340100000895 conserved gate region; other site 340100000896 putative PBP binding loops; other site 340100000897 ABC-ATPase subunit interface; other site 340100000898 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100000899 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100000900 Walker A/P-loop; other site 340100000901 ATP binding site [chemical binding]; other site 340100000902 Q-loop/lid; other site 340100000903 ABC transporter signature motif; other site 340100000904 Walker B; other site 340100000905 D-loop; other site 340100000906 H-loop/switch region; other site 340100000907 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100000908 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100000909 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100000910 Walker A/P-loop; other site 340100000911 ATP binding site [chemical binding]; other site 340100000912 Q-loop/lid; other site 340100000913 ABC transporter signature motif; other site 340100000914 Walker B; other site 340100000915 D-loop; other site 340100000916 H-loop/switch region; other site 340100000917 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100000918 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 340100000919 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000920 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100000921 Amidase; Region: Amidase; cl11426 340100000922 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100000923 active site 340100000924 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100000925 Predicted membrane protein [Function unknown]; Region: COG1470 340100000926 NPCBM-associated, NEW3 domain of alpha-galactosidase; Region: NPCBM_assoc; pfam10633 340100000927 NPCBM-associated, NEW3 domain of alpha-galactosidase; Region: NPCBM_assoc; pfam10633 340100000928 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100000929 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100000930 DNA-binding site [nucleotide binding]; DNA binding site 340100000931 FCD domain; Region: FCD; cl11656 340100000932 urea carboxylase; Region: urea_carbox; TIGR02712 340100000933 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100000934 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 340100000935 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 340100000936 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 340100000937 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 340100000938 carboxyltransferase (CT) interaction site; other site 340100000939 biotinylation site [posttranslational modification]; other site 340100000940 allophanate hydrolase; Provisional; Region: PRK08186 340100000941 Amidase; Region: Amidase; cl11426 340100000942 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100000943 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 340100000944 putative ligand binding site [chemical binding]; other site 340100000945 HEAT repeats; Region: HEAT_2; pfam13646 340100000946 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 340100000947 TM-ABC transporter signature motif; other site 340100000948 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 340100000949 TM-ABC transporter signature motif; other site 340100000950 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 340100000951 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100000952 Walker A/P-loop; other site 340100000953 ATP binding site [chemical binding]; other site 340100000954 Q-loop/lid; other site 340100000955 ABC transporter signature motif; other site 340100000956 Walker B; other site 340100000957 D-loop; other site 340100000958 H-loop/switch region; other site 340100000959 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 340100000960 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100000961 Walker A/P-loop; other site 340100000962 ATP binding site [chemical binding]; other site 340100000963 Q-loop/lid; other site 340100000964 ABC transporter signature motif; other site 340100000965 Walker B; other site 340100000966 D-loop; other site 340100000967 H-loop/switch region; other site 340100000968 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340100000969 putative peptidoglycan binding site; other site 340100000970 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100000971 Helix-turn-helix domains; Region: HTH; cl00088 340100000972 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100000973 NMT1-like family; Region: NMT1_2; cl15260 340100000974 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 340100000975 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000976 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 340100000977 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100000978 Helix-turn-helix domains; Region: HTH; cl00088 340100000979 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 340100000980 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 340100000981 amphipathic channel; other site 340100000982 Asn-Pro-Ala signature motifs; other site 340100000983 Dienelactone hydrolase family; Region: DLH; pfam01738 340100000984 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 340100000985 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100000986 putative choline sulfate-utilization transcription factor; Region: chol_sulf_TF; TIGR03418 340100000987 Helix-turn-helix domains; Region: HTH; cl00088 340100000988 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100000989 dimerization interface [polypeptide binding]; other site 340100000990 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 340100000991 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 340100000992 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 340100000993 putative catalytic residue [active] 340100000994 short chain dehydrogenase; Provisional; Region: PRK06123 340100000995 classical (c) SDRs; Region: SDR_c; cd05233 340100000996 NAD(P) binding site [chemical binding]; other site 340100000997 active site 340100000998 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 340100000999 active site 340100001000 ribulose/triose binding site [chemical binding]; other site 340100001001 phosphate binding site [ion binding]; other site 340100001002 substrate (anthranilate) binding pocket [chemical binding]; other site 340100001003 product (indole) binding pocket [chemical binding]; other site 340100001004 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 340100001005 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 340100001006 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 340100001007 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 340100001008 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 340100001009 glutamine binding [chemical binding]; other site 340100001010 catalytic triad [active] 340100001011 anthranilate synthase component I; Provisional; Region: PRK13565 340100001012 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 340100001013 chorismate binding enzyme; Region: Chorismate_bind; cl10555 340100001014 phosphoglycolate phosphatase; Provisional; Region: PRK13222 340100001015 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 340100001016 motif II; other site 340100001017 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 340100001018 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 340100001019 substrate binding site [chemical binding]; other site 340100001020 hexamer interface [polypeptide binding]; other site 340100001021 metal binding site [ion binding]; metal-binding site 340100001022 Protein of unknown function (DUF525); Region: DUF525; cl01119 340100001023 MltA specific insert domain; Region: MltA; cl08398 340100001024 3D domain; Region: 3D; cl01439 340100001025 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001026 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 340100001027 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 340100001028 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 340100001029 dimerization domain [polypeptide binding]; other site 340100001030 dimer interface [polypeptide binding]; other site 340100001031 catalytic residues [active] 340100001032 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; Region: 2-Hacid_dh; pfam00389 340100001033 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001034 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 340100001035 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 340100001036 Ligand Binding Site [chemical binding]; other site 340100001037 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340100001038 active site 340100001039 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 340100001040 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001041 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 340100001042 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 340100001043 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 340100001044 protein binding site [polypeptide binding]; other site 340100001045 enoyl-CoA hydratase; Provisional; Region: PRK05862 340100001046 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 340100001047 substrate binding site [chemical binding]; other site 340100001048 oxyanion hole (OAH) forming residues; other site 340100001049 trimer interface [polypeptide binding]; other site 340100001050 Uncharacterized conserved protein [Function unknown]; Region: COG5361 340100001051 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 340100001052 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 340100001053 ATP synthase A chain; Region: ATP-synt_A; cl00413 340100001054 ATP synthase subunit C; Region: ATP-synt_C; cl00466 340100001055 Plant ATP synthase F0; Region: YMF19; cl07975 340100001056 Plant ATP synthase F0; Region: YMF19; cl07975 340100001057 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 340100001058 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 340100001059 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 340100001060 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 340100001061 beta subunit interaction interface [polypeptide binding]; other site 340100001062 Walker A motif; other site 340100001063 ATP binding site [chemical binding]; other site 340100001064 Walker B motif; other site 340100001065 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 340100001066 ATP synthase; Region: ATP-synt; cl00365 340100001067 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 340100001068 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 340100001069 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 340100001070 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 340100001071 alpha subunit interaction interface [polypeptide binding]; other site 340100001072 Walker A motif; other site 340100001073 ATP binding site [chemical binding]; other site 340100001074 Walker B motif; other site 340100001075 inhibitor binding site; inhibition site 340100001076 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 340100001077 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 340100001078 Helix-turn-helix domains; Region: HTH; cl00088 340100001079 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 340100001080 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 340100001081 tetramer interface [polypeptide binding]; other site 340100001082 heme binding pocket [chemical binding]; other site 340100001083 NADPH binding site [chemical binding]; other site 340100001084 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 340100001085 methyltransferase, MtaA/CmuA family; Region: mtaA_cmuA; TIGR01463 340100001086 substrate binding site [chemical binding]; other site 340100001087 active site 340100001088 primosome assembly protein PriA; Validated; Region: PRK05580 340100001089 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 340100001090 ATP binding site [chemical binding]; other site 340100001091 putative Mg++ binding site [ion binding]; other site 340100001092 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100001093 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 340100001094 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100001095 Family description; Region: UvrD_C_2; cl15862 340100001096 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100001097 S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic...; Region: S15_NS1_EPRS_RNA-bind; cl00349 340100001098 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100001099 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 340100001100 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 340100001101 metal binding site [ion binding]; metal-binding site 340100001102 dimer interface [polypeptide binding]; other site 340100001103 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 340100001104 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100001105 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100001106 Walker A/P-loop; other site 340100001107 ATP binding site [chemical binding]; other site 340100001108 Q-loop/lid; other site 340100001109 ABC transporter signature motif; other site 340100001110 Walker B; other site 340100001111 D-loop; other site 340100001112 H-loop/switch region; other site 340100001113 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100001114 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100001115 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100001116 Walker A/P-loop; other site 340100001117 ATP binding site [chemical binding]; other site 340100001118 Q-loop/lid; other site 340100001119 ABC transporter signature motif; other site 340100001120 Walker B; other site 340100001121 D-loop; other site 340100001122 H-loop/switch region; other site 340100001123 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100001124 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 340100001125 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 340100001126 dimer interface [polypeptide binding]; other site 340100001127 conserved gate region; other site 340100001128 putative PBP binding loops; other site 340100001129 ABC-ATPase subunit interface; other site 340100001130 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100001131 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 340100001132 dimer interface [polypeptide binding]; other site 340100001133 conserved gate region; other site 340100001134 putative PBP binding loops; other site 340100001135 ABC-ATPase subunit interface; other site 340100001136 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 340100001137 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100001138 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 340100001139 active site 340100001140 Zn binding site [ion binding]; other site 340100001141 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001142 Helix-turn-helix domains; Region: HTH; cl00088 340100001143 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100001144 dimerization interface [polypeptide binding]; other site 340100001145 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 340100001146 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100001147 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 340100001148 putative substrate binding site [chemical binding]; other site 340100001149 putative ATP binding site [chemical binding]; other site 340100001150 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 340100001151 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100001152 substrate binding site [chemical binding]; other site 340100001153 oxyanion hole (OAH) forming residues; other site 340100001154 trimer interface [polypeptide binding]; other site 340100001155 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 340100001156 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100001157 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 340100001158 substrate binding site [chemical binding]; other site 340100001159 oxyanion hole (OAH) forming residues; other site 340100001160 trimer interface [polypeptide binding]; other site 340100001161 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100001162 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100001163 FMN binding site [chemical binding]; other site 340100001164 substrate binding site [chemical binding]; other site 340100001165 putative catalytic residue [active] 340100001166 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100001167 Helix-turn-helix domains; Region: HTH; cl00088 340100001168 YsiA-like protein, C-terminal region; Region: TetR_C_4; pfam08359 340100001169 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100001170 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100001171 active site 340100001172 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100001173 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100001174 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 340100001175 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001176 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100001177 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100001178 Cytochrome c; Region: Cytochrom_C; cl11414 340100001179 Cytochrome c; Region: Cytochrom_C; cl11414 340100001180 Cupin superfamily (DUF985); Region: Cupin_5; cl01418 340100001181 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001182 NMT1-like family; Region: NMT1_2; cl15260 340100001183 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100001184 Helix-turn-helix domains; Region: HTH; cl00088 340100001185 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100001186 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100001187 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 340100001188 substrate binding site [chemical binding]; other site 340100001189 oxyanion hole (OAH) forming residues; other site 340100001190 trimer interface [polypeptide binding]; other site 340100001191 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001192 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100001193 NAD(P) binding site [chemical binding]; other site 340100001194 active site 340100001195 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100001196 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100001197 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 340100001198 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100001199 FMN binding site [chemical binding]; other site 340100001200 substrate binding site [chemical binding]; other site 340100001201 putative catalytic residue [active] 340100001202 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 340100001203 putative active site [active] 340100001204 putative catalytic site [active] 340100001205 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100001206 thiolase; Provisional; Region: PRK06158 340100001207 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100001208 active site 340100001209 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 340100001210 putative substrate translocation pore; other site 340100001211 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100001212 Coenzyme A binding pocket [chemical binding]; other site 340100001213 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340100001214 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 340100001215 active site residue [active] 340100001216 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100001217 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001218 NMT1-like family; Region: NMT1_2; cl15260 340100001219 hypothetical protein; Validated; Region: PRK06201 340100001220 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 340100001221 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100001222 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100001223 DNA-binding site [nucleotide binding]; DNA binding site 340100001224 FCD domain; Region: FCD; cl11656 340100001225 glucose-1-dehydrogenase; Provisional; Region: PRK08936 340100001226 glucose 1 dehydrogenase (GlcDH), classical (c) SDRs; Region: GlcDH_SDR_c; cd05358 340100001227 NAD binding site [chemical binding]; other site 340100001228 homodimer interface [polypeptide binding]; other site 340100001229 active site 340100001230 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 340100001231 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 340100001232 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001233 NMT1-like family; Region: NMT1_2; cl15260 340100001234 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 340100001235 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 340100001236 NAD(P) binding site [chemical binding]; other site 340100001237 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100001238 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100001239 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100001240 Helix-turn-helix domains; Region: HTH; cl00088 340100001241 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 340100001242 putative effector binding pocket; other site 340100001243 dimerization interface [polypeptide binding]; other site 340100001244 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 340100001245 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl15791 340100001246 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 340100001247 DNA binding residues [nucleotide binding] 340100001248 dimerization interface [polypeptide binding]; other site 340100001249 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001250 Helix-turn-helix domains; Region: HTH; cl00088 340100001251 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 340100001252 putative dimerization interface [polypeptide binding]; other site 340100001253 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 340100001254 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100001255 Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR; Region: SQR_QFR_TM; cl00881 340100001256 Iron-sulfur protein interface; other site 340100001257 proximal heme binding site [chemical binding]; other site 340100001258 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 340100001259 Fumarase C-terminus; Region: Fumerase_C; cl00795 340100001260 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK06263 340100001261 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001262 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340100001263 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001264 NMT1-like family; Region: NMT1_2; cl15260 340100001265 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 340100001266 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100001267 PYR/PP interface [polypeptide binding]; other site 340100001268 dimer interface [polypeptide binding]; other site 340100001269 TPP binding site [chemical binding]; other site 340100001270 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100001271 Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL...; Region: TPP_BZL_OCoD_HPCL; cd02004 340100001272 TPP-binding site; other site 340100001273 dimer interface [polypeptide binding]; other site 340100001274 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100001275 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100001276 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100001277 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001278 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001279 NMT1-like family; Region: NMT1_2; cl15260 340100001280 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 340100001281 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100001282 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 340100001283 Walker A/P-loop; other site 340100001284 ATP binding site [chemical binding]; other site 340100001285 Q-loop/lid; other site 340100001286 ABC transporter signature motif; other site 340100001287 Walker B; other site 340100001288 D-loop; other site 340100001289 H-loop/switch region; other site 340100001290 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 340100001291 NMT1-like family; Region: NMT1_2; cl15260 340100001292 Altronate dehydratase [Carbohydrate transport and metabolism]; Region: UxaA; COG2721 340100001293 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 340100001294 SAF domain; Region: SAF; cl00555 340100001295 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100001296 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100001297 DNA-binding site [nucleotide binding]; DNA binding site 340100001298 UTRA domain; Region: UTRA; cl01230 340100001299 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100001300 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 340100001301 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001302 muropeptide transporter; Validated; Region: ampG; PRK11010 340100001303 muropeptide transporter; Reviewed; Region: ampG; PRK11902 340100001304 Predicted membrane protein [Function unknown]; Region: COG2860 340100001305 UPF0126 domain; Region: UPF0126; pfam03458 340100001306 UPF0126 domain; Region: UPF0126; pfam03458 340100001307 glutamate dehydrogenase; Provisional; Region: PRK09414 340100001308 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 340100001309 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 340100001310 NAD(P) binding site [chemical binding]; other site 340100001311 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 340100001312 putative active site [active] 340100001313 putative DNA binding site [nucleotide binding]; other site 340100001314 putative phosphate binding site [ion binding]; other site 340100001315 putative catalytic site [active] 340100001316 metal binding site A [ion binding]; metal-binding site 340100001317 putative AP binding site [nucleotide binding]; other site 340100001318 putative metal binding site B [ion binding]; other site 340100001319 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 340100001320 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100001321 active site 340100001322 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 340100001323 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 340100001324 GatB domain; Region: GatB_Yqey; cl11497 340100001325 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100001326 Amidase; Region: Amidase; cl11426 340100001327 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 340100001328 rod shape-determining protein MreB; Provisional; Region: PRK13927 340100001329 Cell division protein FtsA; Region: FtsA; cl11496 340100001330 rod shape-determining protein MreC; Region: mreC; TIGR00219 340100001331 rod shape-determining protein MreC; Region: MreC; pfam04085 340100001332 rod shape-determining protein MreD; Region: MreD; cl01087 340100001333 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 340100001334 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 340100001335 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100001336 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 340100001337 division inhibitor protein; Provisional; Region: slmA; PRK09480 340100001338 Helix-turn-helix domains; Region: HTH; cl00088 340100001339 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 340100001340 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 340100001341 motif II; other site 340100001342 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 340100001343 feedback inhibition sensing region; other site 340100001344 homohexameric interface [polypeptide binding]; other site 340100001345 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 340100001346 nucleotide binding site [chemical binding]; other site 340100001347 N-acetyl-L-glutamate binding site [chemical binding]; other site 340100001348 NMT1-like family; Region: NMT1_2; cl15260 340100001349 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 340100001350 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 340100001351 catalytic residues [active] 340100001352 BON domain; Region: BON; cl02771 340100001353 BON domain; Region: BON; cl02771 340100001354 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 340100001355 dimer interface [polypeptide binding]; other site 340100001356 active site 340100001357 Restriction endonuclease; Region: Mrr_cat; cl00516 340100001358 Predicted methyltransferases [General function prediction only]; Region: COG0313 340100001359 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340100001360 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 340100001361 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 340100001362 DNA binding site [nucleotide binding] 340100001363 active site 340100001364 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 340100001365 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 340100001366 Sporulation related domain; Region: SPOR; cl10051 340100001367 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 340100001368 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 340100001369 Cytochrome c; Region: Cytochrom_C; cl11414 340100001370 Cytochrome c; Region: Cytochrom_C; cl11414 340100001371 Cytochrome c; Region: Cytochrom_C; cl11414 340100001372 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100001373 Cytochrome c; Region: Cytochrom_C; cl11414 340100001374 HPr kinase/phosphorylase; Provisional; Region: PRK05428 340100001375 DRTGG domain; Region: DRTGG; cl12147 340100001376 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 340100001377 Hpr binding site; other site 340100001378 active site 340100001379 homohexamer subunit interaction site [polypeptide binding]; other site 340100001380 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 340100001381 active site 340100001382 phosphorylation site [posttranslational modification] 340100001383 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 340100001384 30S subunit binding site; other site 340100001385 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 340100001386 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 340100001387 Walker A/P-loop; other site 340100001388 ATP binding site [chemical binding]; other site 340100001389 Q-loop/lid; other site 340100001390 ABC transporter signature motif; other site 340100001391 Walker B; other site 340100001392 D-loop; other site 340100001393 H-loop/switch region; other site 340100001394 OstA-like protein; Region: OstA; cl00844 340100001395 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 340100001396 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 340100001397 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 340100001398 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100001399 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 340100001400 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 340100001401 putative active site [active] 340100001402 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 340100001403 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 340100001404 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001405 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100001406 Predicted transcriptional regulators [Transcription]; Region: COG1510 340100001407 Helix-turn-helix domains; Region: HTH; cl00088 340100001408 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 340100001409 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 340100001410 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 340100001411 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 340100001412 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 340100001413 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100001414 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100001415 Walker A/P-loop; other site 340100001416 ATP binding site [chemical binding]; other site 340100001417 ABC transporter; Region: ABC_tran; pfam00005 340100001418 Q-loop/lid; other site 340100001419 ABC transporter signature motif; other site 340100001420 Walker B; other site 340100001421 D-loop; other site 340100001422 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 340100001423 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100001424 Walker A/P-loop; other site 340100001425 ATP binding site [chemical binding]; other site 340100001426 Q-loop/lid; other site 340100001427 ABC transporter signature motif; other site 340100001428 Walker B; other site 340100001429 D-loop; other site 340100001430 H-loop/switch region; other site 340100001431 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 340100001432 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100001433 active site 340100001434 transcriptional regulator; Provisional; Region: PRK10632 340100001435 Helix-turn-helix domains; Region: HTH; cl00088 340100001436 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 340100001437 putative effector binding pocket; other site 340100001438 dimerization interface [polypeptide binding]; other site 340100001439 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100001440 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 340100001441 trimer interface [polypeptide binding]; other site 340100001442 eyelet of channel; other site 340100001443 threonine dehydratase; Reviewed; Region: PRK09224 340100001444 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 340100001445 tetramer interface [polypeptide binding]; other site 340100001446 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100001447 catalytic residue [active] 340100001448 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 340100001449 putative Ile/Val binding site [chemical binding]; other site 340100001450 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 340100001451 putative Ile/Val binding site [chemical binding]; other site 340100001452 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340100001453 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 340100001454 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100001455 FAD binding domain; Region: FAD_binding_4; pfam01565 340100001456 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 340100001457 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 340100001458 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 340100001459 Cysteine-rich domain; Region: CCG; pfam02754 340100001460 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 340100001461 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001462 NMT1-like family; Region: NMT1_2; cl15260 340100001463 enoyl-CoA hydratase; Provisional; Region: PRK09245 340100001464 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 340100001465 substrate binding site [chemical binding]; other site 340100001466 oxyanion hole (OAH) forming residues; other site 340100001467 trimer interface [polypeptide binding]; other site 340100001468 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100001469 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100001470 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100001471 Helix-turn-helix domains; Region: HTH; cl00088 340100001472 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 340100001473 dimerization interface [polypeptide binding]; other site 340100001474 substrate binding pocket [chemical binding]; other site 340100001475 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100001476 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100001477 tetramerization interface [polypeptide binding]; other site 340100001478 NAD(P) binding site [chemical binding]; other site 340100001479 catalytic residues [active] 340100001480 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 340100001481 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100001482 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100001483 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100001484 LamB/YcsF family; Region: LamB_YcsF; cl00664 340100001485 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 340100001486 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 340100001487 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 340100001488 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_18; cd08357 340100001489 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100001490 putative metal binding site [ion binding]; other site 340100001491 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001492 Helix-turn-helix domains; Region: HTH; cl00088 340100001493 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 340100001494 putative dimerization interface [polypeptide binding]; other site 340100001495 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 340100001496 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001497 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 340100001498 L-serine binding site [chemical binding]; other site 340100001499 ACT domain interface; other site 340100001500 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 340100001501 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 340100001502 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 340100001503 dimer interface [polypeptide binding]; other site 340100001504 phosphorylation site [posttranslational modification] 340100001505 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 340100001506 ATP binding site [chemical binding]; other site 340100001507 Mg2+ binding site [ion binding]; other site 340100001508 G-X-G motif; other site 340100001509 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 340100001510 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100001511 active site 340100001512 phosphorylation site [posttranslational modification] 340100001513 intermolecular recognition site; other site 340100001514 dimerization interface [polypeptide binding]; other site 340100001515 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 340100001516 DNA binding site [nucleotide binding] 340100001517 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 340100001518 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 340100001519 S-adenosylmethionine binding site [chemical binding]; other site 340100001520 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001521 Tim44-like domain; Region: Tim44; cl09208 340100001522 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100001523 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100001524 dinuclear metal binding motif [ion binding]; other site 340100001525 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100001526 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 340100001527 active site 340100001528 nucleotide binding site [chemical binding]; other site 340100001529 HIGH motif; other site 340100001530 KMSKS motif; other site 340100001531 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 340100001532 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 340100001533 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 340100001534 S-adenosylmethionine binding site [chemical binding]; other site 340100001535 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 340100001536 substrate binding site [chemical binding]; other site 340100001537 dimer interface [polypeptide binding]; other site 340100001538 ATP binding site [chemical binding]; other site 340100001539 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 340100001540 ThiS interaction site; other site 340100001541 putative active site [active] 340100001542 tetramer interface [polypeptide binding]; other site 340100001543 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 340100001544 cobalamin binding residues [chemical binding]; other site 340100001545 putative BtuC binding residues; other site 340100001546 dimer interface [polypeptide binding]; other site 340100001547 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 340100001548 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 340100001549 N-terminal plug; other site 340100001550 ligand-binding site [chemical binding]; other site 340100001551 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 340100001552 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 340100001553 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 340100001554 substrate binding pocket [chemical binding]; other site 340100001555 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 340100001556 B12 binding site [chemical binding]; other site 340100001557 cobalt ligand [ion binding]; other site 340100001558 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 340100001559 Methyltransferase domain; Region: Methyltransf_31; pfam13847 340100001560 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 340100001561 S-adenosylmethionine binding site [chemical binding]; other site 340100001562 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100001563 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 340100001564 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100001565 minor groove reading motif; other site 340100001566 helix-hairpin-helix signature motif; other site 340100001567 substrate binding pocket [chemical binding]; other site 340100001568 active site 340100001569 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 340100001570 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 340100001571 DNA binding and oxoG recognition site [nucleotide binding] 340100001572 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 340100001573 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 340100001574 dimer interface [polypeptide binding]; other site 340100001575 PYR/PP interface [polypeptide binding]; other site 340100001576 TPP binding site [chemical binding]; other site 340100001577 substrate binding site [chemical binding]; other site 340100001578 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 340100001579 TPP-binding site [chemical binding]; other site 340100001580 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 340100001581 CheD chemotactic sensory transduction; Region: CheD; cl00810 340100001582 FtsX-like permease family; Region: FtsX; cl15850 340100001583 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 340100001584 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100001585 Walker A/P-loop; other site 340100001586 ATP binding site [chemical binding]; other site 340100001587 Q-loop/lid; other site 340100001588 ABC transporter signature motif; other site 340100001589 Walker B; other site 340100001590 D-loop; other site 340100001591 H-loop/switch region; other site 340100001592 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 340100001593 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 340100001594 substrate binding pocket [chemical binding]; other site 340100001595 membrane-bound complex binding site; other site 340100001596 hinge residues; other site 340100001597 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 340100001598 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 340100001599 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 340100001600 dimer interface [polypeptide binding]; other site 340100001601 conserved gate region; other site 340100001602 putative PBP binding loops; other site 340100001603 ABC-ATPase subunit interface; other site 340100001604 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 340100001605 dimer interface [polypeptide binding]; other site 340100001606 conserved gate region; other site 340100001607 putative PBP binding loops; other site 340100001608 ABC-ATPase subunit interface; other site 340100001609 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100001610 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100001611 Walker A/P-loop; other site 340100001612 ATP binding site [chemical binding]; other site 340100001613 Q-loop/lid; other site 340100001614 ABC transporter signature motif; other site 340100001615 Walker B; other site 340100001616 D-loop; other site 340100001617 H-loop/switch region; other site 340100001618 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001619 NMT1-like family; Region: NMT1_2; cl15260 340100001620 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100001621 Helix-turn-helix domains; Region: HTH; cl00088 340100001622 Helix-turn-helix domains; Region: HTH; cl00088 340100001623 putative transposase OrfB; Reviewed; Region: PHA02517 340100001624 HTH-like domain; Region: HTH_21; pfam13276 340100001625 Integrase core domain; Region: rve; cl01316 340100001626 Integrase core domain; Region: rve_3; cl15866 340100001627 salicylate hydroxylase; Provisional; Region: PRK08163 340100001628 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001629 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 340100001630 NMT1-like family; Region: NMT1_2; cl15260 340100001631 Chorismate mutase type II; Region: CM_2; cl00693 340100001632 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 340100001633 maleylacetoacetate isomerase; Region: maiA; TIGR01262 340100001634 C-terminal domain interface [polypeptide binding]; other site 340100001635 GSH binding site (G-site) [chemical binding]; other site 340100001636 putative dimer interface [polypeptide binding]; other site 340100001637 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 340100001638 dimer interface [polypeptide binding]; other site 340100001639 N-terminal domain interface [polypeptide binding]; other site 340100001640 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 340100001641 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001642 NMT1-like family; Region: NMT1_2; cl15260 340100001643 hypothetical protein; Provisional; Region: PRK07538 340100001644 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001645 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100001646 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 340100001647 Cupin domain; Region: Cupin_2; cl09118 340100001648 Cupin domain; Region: Cupin_2; cl09118 340100001649 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100001650 Helix-turn-helix domains; Region: HTH; cl00088 340100001651 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100001652 dimerization interface [polypeptide binding]; other site 340100001653 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 340100001654 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 340100001655 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340100001656 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 340100001657 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 340100001658 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100001659 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001660 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001661 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340100001662 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100001663 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001664 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001665 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340100001666 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100001667 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001668 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001669 PAAR motif; Region: PAAR_motif; cl15808 340100001670 HNH/ENDO VII superfamily nuclease with conserved GHE residues; Region: GH-E; pfam14410 340100001671 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 340100001672 glycerol kinase; Provisional; Region: glpK; PRK00047 340100001673 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 340100001674 N- and C-terminal domain interface [polypeptide binding]; other site 340100001675 active site 340100001676 MgATP binding site [chemical binding]; other site 340100001677 catalytic site [active] 340100001678 metal binding site [ion binding]; metal-binding site 340100001679 glycerol binding site [chemical binding]; other site 340100001680 homotetramer interface [polypeptide binding]; other site 340100001681 homodimer interface [polypeptide binding]; other site 340100001682 FBP binding site [chemical binding]; other site 340100001683 putative transporter; Provisional; Region: PRK10504 340100001684 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 340100001685 putative substrate translocation pore; other site 340100001686 ScpA/B protein; Region: ScpA_ScpB; cl00598 340100001687 Pantoate-beta-alanine ligase; Region: PanC; cd00560 340100001688 pantoate--beta-alanine ligase; Region: panC; TIGR00018 340100001689 active site 340100001690 ATP-binding site [chemical binding]; other site 340100001691 pantoate-binding site; other site 340100001692 HXXH motif; other site 340100001693 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 340100001694 DNA binding residues [nucleotide binding] 340100001695 dimerization interface [polypeptide binding]; other site 340100001696 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 340100001697 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 340100001698 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 340100001699 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 340100001700 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 340100001701 CoA-binding site [chemical binding]; other site 340100001702 ATP-binding [chemical binding]; other site 340100001703 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 340100001704 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 340100001705 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 340100001706 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 340100001707 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 340100001708 Protein export membrane protein; Region: SecD_SecF; cl14618 340100001709 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 340100001710 Protein export membrane protein; Region: SecD_SecF; cl14618 340100001711 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100001712 hypothetical protein; Provisional; Region: PRK08999 340100001713 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 340100001714 active site 340100001715 8-oxo-dGMP binding site [chemical binding]; other site 340100001716 nudix motif; other site 340100001717 metal binding site [ion binding]; metal-binding site 340100001718 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 340100001719 active site 340100001720 thiamine phosphate binding site [chemical binding]; other site 340100001721 pyrophosphate binding site [ion binding]; other site 340100001722 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 340100001723 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 340100001724 Walker A motif; other site 340100001725 ATP binding site [chemical binding]; other site 340100001726 Walker B motif; other site 340100001727 arginine finger; other site 340100001728 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 340100001729 heterotetramer interface [polypeptide binding]; other site 340100001730 active site pocket [active] 340100001731 cleavage site 340100001732 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100001733 Helix-turn-helix domains; Region: HTH; cl00088 340100001734 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 340100001735 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100001736 substrate binding pocket [chemical binding]; other site 340100001737 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100001738 Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; Region: PBP1_Nba_like; cd06359 340100001739 putative ligand binding site [chemical binding]; other site 340100001740 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 340100001741 TM-ABC transporter signature motif; other site 340100001742 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 340100001743 TM-ABC transporter signature motif; other site 340100001744 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100001745 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100001746 Walker A/P-loop; other site 340100001747 ATP binding site [chemical binding]; other site 340100001748 Q-loop/lid; other site 340100001749 ABC transporter signature motif; other site 340100001750 Walker B; other site 340100001751 D-loop; other site 340100001752 H-loop/switch region; other site 340100001753 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100001754 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100001755 Walker A/P-loop; other site 340100001756 ATP binding site [chemical binding]; other site 340100001757 Q-loop/lid; other site 340100001758 ABC transporter signature motif; other site 340100001759 Walker B; other site 340100001760 D-loop; other site 340100001761 H-loop/switch region; other site 340100001762 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 340100001763 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001764 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 340100001765 active site 340100001766 FMN binding site [chemical binding]; other site 340100001767 substrate binding site [chemical binding]; other site 340100001768 homotetramer interface [polypeptide binding]; other site 340100001769 catalytic residue [active] 340100001770 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100001771 classical (c) SDRs; Region: SDR_c; cd05233 340100001772 NAD(P) binding site [chemical binding]; other site 340100001773 active site 340100001774 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100001775 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 340100001776 substrate binding site [chemical binding]; other site 340100001777 oxyanion hole (OAH) forming residues; other site 340100001778 trimer interface [polypeptide binding]; other site 340100001779 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100001780 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100001781 active site 340100001782 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 340100001783 AMP-binding enzyme; Region: AMP-binding; cl15778 340100001784 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100001785 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 340100001786 active site 340100001787 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 340100001788 homotrimer interaction site [polypeptide binding]; other site 340100001789 putative active site [active] 340100001790 Protein of unknown function (DUF342); Region: DUF342; pfam03961 340100001791 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 340100001792 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 340100001793 inhibitor-cofactor binding pocket; inhibition site 340100001794 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100001795 catalytic residue [active] 340100001796 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 340100001797 thiamine phosphate binding site [chemical binding]; other site 340100001798 active site 340100001799 pyrophosphate binding site [ion binding]; other site 340100001800 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 340100001801 substrate binding site [chemical binding]; other site 340100001802 ATP binding site [chemical binding]; other site 340100001803 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 340100001804 Rubredoxin; Region: Rubredoxin; pfam00301 340100001805 iron binding site [ion binding]; other site 340100001806 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 340100001807 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 340100001808 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340100001809 putative acyl-acceptor binding pocket; other site 340100001810 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 340100001811 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 340100001812 active site 340100001813 metal binding site [ion binding]; metal-binding site 340100001814 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 340100001815 Transglycosylase; Region: Transgly; cl07896 340100001816 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 340100001817 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 340100001818 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 340100001819 shikimate binding site; other site 340100001820 NAD(P) binding site [chemical binding]; other site 340100001821 Gram-negative bacterial tonB protein; Region: TonB; cl10048 340100001822 RNB domain; Region: RNB; pfam00773 340100001823 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 340100001824 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 340100001825 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100001826 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 340100001827 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100001828 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100001829 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100001830 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 340100001831 catalytic residues [active] 340100001832 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 340100001833 trimer interface [polypeptide binding]; other site 340100001834 active site 340100001835 dimer interface [polypeptide binding]; other site 340100001836 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 340100001837 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 340100001838 carboxyltransferase (CT) interaction site; other site 340100001839 biotinylation site [posttranslational modification]; other site 340100001840 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 340100001841 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100001842 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100001843 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 340100001844 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 340100001845 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 340100001846 S-adenosylmethionine binding site [chemical binding]; other site 340100001847 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 340100001848 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 340100001849 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 340100001850 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 340100001851 substrate binding site [chemical binding]; other site 340100001852 ATP binding site [chemical binding]; other site 340100001853 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 340100001854 YGGT family; Region: YGGT; cl00508 340100001855 YGGT family; Region: YGGT; cl00508 340100001856 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 340100001857 dimer interface [polypeptide binding]; other site 340100001858 putative radical transfer pathway; other site 340100001859 diiron center [ion binding]; other site 340100001860 tyrosyl radical; other site 340100001861 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 340100001862 ATP cone domain; Region: ATP-cone; pfam03477 340100001863 Class I ribonucleotide reductase; Region: RNR_I; cd01679 340100001864 active site 340100001865 dimer interface [polypeptide binding]; other site 340100001866 catalytic residues [active] 340100001867 effector binding site; other site 340100001868 R2 peptide binding site; other site 340100001869 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 340100001870 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 340100001871 dimer interface [polypeptide binding]; other site 340100001872 PYR/PP interface [polypeptide binding]; other site 340100001873 TPP binding site [chemical binding]; other site 340100001874 substrate binding site [chemical binding]; other site 340100001875 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 340100001876 TPP-binding site [chemical binding]; other site 340100001877 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 340100001878 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100001879 Helix-turn-helix domains; Region: HTH; cl00088 340100001880 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 340100001881 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100001882 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 340100001883 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 340100001884 HIGH motif; other site 340100001885 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 340100001886 active site 340100001887 KMSKS motif; other site 340100001888 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 340100001889 CoA-ligase; Region: Ligase_CoA; cl02894 340100001890 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100001891 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 340100001892 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100001893 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 340100001894 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100001895 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 340100001896 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 340100001897 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100001898 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 340100001899 23S rRNA interface [nucleotide binding]; other site 340100001900 L3 interface [polypeptide binding]; other site 340100001901 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 340100001902 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 340100001903 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001904 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 340100001905 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 340100001906 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 340100001907 putative substrate translocation pore; other site 340100001908 Helix-turn-helix domains; Region: HTH; cl00088 340100001909 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 340100001910 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340100001911 Surface antigen; Region: Bac_surface_Ag; cl03097 340100001912 haemagglutination activity domain; Region: Haemagg_act; cl05436 340100001913 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100001914 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100001915 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100001916 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100001917 Colicin D; Region: Colicin_D; pfam11429 340100001918 Bacterial self-protective colicin-like immunity; Region: Colicin_immun; pfam09204 340100001919 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100001920 Integrase core domain; Region: rve; cl01316 340100001921 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100001922 Integrase core domain; Region: rve_3; cl15866 340100001923 Helix-turn-helix domains; Region: HTH; cl00088 340100001924 Helix-turn-helix domains; Region: HTH; cl00088 340100001925 HTH-like domain; Region: HTH_21; pfam13276 340100001926 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100001927 Integrase core domain; Region: rve; cl01316 340100001928 Integrase core domain; Region: rve_3; cl15866 340100001929 Integrase core domain; Region: rve_3; cl15866 340100001930 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 340100001931 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100001932 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 340100001933 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 340100001934 active site 340100001935 HIGH motif; other site 340100001936 dimer interface [polypeptide binding]; other site 340100001937 KMSKS motif; other site 340100001938 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 340100001939 RNA binding surface [nucleotide binding]; other site 340100001940 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 340100001941 substrate binding site [chemical binding]; other site 340100001942 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 340100001943 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 340100001944 dimer interface [polypeptide binding]; other site 340100001945 glycine-pyridoxal phosphate binding site [chemical binding]; other site 340100001946 active site 340100001947 folate binding site [chemical binding]; other site 340100001948 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 340100001949 ATP cone domain; Region: ATP-cone; pfam03477 340100001950 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 340100001951 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 340100001952 catalytic motif [active] 340100001953 Zn binding site [ion binding]; other site 340100001954 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; cl00161 340100001955 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 340100001956 Lumazine binding domain; Region: Lum_binding; pfam00677 340100001957 Lumazine binding domain; Region: Lum_binding; pfam00677 340100001958 PrkA family serine protein kinase; Provisional; Region: PRK15455 340100001959 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100001960 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 340100001961 Uncharacterized conserved protein [Function unknown]; Region: COG2718 340100001962 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 340100001963 SpoVR family protein; Provisional; Region: PRK11767 340100001964 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 340100001965 Helix-turn-helix domains; Region: HTH; cl00088 340100001966 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 340100001967 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100001968 active site 340100001969 phosphorylation site [posttranslational modification] 340100001970 intermolecular recognition site; other site 340100001971 dimerization interface [polypeptide binding]; other site 340100001972 LytTr DNA-binding domain; Region: LytTR; cl04498 340100001973 Conserved TM helix; Region: TM_helix; pfam05552 340100001974 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 340100001975 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 340100001976 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 340100001977 dimerization interface [polypeptide binding]; other site 340100001978 active site 340100001979 OsmC-like protein; Region: OsmC; cl00767 340100001980 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 340100001981 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 340100001982 NAD binding site [chemical binding]; other site 340100001983 homotetramer interface [polypeptide binding]; other site 340100001984 homodimer interface [polypeptide binding]; other site 340100001985 substrate binding site [chemical binding]; other site 340100001986 active site 340100001987 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 340100001988 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100001989 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100001990 catalytic residue [active] 340100001991 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340100001992 putative peptidoglycan binding site; other site 340100001993 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 340100001994 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 340100001995 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100001996 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 340100001997 RNA/DNA hybrid binding site [nucleotide binding]; other site 340100001998 active site 340100001999 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 340100002000 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 340100002001 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 340100002002 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 340100002003 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 340100002004 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 340100002005 active site 340100002006 substrate binding site [chemical binding]; other site 340100002007 catalytic site [active] 340100002008 Protein of unknown function (DUF3251); Region: DUF3251; cl08186 340100002009 Phage capsid family; Region: Phage_capsid; pfam05065 340100002010 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 340100002011 PAS domain; Region: PAS_9; pfam13426 340100002012 putative active site [active] 340100002013 heme pocket [chemical binding]; other site 340100002014 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100002015 dimer interface [polypeptide binding]; other site 340100002016 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 340100002017 putative CheW interface [polypeptide binding]; other site 340100002018 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 340100002019 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 340100002020 Ligand binding site; other site 340100002021 Putative Catalytic site; other site 340100002022 DXD motif; other site 340100002023 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 340100002024 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 340100002025 YdjC-like protein; Region: YdjC; cl01344 340100002026 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100002027 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 340100002028 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100002029 LysE type translocator; Region: LysE; cl00565 340100002030 EamA-like transporter family; Region: EamA; cl01037 340100002031 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100002032 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100002033 DNA-binding site [nucleotide binding]; DNA binding site 340100002034 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 340100002035 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100002036 homodimer interface [polypeptide binding]; other site 340100002037 catalytic residue [active] 340100002038 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 340100002039 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 340100002040 Ligand Binding Site [chemical binding]; other site 340100002041 elongation factor G; Reviewed; Region: PRK00007 340100002042 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 340100002043 G1 box; other site 340100002044 putative GEF interaction site [polypeptide binding]; other site 340100002045 GTP/Mg2+ binding site [chemical binding]; other site 340100002046 Switch I region; other site 340100002047 G2 box; other site 340100002048 G3 box; other site 340100002049 Switch II region; other site 340100002050 G4 box; other site 340100002051 G5 box; other site 340100002052 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 340100002053 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 340100002054 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 340100002055 putative transposase OrfB; Reviewed; Region: PHA02517 340100002056 HTH-like domain; Region: HTH_21; pfam13276 340100002057 Integrase core domain; Region: rve; cl01316 340100002058 Integrase core domain; Region: rve_3; cl15866 340100002059 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100002060 Helix-turn-helix domains; Region: HTH; cl00088 340100002061 Helix-turn-helix domains; Region: HTH; cl00088 340100002062 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100002063 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 340100002064 putative deacylase active site [active] 340100002065 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 340100002066 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100002067 ligand binding site [chemical binding]; other site 340100002068 translocation protein TolB; Provisional; Region: tolB; PRK02889 340100002069 TolB amino-terminal domain; Region: TolB_N; cl00639 340100002070 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002071 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002072 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002073 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002074 TolA protein; Region: tolA_full; TIGR02794 340100002075 Gram-negative bacterial tonB protein; Region: TonB; cl10048 340100002076 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 340100002077 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340100002078 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 340100002079 active site 340100002080 prolyl-tRNA synthetase; Provisional; Region: PRK09194 340100002081 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 340100002082 dimer interface [polypeptide binding]; other site 340100002083 motif 1; other site 340100002084 active site 340100002085 motif 2; other site 340100002086 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 340100002087 putative deacylase active site [active] 340100002088 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 attaches...; Region: class_II_aaRS-like_core; cl00268 340100002089 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 340100002090 anticodon binding site; other site 340100002091 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 340100002092 putative active site [active] 340100002093 Ap4A binding site [chemical binding]; other site 340100002094 nudix motif; other site 340100002095 putative metal binding site [ion binding]; other site 340100002096 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 340100002097 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100002098 active site 340100002099 phosphorylation site [posttranslational modification] 340100002100 intermolecular recognition site; other site 340100002101 dimerization interface [polypeptide binding]; other site 340100002102 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 340100002103 DNA binding site [nucleotide binding] 340100002104 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 340100002105 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100002106 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 340100002107 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 340100002108 dimer interface [polypeptide binding]; other site 340100002109 phosphorylation site [posttranslational modification] 340100002110 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 340100002111 ATP binding site [chemical binding]; other site 340100002112 Mg2+ binding site [ion binding]; other site 340100002113 G-X-G motif; other site 340100002114 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100002115 Helix-turn-helix domains; Region: HTH; cl00088 340100002116 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 340100002117 putative effector binding pocket; other site 340100002118 putative dimerization interface [polypeptide binding]; other site 340100002119 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100002120 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002121 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100002122 NAD(P) binding pocket [chemical binding]; other site 340100002123 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 340100002124 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100002125 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340100002126 Cell division protein ZapA; Region: ZapA; cl01146 340100002127 Protein of unknown function (DUF541); Region: SIMPL; cl01077 340100002128 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 340100002129 Dehydratase family; Region: ILVD_EDD; cl00340 340100002130 Cytochrome c; Region: Cytochrom_C; cl11414 340100002131 RNA polymerase sigma factor; Provisional; Region: PRK11922 340100002132 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 340100002133 DNA binding residues [nucleotide binding] 340100002134 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 340100002135 dinuclear metal binding motif [ion binding]; other site 340100002136 Cytochrome c; Region: Cytochrom_C; cl11414 340100002137 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 340100002138 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 340100002139 dimer interface [polypeptide binding]; other site 340100002140 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 340100002141 active site 340100002142 Fe binding site [ion binding]; other site 340100002143 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 340100002144 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 340100002145 putative DNA binding site [nucleotide binding]; other site 340100002146 putative Zn2+ binding site [ion binding]; other site 340100002147 Helix-turn-helix domains; Region: HTH; cl00088 340100002148 Predicted membrane protein [Function unknown]; Region: COG3671 340100002149 SWIB/MDM2 domain; Region: SWIB; cl02489 340100002150 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100002151 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100002152 metal binding site [ion binding]; metal-binding site 340100002153 putative dimer interface [polypeptide binding]; other site 340100002154 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 340100002155 active site 340100002156 substrate binding pocket [chemical binding]; other site 340100002157 dimer interface [polypeptide binding]; other site 340100002158 ABC transporter ATPase component; Reviewed; Region: PRK11147 340100002159 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100002160 ABC transporter; Region: ABC_tran_2; pfam12848 340100002161 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100002162 cell division protein MraZ; Reviewed; Region: PRK00326 340100002163 MraZ protein; Region: MraZ; pfam02381 340100002164 MraZ protein; Region: MraZ; pfam02381 340100002165 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 340100002166 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002167 Septum formation initiator; Region: DivIC; cl11433 340100002168 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 340100002169 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 340100002170 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100002171 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional; Region: PRK11929 340100002172 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100002173 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002174 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100002175 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100002176 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002177 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 340100002178 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 340100002179 Mg++ binding site [ion binding]; other site 340100002180 putative catalytic motif [active] 340100002181 putative substrate binding site [chemical binding]; other site 340100002182 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 340100002183 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002184 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100002185 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 340100002186 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 340100002187 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 340100002188 active site 340100002189 homodimer interface [polypeptide binding]; other site 340100002190 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 340100002191 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100002192 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002193 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100002194 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 340100002195 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 340100002196 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100002197 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 340100002198 Cell division protein FtsQ; Region: FtsQ; pfam03799 340100002199 cell division protein FtsA; Region: ftsA; TIGR01174 340100002200 Cell division protein FtsA; Region: FtsA; cl11496 340100002201 Cell division protein FtsA; Region: FtsA; cl11496 340100002202 cell division protein FtsZ; Validated; Region: PRK09330 340100002203 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 340100002204 nucleotide binding site [chemical binding]; other site 340100002205 SulA interaction site; other site 340100002206 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 340100002207 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 340100002208 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100002209 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 340100002210 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002211 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 340100002212 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002213 nucleotide binding region [chemical binding]; other site 340100002214 ATP-binding site [chemical binding]; other site 340100002215 hypothetical protein; Provisional; Region: PRK10396 340100002216 SEC-C motif; Region: SEC-C; pfam02810 340100002217 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 340100002218 Cysteine dioxygenase type I; Region: CDO_I; cl15835 340100002219 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100002220 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100002221 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 340100002222 putative DNA binding site [nucleotide binding]; other site 340100002223 putative Zn2+ binding site [ion binding]; other site 340100002224 Helix-turn-helix domains; Region: HTH; cl00088 340100002225 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 340100002226 MgtE intracellular N domain; Region: MgtE_N; cl15244 340100002227 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 340100002228 Divalent cation transporter; Region: MgtE; cl00786 340100002229 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 340100002230 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 340100002231 Helix-turn-helix domains; Region: HTH; cl00088 340100002232 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 340100002233 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 340100002234 putative dimerization interface [polypeptide binding]; other site 340100002235 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100002236 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100002237 metal binding site [ion binding]; metal-binding site 340100002238 putative dimer interface [polypeptide binding]; other site 340100002239 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 340100002240 AMP-binding enzyme; Region: AMP-binding; cl15778 340100002241 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100002242 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 340100002243 active site 340100002244 dimerization interface [polypeptide binding]; other site 340100002245 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; cl15754 340100002246 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 340100002247 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 340100002248 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase; Region: GH31; cl11402 340100002249 active site 340100002250 catalytic site [active] 340100002251 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 340100002252 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 340100002253 Walker A/P-loop; other site 340100002254 ATP binding site [chemical binding]; other site 340100002255 Q-loop/lid; other site 340100002256 ABC transporter signature motif; other site 340100002257 Walker B; other site 340100002258 D-loop; other site 340100002259 H-loop/switch region; other site 340100002260 NIL domain; Region: NIL; cl09633 340100002261 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 340100002262 dimer interface [polypeptide binding]; other site 340100002263 conserved gate region; other site 340100002264 ABC-ATPase subunit interface; other site 340100002265 NMT1-like family; Region: NMT1_2; cl15260 340100002266 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100002267 active site 2 [active] 340100002268 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100002269 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100002270 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 340100002271 putative PBP binding loops; other site 340100002272 dimer interface [polypeptide binding]; other site 340100002273 ABC-ATPase subunit interface; other site 340100002274 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 340100002275 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002276 Walker A/P-loop; other site 340100002277 ATP binding site [chemical binding]; other site 340100002278 Q-loop/lid; other site 340100002279 ABC transporter signature motif; other site 340100002280 Walker B; other site 340100002281 D-loop; other site 340100002282 H-loop/switch region; other site 340100002283 TOBE domain; Region: TOBE_2; cl01440 340100002284 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 340100002285 Helix-turn-helix domains; Region: HTH; cl00088 340100002286 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100002287 putative dimerization interface [polypeptide binding]; other site 340100002288 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100002289 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 340100002290 active site 340100002291 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100002292 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100002293 classical (c) SDRs; Region: SDR_c; cd05233 340100002294 NAD(P) binding site [chemical binding]; other site 340100002295 active site 340100002296 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 340100002297 NMT1-like family; Region: NMT1_2; cl15260 340100002298 Flagellin N-methylase; Region: FliB; cl00497 340100002299 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 340100002300 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 340100002301 AsmA-like C-terminal region; Region: AsmA_2; cl15864 340100002302 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100002303 Helix-turn-helix domains; Region: HTH; cl00088 340100002304 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100002305 classical (c) SDRs; Region: SDR_c; cd05233 340100002306 NAD(P) binding site [chemical binding]; other site 340100002307 active site 340100002308 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100002309 Helix-turn-helix domains; Region: HTH; cl00088 340100002310 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100002311 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 340100002312 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100002313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002314 NMT1-like family; Region: NMT1_2; cl15260 340100002315 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 340100002316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002317 NIPSNAP; Region: NIPSNAP; pfam07978 340100002318 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 340100002319 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; cl09155 340100002320 Protein of unknown function (DUF1810); Region: DUF1810; cl02370 340100002321 ornithine cyclodeaminase; Validated; Region: PRK07589 340100002322 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002323 Helix-turn-helix domains; Region: HTH; cl00088 340100002324 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 340100002325 putative substrate translocation pore; other site 340100002326 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002327 Helix-turn-helix domains; Region: HTH; cl00088 340100002328 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100002329 dimerization interface [polypeptide binding]; other site 340100002330 NMT1-like family; Region: NMT1_2; cl15260 340100002331 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100002332 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 340100002333 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100002334 ligand binding site [chemical binding]; other site 340100002335 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 340100002336 aromatic arch; other site 340100002337 DCoH dimer interaction site [polypeptide binding]; other site 340100002338 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 340100002339 DCoH tetramer interaction site [polypeptide binding]; other site 340100002340 substrate binding site [chemical binding]; other site 340100002341 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340100002342 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 340100002343 Substrate binding site; other site 340100002344 metal-binding site 340100002345 Phosphotransferase enzyme family; Region: APH; pfam01636 340100002346 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; cd05120 340100002347 active site 340100002348 ATP binding site [chemical binding]; other site 340100002349 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 340100002350 Organic solvent tolerance protein; Region: OstA_C; pfam04453 340100002351 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 340100002352 SurA N-terminal domain; Region: SurA_N_3; cl07813 340100002353 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100002354 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100002355 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002356 Glycerate kinase family; Region: Gly_kinase; cl00841 340100002357 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; cl09155 340100002358 pyruvate kinase; Provisional; Region: PRK05826 340100002359 domain interfaces; other site 340100002360 active site 340100002361 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100002362 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 340100002363 active site 340100002364 putative substrate binding pocket [chemical binding]; other site 340100002365 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100002366 Response regulator receiver domain; Region: Response_reg; pfam00072 340100002367 active site 340100002368 phosphorylation site [posttranslational modification] 340100002369 intermolecular recognition site; other site 340100002370 dimerization interface [polypeptide binding]; other site 340100002371 Helix-turn-helix domains; Region: HTH; cl00088 340100002372 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002373 Walker B; other site 340100002374 D-loop; other site 340100002375 H-loop/switch region; other site 340100002376 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100002377 Nucleoside recognition; Region: Gate; cl00486 340100002378 Nucleoside recognition; Region: Gate; cl00486 340100002379 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100002380 active site 340100002381 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 340100002382 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 340100002383 active site 340100002384 catalytic residues [active] 340100002385 metal binding site [ion binding]; metal-binding site 340100002386 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100002387 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 340100002388 dimer interface [polypeptide binding]; other site 340100002389 active site 340100002390 metal binding site [ion binding]; metal-binding site 340100002391 glutathione binding site [chemical binding]; other site 340100002392 tricarballylate utilization protein B; Provisional; Region: PRK15033 340100002393 tricarballylate dehydrogenase; Validated; Region: PRK08274 340100002394 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 340100002395 Helix-turn-helix domains; Region: HTH; cl00088 340100002396 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100002397 putative dimerization interface [polypeptide binding]; other site 340100002398 Protein of unknown function DUF45; Region: DUF45; cl00636 340100002399 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 340100002400 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340100002401 putative acyl-acceptor binding pocket; other site 340100002402 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 340100002403 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 340100002404 active site 340100002405 motif I; other site 340100002406 motif II; other site 340100002407 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 340100002408 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 340100002409 dimer interface [polypeptide binding]; other site 340100002410 motif 1; other site 340100002411 active site 340100002412 motif 2; other site 340100002413 motif 3; other site 340100002414 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100002415 Helix-turn-helix domains; Region: HTH; cl00088 340100002416 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 340100002417 dimerization interface [polypeptide binding]; other site 340100002418 substrate binding pocket [chemical binding]; other site 340100002419 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 340100002420 homotrimer interaction site [polypeptide binding]; other site 340100002421 putative active site [active] 340100002422 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 340100002423 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 340100002424 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100002425 catalytic residue [active] 340100002426 enoyl-CoA hydratase; Provisional; Region: PRK08252 340100002427 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 340100002428 substrate binding site [chemical binding]; other site 340100002429 oxyanion hole (OAH) forming residues; other site 340100002430 trimer interface [polypeptide binding]; other site 340100002431 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 340100002432 Fumarase C-terminus; Region: Fumerase_C; cl00795 340100002433 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100002434 Helix-turn-helix domains; Region: HTH; cl00088 340100002435 Helix-turn-helix domains; Region: HTH; cl00088 340100002436 putative transposase OrfB; Reviewed; Region: PHA02517 340100002437 HTH-like domain; Region: HTH_21; pfam13276 340100002438 Integrase core domain; Region: rve; cl01316 340100002439 Integrase core domain; Region: rve_3; cl15866 340100002440 Domain of unknown function DUF21; Region: DUF21; pfam01595 340100002441 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 340100002442 Transporter associated domain; Region: CorC_HlyC; cl08393 340100002443 Acetyltransferase (GNAT) domain; Region: Acetyltransf_4; pfam13420 340100002444 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100002445 Coenzyme A binding pocket [chemical binding]; other site 340100002446 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100002447 Protein of unknown function (DUF419); Region: DUF419; cl15265 340100002448 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 340100002449 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002450 Walker A/P-loop; other site 340100002451 ATP binding site [chemical binding]; other site 340100002452 Q-loop/lid; other site 340100002453 ABC transporter signature motif; other site 340100002454 Walker B; other site 340100002455 D-loop; other site 340100002456 H-loop/switch region; other site 340100002457 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 340100002458 MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: MaoC_like; cd03446 340100002459 homodimer interaction site [polypeptide binding]; other site 340100002460 putative active site [active] 340100002461 putative catalytic site [active] 340100002462 acyl-CoA synthetase; Validated; Region: PRK06164 340100002463 AMP-binding enzyme; Region: AMP-binding; cl15778 340100002464 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100002465 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100002466 Walker A/P-loop; other site 340100002467 ATP binding site [chemical binding]; other site 340100002468 Q-loop/lid; other site 340100002469 ABC transporter signature motif; other site 340100002470 Walker B; other site 340100002471 D-loop; other site 340100002472 H-loop/switch region; other site 340100002473 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100002474 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100002475 Walker A/P-loop; other site 340100002476 ATP binding site [chemical binding]; other site 340100002477 Q-loop/lid; other site 340100002478 ABC transporter signature motif; other site 340100002479 Walker B; other site 340100002480 D-loop; other site 340100002481 H-loop/switch region; other site 340100002482 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 340100002483 TM-ABC transporter signature motif; other site 340100002484 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 340100002485 TM-ABC transporter signature motif; other site 340100002486 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100002487 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 340100002488 ligand binding site [chemical binding]; other site 340100002489 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002490 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002491 enoyl-CoA hydratase; Region: PLN02864 340100002492 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100002493 HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit; Region: HDE_HSD; cd03448 340100002494 dimer interaction site [polypeptide binding]; other site 340100002495 substrate-binding tunnel; other site 340100002496 active site 340100002497 catalytic site [active] 340100002498 substrate binding site [chemical binding]; other site 340100002499 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002500 NAD(P) binding site [chemical binding]; other site 340100002501 short chain dehydrogenase; Provisional; Region: PRK07060 340100002502 active site 340100002503 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002504 Helix-turn-helix domains; Region: HTH; cl00088 340100002505 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 340100002506 putative dimerization interface [polypeptide binding]; other site 340100002507 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 340100002508 non-specific DNA binding site [nucleotide binding]; other site 340100002509 salt bridge; other site 340100002510 sequence-specific DNA binding site [nucleotide binding]; other site 340100002511 Cupin domain; Region: Cupin_2; cl09118 340100002512 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100002513 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 340100002514 active site 340100002515 putative substrate binding pocket [chemical binding]; other site 340100002516 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_16; cd08502 340100002517 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100002518 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100002519 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100002520 MlrC C-terminus; Region: MlrC_C; pfam07171 340100002521 FAD dependent oxidoreductase; Region: DAO; pfam01266 340100002522 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002523 NMT1-like family; Region: NMT1_2; cl15260 340100002524 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100002525 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100002526 FMN binding site [chemical binding]; other site 340100002527 substrate binding site [chemical binding]; other site 340100002528 putative catalytic residue [active] 340100002529 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002530 NMT1-like family; Region: NMT1_2; cl15260 340100002531 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100002532 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 340100002533 FAD binding site [chemical binding]; other site 340100002534 substrate binding site [chemical binding]; other site 340100002535 catalytic base [active] 340100002536 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 340100002537 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 340100002538 active site 340100002539 enoyl-CoA hydratase; Provisional; Region: PRK08140 340100002540 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 340100002541 substrate binding site [chemical binding]; other site 340100002542 oxyanion hole (OAH) forming residues; other site 340100002543 trimer interface [polypeptide binding]; other site 340100002544 Uncharacterized conserved protein [Function unknown]; Region: COG3777 340100002545 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100002546 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100002547 active site 2 [active] 340100002548 active site 1 [active] 340100002549 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002550 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002551 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; cl09155 340100002552 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 340100002553 catalytic center binding site [active] 340100002554 ATP binding site [chemical binding]; other site 340100002555 poly(A) polymerase; Region: pcnB; TIGR01942 340100002556 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 340100002557 active site 340100002558 NTP binding site [chemical binding]; other site 340100002559 metal binding triad [ion binding]; metal-binding site 340100002560 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 340100002561 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 340100002562 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 340100002563 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100002564 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002565 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 340100002566 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 340100002567 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 340100002568 dimerization interface [polypeptide binding]; other site 340100002569 putative ATP binding site [chemical binding]; other site 340100002570 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002571 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 340100002572 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 340100002573 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 340100002574 ATP binding site [chemical binding]; other site 340100002575 Mg2+ binding site [ion binding]; other site 340100002576 G-X-G motif; other site 340100002577 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 340100002578 ATP binding site [chemical binding]; other site 340100002579 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 340100002580 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340100002581 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 340100002582 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_14; cd08355 340100002583 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100002584 AMIN domain; Region: AMIN; pfam11741 340100002585 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 340100002586 active site 340100002587 metal binding site [ion binding]; metal-binding site 340100002588 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 340100002589 fumarate hydratase; Reviewed; Region: fumC; PRK00485 340100002590 Class II fumarases; Region: Fumarase_classII; cd01362 340100002591 active site 340100002592 tetramer interface [polypeptide binding]; other site 340100002593 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002594 NMT1-like family; Region: NMT1_2; cl15260 340100002595 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 340100002596 Helix-turn-helix domains; Region: HTH; cl00088 340100002597 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100002598 dimerization interface [polypeptide binding]; other site 340100002599 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100002600 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100002601 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002602 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002603 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002604 NMT1-like family; Region: NMT1_2; cl15260 340100002605 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100002606 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100002607 active site 340100002608 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100002609 Helix-turn-helix domains; Region: HTH; cl00088 340100002610 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like_2; cd08448 340100002611 putative dimerization interface [polypeptide binding]; other site 340100002612 putative substrate binding pocket [chemical binding]; other site 340100002613 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 340100002614 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 340100002615 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 340100002616 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 340100002617 dimer interface [polypeptide binding]; other site 340100002618 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 340100002619 putative active site [active] 340100002620 putative catalytic site [active] 340100002621 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100002622 amidase; Provisional; Region: PRK06061 340100002623 Amidase; Region: Amidase; cl11426 340100002624 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100002625 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100002626 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100002627 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100002628 DctM-like transporters; Region: DctM; pfam06808 340100002629 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100002630 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100002631 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100002632 active site 340100002633 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002634 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002635 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100002636 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100002637 DNA-binding site [nucleotide binding]; DNA binding site 340100002638 UTRA domain; Region: UTRA; cl01230 340100002639 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 340100002640 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; cl09155 340100002641 LysE type translocator; Region: LysE; cl00565 340100002642 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 340100002643 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 340100002644 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 340100002645 putative active site [active] 340100002646 putative substrate binding site [chemical binding]; other site 340100002647 putative cosubstrate binding site; other site 340100002648 catalytic site [active] 340100002649 Predicted dehydrogenase [General function prediction only]; Region: COG0579 340100002650 Flavin Reductases; Region: FlaRed; cl00801 340100002651 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 340100002652 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340100002653 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 340100002654 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl15777 340100002655 Helix-turn-helix domains; Region: HTH; cl00088 340100002656 putative transposase OrfB; Reviewed; Region: PHA02517 340100002657 HTH-like domain; Region: HTH_21; pfam13276 340100002658 Integrase core domain; Region: rve; cl01316 340100002659 Integrase core domain; Region: rve_3; cl15866 340100002660 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl15777 340100002661 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 340100002662 putative substrate translocation pore; other site 340100002663 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 340100002664 putative ATP binding site [chemical binding]; other site 340100002665 putative substrate interface [chemical binding]; other site 340100002666 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100002667 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100002668 DNA-binding site [nucleotide binding]; DNA binding site 340100002669 UTRA domain; Region: UTRA; cl01230 340100002670 acyl-CoA synthetase; Validated; Region: PRK06164 340100002671 AMP-binding enzyme; Region: AMP-binding; cl15778 340100002672 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002673 NMT1-like family; Region: NMT1_2; cl15260 340100002674 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100002675 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002676 NAD(P) binding site [chemical binding]; other site 340100002677 active site 340100002678 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 340100002679 substrate-cofactor binding pocket; other site 340100002680 homodimer interface [polypeptide binding]; other site 340100002681 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100002682 catalytic residue [active] 340100002683 aminodeoxychorismate synthase; Provisional; Region: PRK07508 340100002684 chorismate binding enzyme; Region: Chorismate_bind; cl10555 340100002685 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002686 Walker A/P-loop; other site 340100002687 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 340100002688 ATP binding site [chemical binding]; other site 340100002689 Q-loop/lid; other site 340100002690 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002691 ABC transporter signature motif; other site 340100002692 Walker B; other site 340100002693 D-loop; other site 340100002694 H-loop/switch region; other site 340100002695 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 340100002696 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 340100002697 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 340100002698 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 340100002699 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002700 Walker A/P-loop; other site 340100002701 ATP binding site [chemical binding]; other site 340100002702 Q-loop/lid; other site 340100002703 ABC transporter signature motif; other site 340100002704 Walker B; other site 340100002705 D-loop; other site 340100002706 H-loop/switch region; other site 340100002707 Helix-turn-helix domains; Region: HTH; cl00088 340100002708 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100002709 KDPG and KHG aldolase; Region: Aldolase; pfam01081 340100002710 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 340100002711 active site 340100002712 intersubunit interface [polypeptide binding]; other site 340100002713 catalytic residue [active] 340100002714 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 340100002715 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 340100002716 substrate binding site [chemical binding]; other site 340100002717 ATP binding site [chemical binding]; other site 340100002718 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002719 Helix-turn-helix domains; Region: HTH; cl00088 340100002720 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 340100002721 putative effector binding pocket; other site 340100002722 dimerization interface [polypeptide binding]; other site 340100002723 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 340100002724 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 340100002725 active site 340100002726 EamA-like transporter family; Region: EamA; cl01037 340100002727 EamA-like transporter family; Region: EamA; cl01037 340100002728 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 340100002729 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100002730 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100002731 ABC transporter; Region: ABC_tran_2; pfam12848 340100002732 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100002733 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 340100002734 catalytic triad [active] 340100002735 conserved cis-peptide bond; other site 340100002736 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 340100002737 putative active site [active] 340100002738 heme pocket [chemical binding]; other site 340100002739 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 340100002740 DNA binding residues [nucleotide binding] 340100002741 dimerization interface [polypeptide binding]; other site 340100002742 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 340100002743 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100002744 active site 340100002745 AMP-binding enzyme; Region: AMP-binding; cl15778 340100002746 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 340100002747 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100002748 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100002749 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100002750 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100002751 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100002752 classical (c) SDRs; Region: SDR_c; cd05233 340100002753 NAD(P) binding site [chemical binding]; other site 340100002754 active site 340100002755 Septum formation topological specificity factor MinE; Region: MinE; cl00538 340100002756 cell division inhibitor MinD; Provisional; Region: PRK10818 340100002757 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 340100002758 Switch I; other site 340100002759 Switch II; other site 340100002760 septum formation inhibitor; Provisional; Region: minC; PRK00030 340100002761 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 340100002762 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 340100002763 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 340100002764 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100002765 active site 340100002766 HIGH motif; other site 340100002767 nucleotide binding site [chemical binding]; other site 340100002768 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 340100002769 KMSKS motif; other site 340100002770 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 340100002771 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 340100002772 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 340100002773 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 340100002774 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 340100002775 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 340100002776 dimerization interface [polypeptide binding]; other site 340100002777 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 340100002778 ATP binding site [chemical binding]; other site 340100002779 Mg2+ binding site [ion binding]; other site 340100002780 G-X-G motif; other site 340100002781 osmolarity response regulator; Provisional; Region: ompR; PRK09468 340100002782 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100002783 active site 340100002784 phosphorylation site [posttranslational modification] 340100002785 intermolecular recognition site; other site 340100002786 dimerization interface [polypeptide binding]; other site 340100002787 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 340100002788 DNA binding site [nucleotide binding] 340100002789 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100002790 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 340100002791 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 340100002792 ATP binding site [chemical binding]; other site 340100002793 putative Mg++ binding site [ion binding]; other site 340100002794 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 340100002795 nucleotide binding region [chemical binding]; other site 340100002796 ATP-binding site [chemical binding]; other site 340100002797 RQC domain; Region: RQC; cl09632 340100002798 HRDC domain; Region: HRDC; cl02578 340100002799 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 340100002800 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 340100002801 Walker A motif; other site 340100002802 ATP binding site [chemical binding]; other site 340100002803 Walker B motif; other site 340100002804 arginine finger; other site 340100002805 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 340100002806 serine racemase; Region: PLN02970 340100002807 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 340100002808 tetramer interface [polypeptide binding]; other site 340100002809 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100002810 catalytic residue [active] 340100002811 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 340100002812 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 340100002813 putative NAD(P) binding site [chemical binding]; other site 340100002814 active site 340100002815 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 340100002816 RuvA N terminal domain; Region: RuvA_N; pfam01330 340100002817 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 340100002818 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 340100002819 active site 340100002820 putative DNA-binding cleft [nucleotide binding]; other site 340100002821 dimer interface [polypeptide binding]; other site 340100002822 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 340100002823 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 340100002824 purine monophosphate binding site [chemical binding]; other site 340100002825 dimer interface [polypeptide binding]; other site 340100002826 putative catalytic residues [active] 340100002827 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 340100002828 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 340100002829 Helix-turn-helix domains; Region: HTH; cl00088 340100002830 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 340100002831 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 340100002832 FMN binding site [chemical binding]; other site 340100002833 active site 340100002834 catalytic residues [active] 340100002835 substrate binding site [chemical binding]; other site 340100002836 hypothetical protein; Provisional; Region: PRK06996 340100002837 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002838 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 340100002839 proline aminopeptidase P II; Provisional; Region: PRK10879 340100002840 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 340100002841 active site 340100002842 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 340100002843 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 340100002844 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; cl09173 340100002845 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 340100002846 active site 340100002847 tetramer interface; other site 340100002848 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 340100002849 Peptidase family M48; Region: Peptidase_M48; cl12018 340100002850 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 340100002851 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 340100002852 Zinc-finger domain; Region: zf-CHCC; cl01821 340100002853 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 340100002854 homodimer interface [polypeptide binding]; other site 340100002855 substrate-cofactor binding pocket; other site 340100002856 catalytic residue [active] 340100002857 AzlC protein; Region: AzlC; cl00570 340100002858 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 340100002859 helicase 45; Provisional; Region: PTZ00424 340100002860 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 340100002861 ATP binding site [chemical binding]; other site 340100002862 Mg++ binding site [ion binding]; other site 340100002863 motif III; other site 340100002864 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 340100002865 nucleotide binding region [chemical binding]; other site 340100002866 ATP-binding site [chemical binding]; other site 340100002867 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 340100002868 catalytic residues [active] 340100002869 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 340100002870 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 340100002871 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 340100002872 putative MPT binding site; other site 340100002873 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100002874 Helix-turn-helix domains; Region: HTH; cl00088 340100002875 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100002876 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002877 NMT1-like family; Region: NMT1_2; cl15260 340100002878 Phasin protein; Region: Phasin_2; cl11491 340100002879 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 340100002880 quinone interaction residues [chemical binding]; other site 340100002881 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 340100002882 active site 340100002883 catalytic residues [active] 340100002884 FMN binding site [chemical binding]; other site 340100002885 substrate binding site [chemical binding]; other site 340100002886 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 340100002887 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 340100002888 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100002889 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100002890 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 340100002891 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 340100002892 nudix motif; other site 340100002893 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 340100002894 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100002895 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 340100002896 DNA binding residues [nucleotide binding] 340100002897 dimerization interface [polypeptide binding]; other site 340100002898 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100002899 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100002900 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 340100002901 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 340100002902 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 340100002903 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 340100002904 DNA binding site [nucleotide binding] 340100002905 Int/Topo IB signature motif; other site 340100002906 active site 340100002907 TraU protein; Region: TraU; cl06067 340100002908 Protein of unknown function (DUF4031); Region: DUF4031; pfam13223 340100002909 Protein of unknown function (DUF550); Region: DUF550; pfam04447 340100002910 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; cl15754 340100002911 DNA binding site [nucleotide binding] 340100002912 substrate interaction site [chemical binding]; other site 340100002913 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; cl15754 340100002914 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002915 Walker A/P-loop; other site 340100002916 ATP binding site [chemical binding]; other site 340100002917 Q-loop/lid; other site 340100002918 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 340100002919 RecT family; Region: RecT; cl04285 340100002920 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 340100002921 Amino acid synthesis; Region: AA_synth; pfam06684 340100002922 HNH endonuclease; Region: HNH_3; pfam13392 340100002923 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 340100002924 TM2 domain; Region: TM2; cl00984 340100002925 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 340100002926 Catalytic site [active] 340100002927 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100002928 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 340100002929 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100002930 Endodeoxyribonuclease RusA; Region: RusA; cl01885 340100002931 Terminase small subunit; Region: Terminase_2; cl01513 340100002932 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 340100002933 Terminase-like family; Region: Terminase_6; pfam03237 340100002934 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 340100002935 Protein of unknown function (DUF1073); Region: DUF1073; pfam06381 340100002936 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3567; cl12082 340100002937 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 340100002938 Uncharacterized protein conserved in bacteria (DUF2213); Region: DUF2213; cl15403 340100002939 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100002940 Encapsulating protein for peroxidase; Region: Linocin_M18; cl12047 340100002941 Uncharacterized protein conserved in bacteria (DUF2184); Region: DUF2184; pfam09950 340100002942 HeH/LEM domain; Region: HeH; pfam12949 340100002943 Protein of unknown function (DUF4054); Region: DUF4054; pfam13262 340100002944 Protein of unknown function (DUF3383); Region: DUF3383; pfam11863 340100002945 Protein of unknown function (DUF3383); Region: DUF3383; pfam11863 340100002946 Protein of unknown function (DUF3277); Region: DUF3277; pfam11681 340100002947 tape measure domain; Region: tape_meas_nterm; TIGR02675 340100002948 Baseplate J-like protein; Region: Baseplate_J; cl01294 340100002949 Protein of unknown function (DUF2612); Region: DUF2612; pfam11041 340100002950 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 340100002951 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340100002952 catalytic residue [active] 340100002953 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 340100002954 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 340100002955 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100002956 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 340100002957 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 340100002958 DNA binding residues [nucleotide binding] 340100002959 dimer interface [polypeptide binding]; other site 340100002960 putative metal binding site [ion binding]; other site 340100002961 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 340100002962 Integrase core domain; Region: rve; cl01316 340100002963 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100002964 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 340100002965 Cation efflux family; Region: Cation_efflux; cl00316 340100002966 HTH-like domain; Region: HTH_21; pfam13276 340100002967 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100002968 Integrase core domain; Region: rve; cl01316 340100002969 Integrase core domain; Region: rve_3; cl15866 340100002970 Helix-turn-helix domains; Region: HTH; cl00088 340100002971 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 340100002972 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 340100002973 DNA binding residues [nucleotide binding] 340100002974 dimer interface [polypeptide binding]; other site 340100002975 putative metal binding site [ion binding]; other site 340100002976 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100002977 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100002978 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 340100002979 ArsC family; Region: ArsC; pfam03960 340100002980 catalytic residues [active] 340100002981 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 340100002982 Membrane transport protein; Region: Mem_trans; cl09117 340100002983 Low molecular weight phosphatase family; Region: LMWPc; cd00115 340100002984 active site 340100002985 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 340100002986 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100002987 putative metal binding site [ion binding]; other site 340100002988 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 340100002989 putative DNA binding site [nucleotide binding]; other site 340100002990 putative Zn2+ binding site [ion binding]; other site 340100002991 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100002992 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100002993 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 340100002994 Magnesium ion binding site [ion binding]; other site 340100002995 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100002996 ParB-like nuclease domain; Region: ParBc; cl02129 340100002997 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100002998 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 340100002999 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100003000 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 340100003001 ssDNA binding site [nucleotide binding]; other site 340100003002 dimer interface [polypeptide binding]; other site 340100003003 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100003004 DNA topoisomerase III; Provisional; Region: PRK07726 340100003005 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 340100003006 active site 340100003007 putative interdomain interaction site [polypeptide binding]; other site 340100003008 putative metal-binding site [ion binding]; other site 340100003009 putative nucleotide binding site [chemical binding]; other site 340100003010 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 340100003011 domain I; other site 340100003012 DNA binding groove [nucleotide binding] 340100003013 phosphate binding site [ion binding]; other site 340100003014 domain II; other site 340100003015 domain III; other site 340100003016 nucleotide binding site [chemical binding]; other site 340100003017 catalytic site [active] 340100003018 domain IV; other site 340100003019 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100003020 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; cl15754 340100003021 cofactor binding site; other site 340100003022 DNA binding site [nucleotide binding] 340100003023 substrate interaction site [chemical binding]; other site 340100003024 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100003025 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 340100003026 DNA binding site [nucleotide binding] 340100003027 Int/Topo IB signature motif; other site 340100003028 active site 340100003029 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 340100003030 DNA binding site [nucleotide binding] 340100003031 Int/Topo IB signature motif; other site 340100003032 active site 340100003033 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 340100003034 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 340100003035 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 340100003036 DNA binding site [nucleotide binding] 340100003037 Int/Topo IB signature motif; other site 340100003038 active site 340100003039 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; cl15754 340100003040 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 340100003041 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100003042 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100003043 Domain of unknown function (DUF932); Region: DUF932; cl12129 340100003044 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100003045 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100003046 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100003047 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100003048 putative active site [active] 340100003049 putative NTP binding site [chemical binding]; other site 340100003050 putative nucleic acid binding site [nucleotide binding]; other site 340100003051 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100003052 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 340100003053 active site 340100003054 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100003055 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100003056 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100003057 putative active site [active] 340100003058 putative NTP binding site [chemical binding]; other site 340100003059 putative nucleic acid binding site [nucleotide binding]; other site 340100003060 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100003061 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 340100003062 active site 340100003063 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003064 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100003065 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 340100003066 nucleotide binding region [chemical binding]; other site 340100003067 ATP-binding site [chemical binding]; other site 340100003068 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100003069 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100003070 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340100003071 Protein of unknown function (DUF2859); Region: DUF2859; cl12633 340100003072 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100003073 Domain of unknown function DUF87; Region: DUF87; pfam01935 340100003074 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100003075 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 340100003076 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100003077 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100003078 Protein of unknown function (DUF3262); Region: DUF3262; cl13160 340100003079 Protein of unknown function (DUF2976); Region: DUF2976; cl12739 340100003080 Protein of unknown function (DUF3487); Region: DUF3487; cl13432 340100003081 Protein of unknown function (DUF2895); Region: DUF2895; cl12968 340100003082 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 340100003083 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100003084 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100003085 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100003086 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100003087 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100003088 MPN+ (JAMM) motif; other site 340100003089 Zinc-binding site [ion binding]; other site 340100003090 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 340100003091 TraU protein; Region: TraU; cl06067 340100003092 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100003093 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100003094 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 340100003095 RES domain; Region: RES; cl02411 340100003096 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100003097 Putative helicase; Region: TraI_2; pfam07514 340100003098 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100003099 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100003100 Helix-turn-helix domains; Region: HTH; cl00088 340100003101 Transposase, Mutator family; Region: Transposase_mut; pfam00872 340100003102 inactivated transposase 340100003103 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003104 NMT1-like family; Region: NMT1_2; cl15260 340100003105 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 340100003106 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 340100003107 Transposase; Region: DDE_Tnp_ISL3; pfam01610 340100003108 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 340100003109 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 340100003110 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340100003111 Helix-turn-helix domains; Region: HTH; cl00088 340100003112 Integrase core domain; Region: rve; cl01316 340100003113 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003114 Integrase core domain; Region: rve_3; cl15866 340100003115 Fusaric acid resistance protein family; Region: FUSC; pfam04632 340100003116 HTH-like domain; Region: HTH_21; pfam13276 340100003117 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100003118 Integrase core domain; Region: rve; cl01316 340100003119 Integrase core domain; Region: rve_3; cl15866 340100003120 Helix-turn-helix domains; Region: HTH; cl00088 340100003121 Fusaric acid resistance protein family; Region: FUSC; pfam04632 340100003122 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 340100003123 Transposase; Region: DDE_Tnp_ISL3; pfam01610 340100003124 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340100003125 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 340100003126 Integrase core domain; Region: rve; cl01316 340100003127 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003128 Integrase core domain; Region: rve_3; cl15866 340100003129 Helix-turn-helix domains; Region: HTH; cl00088 340100003130 Helix-turn-helix domains; Region: HTH; cl00088 340100003131 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003132 active site 340100003133 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100003134 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003135 acyl-CoA synthetase; Validated; Region: PRK06178 340100003136 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003137 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 340100003138 substrate binding site [chemical binding]; other site 340100003139 oxyanion hole (OAH) forming residues; other site 340100003140 trimer interface [polypeptide binding]; other site 340100003141 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003142 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003143 acetyl-CoA acetyltransferase; Provisional; Region: PRK06064 340100003144 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100003145 active site 340100003146 acyl-CoA synthetase; Validated; Region: PRK06188 340100003147 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003148 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003149 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003150 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003151 NAD(P) binding site [chemical binding]; other site 340100003152 active site 340100003153 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100003154 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100003155 Walker A/P-loop; other site 340100003156 ATP binding site [chemical binding]; other site 340100003157 Q-loop/lid; other site 340100003158 ABC transporter signature motif; other site 340100003159 Walker B; other site 340100003160 D-loop; other site 340100003161 H-loop/switch region; other site 340100003162 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003163 putative transposase OrfB; Reviewed; Region: PHA02517 340100003164 HTH-like domain; Region: HTH_21; pfam13276 340100003165 Integrase core domain; Region: rve; cl01316 340100003166 Integrase core domain; Region: rve_3; cl15866 340100003167 Helix-turn-helix domains; Region: HTH; cl00088 340100003168 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 340100003169 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003170 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 340100003171 TM-ABC transporter signature motif; other site 340100003172 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 340100003173 TM-ABC transporter signature motif; other site 340100003174 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003175 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 340100003176 ligand binding site [chemical binding]; other site 340100003177 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100003178 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100003179 Walker A/P-loop; other site 340100003180 ATP binding site [chemical binding]; other site 340100003181 Q-loop/lid; other site 340100003182 ABC transporter signature motif; other site 340100003183 Walker B; other site 340100003184 D-loop; other site 340100003185 H-loop/switch region; other site 340100003186 enoyl-CoA hydratase; Validated; Region: PRK08139 340100003187 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 340100003188 substrate binding site [chemical binding]; other site 340100003189 oxyanion hole (OAH) forming residues; other site 340100003190 trimer interface [polypeptide binding]; other site 340100003191 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003192 classical (c) SDRs; Region: SDR_c; cd05233 340100003193 NAD(P) binding site [chemical binding]; other site 340100003194 active site 340100003195 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100003196 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100003197 FMN binding site [chemical binding]; other site 340100003198 substrate binding site [chemical binding]; other site 340100003199 putative catalytic residue [active] 340100003200 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003201 Helix-turn-helix domains; Region: HTH; cl00088 340100003202 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340100003203 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340100003204 Integrase core domain; Region: rve; cl01316 340100003205 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003206 Integrase core domain; Region: rve_3; cl15866 340100003207 Helix-turn-helix domains; Region: HTH; cl00088 340100003208 Helix-turn-helix domains; Region: HTH; cl00088 340100003209 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 340100003210 Integrase core domain; Region: rve; cl01316 340100003211 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 340100003212 transposase/IS protein; Provisional; Region: PRK09183 340100003213 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 340100003214 Walker A motif; other site 340100003215 ATP binding site [chemical binding]; other site 340100003216 Walker B motif; other site 340100003217 arginine finger; other site 340100003218 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 340100003219 Integrase core domain; Region: rve; cl01316 340100003220 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 340100003221 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 340100003222 Helix-turn-helix domains; Region: HTH; cl00088 340100003223 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100003224 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 340100003225 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340100003226 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340100003227 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 340100003228 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100003229 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100003230 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 340100003231 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 340100003232 carboxyltransferase (CT) interaction site; other site 340100003233 biotinylation site [posttranslational modification]; other site 340100003234 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003235 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003236 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100003237 active site 2 [active] 340100003238 active site 1 [active] 340100003239 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003240 NMT1-like family; Region: NMT1_2; cl15260 340100003241 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100003242 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 340100003243 substrate binding site [chemical binding]; other site 340100003244 oxyanion hole (OAH) forming residues; other site 340100003245 trimer interface [polypeptide binding]; other site 340100003246 enoyl-CoA hydratase; Provisional; Region: PRK09245 340100003247 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 340100003248 substrate binding site [chemical binding]; other site 340100003249 oxyanion hole (OAH) forming residues; other site 340100003250 trimer interface [polypeptide binding]; other site 340100003251 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100003252 Helix-turn-helix domains; Region: HTH; cl00088 340100003253 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100003254 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100003255 Helix-turn-helix domains; Region: HTH; cl00088 340100003256 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100003257 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 340100003258 active site 340100003259 FMN binding site [chemical binding]; other site 340100003260 substrate binding site [chemical binding]; other site 340100003261 homotetramer interface [polypeptide binding]; other site 340100003262 catalytic residue [active] 340100003263 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 340100003264 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 340100003265 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003266 NAD(P) binding site [chemical binding]; other site 340100003267 active site 340100003268 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100003269 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100003270 Walker A/P-loop; other site 340100003271 ATP binding site [chemical binding]; other site 340100003272 Q-loop/lid; other site 340100003273 ABC transporter signature motif; other site 340100003274 Walker B; other site 340100003275 D-loop; other site 340100003276 H-loop/switch region; other site 340100003277 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100003278 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100003279 Walker A/P-loop; other site 340100003280 ATP binding site [chemical binding]; other site 340100003281 Q-loop/lid; other site 340100003282 ABC transporter signature motif; other site 340100003283 Walker B; other site 340100003284 D-loop; other site 340100003285 H-loop/switch region; other site 340100003286 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 340100003287 TM-ABC transporter signature motif; other site 340100003288 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 340100003289 TM-ABC transporter signature motif; other site 340100003290 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003291 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_3; cd06336 340100003292 putative ligand binding site [chemical binding]; other site 340100003293 NAD binding domain of 6-phosphogluconate dehydrogenase; Region: NAD_binding_2; pfam03446 340100003294 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003295 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003296 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 340100003297 substrate binding site [chemical binding]; other site 340100003298 oxyanion hole (OAH) forming residues; other site 340100003299 trimer interface [polypeptide binding]; other site 340100003300 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003301 Helix-turn-helix domains; Region: HTH; cl00088 340100003302 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100003303 dimerization interface [polypeptide binding]; other site 340100003304 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100003305 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100003306 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 340100003307 putative active site pocket [active] 340100003308 dimerization interface [polypeptide binding]; other site 340100003309 putative catalytic residue [active] 340100003310 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 340100003311 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100003312 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 340100003313 FMN binding site [chemical binding]; other site 340100003314 active site 340100003315 substrate binding site [chemical binding]; other site 340100003316 catalytic residue [active] 340100003317 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 340100003318 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100003319 Helix-turn-helix domains; Region: HTH; cl00088 340100003320 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100003321 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 340100003322 putative effector binding pocket; other site 340100003323 dimerization interface [polypeptide binding]; other site 340100003324 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 340100003325 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100003326 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 340100003327 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003328 hypothetical protein; Provisional; Region: PRK06753 340100003329 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100003330 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_9; cd07245 340100003331 dimer interface [polypeptide binding]; other site 340100003332 putative metal binding site [ion binding]; other site 340100003333 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003334 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 340100003335 putative ligand binding site [chemical binding]; other site 340100003336 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 340100003337 TM-ABC transporter signature motif; other site 340100003338 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 340100003339 TM-ABC transporter signature motif; other site 340100003340 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100003341 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100003342 Walker A/P-loop; other site 340100003343 ATP binding site [chemical binding]; other site 340100003344 Q-loop/lid; other site 340100003345 ABC transporter signature motif; other site 340100003346 Walker B; other site 340100003347 D-loop; other site 340100003348 H-loop/switch region; other site 340100003349 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100003350 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100003351 Walker A/P-loop; other site 340100003352 ATP binding site [chemical binding]; other site 340100003353 Q-loop/lid; other site 340100003354 ABC transporter signature motif; other site 340100003355 Walker B; other site 340100003356 D-loop; other site 340100003357 H-loop/switch region; other site 340100003358 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003359 Helix-turn-helix domains; Region: HTH; cl00088 340100003360 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100003361 Helix-turn-helix domains; Region: HTH; cl00088 340100003362 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 340100003363 dimerization interface [polypeptide binding]; other site 340100003364 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003365 NMT1-like family; Region: NMT1_2; cl15260 340100003366 Predicted acyl esterases [General function prediction only]; Region: COG2936 340100003367 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 340100003368 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 340100003369 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 340100003370 putative DNA binding site [nucleotide binding]; other site 340100003371 putative Zn2+ binding site [ion binding]; other site 340100003372 Helix-turn-helix domains; Region: HTH; cl00088 340100003373 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100003374 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003375 Membrane transport protein; Region: Mem_trans; cl09117 340100003376 Helix-turn-helix domains; Region: HTH; cl00088 340100003377 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 340100003378 putative effector binding pocket; other site 340100003379 dimerization interface [polypeptide binding]; other site 340100003380 Helix-turn-helix domains; Region: HTH; cl00088 340100003381 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 340100003382 Integrase core domain; Region: rve; cl01316 340100003383 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003384 Integrase core domain; Region: rve_3; cl15866 340100003385 Helix-turn-helix domains; Region: HTH; cl00088 340100003386 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003387 Helix-turn-helix domains; Region: HTH; cl00088 340100003388 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 340100003389 putative effector binding pocket; other site 340100003390 dimerization interface [polypeptide binding]; other site 340100003391 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100003392 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 340100003393 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 340100003394 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 340100003395 Helix-turn-helix domains; Region: HTH; cl00088 340100003396 Integrase core domain; Region: rve; cl01316 340100003397 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003398 Integrase core domain; Region: rve_3; cl15866 340100003399 Helix-turn-helix domains; Region: HTH; cl00088 340100003400 Integrase core domain; Region: rve; cl01316 340100003401 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003402 Integrase core domain; Region: rve_3; cl15866 340100003403 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003404 NMT1-like family; Region: NMT1_2; cl15260 340100003405 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100003406 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003407 CoA-ligase; Region: Ligase_CoA; cl02894 340100003408 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100003409 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003410 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003411 active site 340100003412 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003413 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 340100003414 substrate binding site [chemical binding]; other site 340100003415 oxyanion hole (OAH) forming residues; other site 340100003416 trimer interface [polypeptide binding]; other site 340100003417 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 340100003418 short chain dehydrogenase; Provisional; Region: PRK07576 340100003419 NAD(P) binding site [chemical binding]; other site 340100003420 substrate binding site [chemical binding]; other site 340100003421 homotetramer interface [polypeptide binding]; other site 340100003422 active site 340100003423 homodimer interface [polypeptide binding]; other site 340100003424 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003425 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003426 active site 340100003427 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100003428 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003429 CoA-ligase; Region: Ligase_CoA; cl02894 340100003430 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100003431 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 340100003432 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100003433 FMN binding site [chemical binding]; other site 340100003434 substrate binding site [chemical binding]; other site 340100003435 putative catalytic residue [active] 340100003436 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100003437 DctM-like transporters; Region: DctM; pfam06808 340100003438 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100003439 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100003440 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003441 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003442 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003443 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003444 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003445 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 340100003446 substrate binding site [chemical binding]; other site 340100003447 oxyanion hole (OAH) forming residues; other site 340100003448 trimer interface [polypeptide binding]; other site 340100003449 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003450 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003451 enoyl-CoA hydratase; Region: PLN02864 340100003452 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100003453 HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit; Region: HDE_HSD; cd03448 340100003454 dimer interaction site [polypeptide binding]; other site 340100003455 substrate-binding tunnel; other site 340100003456 active site 340100003457 catalytic site [active] 340100003458 substrate binding site [chemical binding]; other site 340100003459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003460 NMT1-like family; Region: NMT1_2; cl15260 340100003461 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003462 NMT1-like family; Region: NMT1_2; cl15260 340100003463 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003464 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003465 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100003466 active site 2 [active] 340100003467 active site 1 [active] 340100003468 thiolase; Provisional; Region: PRK06158 340100003469 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100003470 active site 340100003471 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 340100003472 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100003473 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003474 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 340100003475 substrate binding site [chemical binding]; other site 340100003476 oxyanion hole (OAH) forming residues; other site 340100003477 trimer interface [polypeptide binding]; other site 340100003478 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003479 NMT1-like family; Region: NMT1_2; cl15260 340100003480 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 340100003481 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 340100003482 Walker A motif; other site 340100003483 ATP binding site [chemical binding]; other site 340100003484 Walker B motif; other site 340100003485 arginine finger; other site 340100003486 Helix-turn-helix domains; Region: HTH; cl00088 340100003487 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 340100003488 CoenzymeA binding site [chemical binding]; other site 340100003489 subunit interaction site [polypeptide binding]; other site 340100003490 PHB binding site; other site 340100003491 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003492 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 340100003493 putative ligand binding site [chemical binding]; other site 340100003494 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 340100003495 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 340100003496 ATP binding site [chemical binding]; other site 340100003497 Walker B motif; other site 340100003498 arginine finger; other site 340100003499 Helix-turn-helix domains; Region: HTH; cl00088 340100003500 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003501 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003502 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 340100003503 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003504 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 340100003505 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 340100003506 substrate binding site [chemical binding]; other site 340100003507 oxyanion hole (OAH) forming residues; other site 340100003508 trimer interface [polypeptide binding]; other site 340100003509 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100003510 classical (c) SDRs; Region: SDR_c; cd05233 340100003511 NAD(P) binding site [chemical binding]; other site 340100003512 active site 340100003513 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003514 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003515 active site 340100003516 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07819 340100003517 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003518 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100003519 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100003520 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003521 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003522 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 340100003523 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 340100003524 NAD(P) binding site [chemical binding]; other site 340100003525 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100003526 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 340100003527 substrate binding site [chemical binding]; other site 340100003528 oxyanion hole (OAH) forming residues; other site 340100003529 trimer interface [polypeptide binding]; other site 340100003530 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 340100003531 Transposase, Mutator family; Region: Transposase_mut; pfam00872 340100003532 Nucleotide-sugar transporter; Region: Nuc_sug_transp; pfam04142 340100003533 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003534 NMT1-like family; Region: NMT1_2; cl15260 340100003535 GAF domain; Region: GAF; cl15785 340100003536 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100003537 Helix-turn-helix domains; Region: HTH; cl00088 340100003538 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100003539 dimerization interface [polypeptide binding]; other site 340100003540 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100003541 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100003542 Predicted acyl esterases [General function prediction only]; Region: COG2936 340100003543 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 340100003544 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003545 NMT1-like family; Region: NMT1_2; cl15260 340100003546 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 340100003547 Helix-turn-helix domains; Region: HTH; cl00088 340100003548 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100003549 putative dimerization interface [polypeptide binding]; other site 340100003550 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003551 NMT1-like family; Region: NMT1_2; cl15260 340100003552 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100003553 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 340100003554 dimer interface [polypeptide binding]; other site 340100003555 NADP binding site [chemical binding]; other site 340100003556 catalytic residues [active] 340100003557 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 340100003558 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 340100003559 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100003560 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100003561 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003562 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100003563 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 340100003564 Proline racemase; Region: Pro_racemase; pfam05544 340100003565 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 340100003566 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 340100003567 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 340100003568 active site 340100003569 benzoate transport; Region: 2A0115; TIGR00895 340100003570 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 340100003571 putative substrate translocation pore; other site 340100003572 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 340100003573 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100003574 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100003575 Walker A/P-loop; other site 340100003576 ATP binding site [chemical binding]; other site 340100003577 Q-loop/lid; other site 340100003578 ABC transporter signature motif; other site 340100003579 Walker B; other site 340100003580 D-loop; other site 340100003581 H-loop/switch region; other site 340100003582 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 340100003583 dimer interface [polypeptide binding]; other site 340100003584 conserved gate region; other site 340100003585 putative PBP binding loops; other site 340100003586 ABC-ATPase subunit interface; other site 340100003587 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100003588 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 340100003589 dimer interface [polypeptide binding]; other site 340100003590 conserved gate region; other site 340100003591 putative PBP binding loops; other site 340100003592 ABC-ATPase subunit interface; other site 340100003593 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100003594 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 340100003595 substrate binding pocket [chemical binding]; other site 340100003596 membrane-bound complex binding site; other site 340100003597 hinge residues; other site 340100003598 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100003599 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 340100003600 inhibitor site; inhibition site 340100003601 active site 340100003602 dimer interface [polypeptide binding]; other site 340100003603 catalytic residue [active] 340100003604 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100003605 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100003606 DNA-binding site [nucleotide binding]; DNA binding site 340100003607 FCD domain; Region: FCD; cl11656 340100003608 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100003609 Helix-turn-helix domains; Region: HTH; cl00088 340100003610 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100003611 dimerization interface [polypeptide binding]; other site 340100003612 substrate binding pocket [chemical binding]; other site 340100003613 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 340100003614 non-specific DNA binding site [nucleotide binding]; other site 340100003615 salt bridge; other site 340100003616 sequence-specific DNA binding site [nucleotide binding]; other site 340100003617 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100003618 dimerization interface [polypeptide binding]; other site 340100003619 substrate binding pocket [chemical binding]; other site 340100003620 integrase; Provisional; Region: PRK09692 340100003621 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 340100003622 active site 340100003623 Int/Topo IB signature motif; other site 340100003624 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100003625 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003626 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 340100003627 glutathionine S-transferase; Provisional; Region: PRK10542 340100003628 C-terminal domain interface [polypeptide binding]; other site 340100003629 GSH binding site (G-site) [chemical binding]; other site 340100003630 dimer interface [polypeptide binding]; other site 340100003631 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100003632 dimer interface [polypeptide binding]; other site 340100003633 substrate binding pocket (H-site) [chemical binding]; other site 340100003634 N-terminal domain interface [polypeptide binding]; other site 340100003635 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100003636 Helix-turn-helix domains; Region: HTH; cl00088 340100003637 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 340100003638 dimerization interface [polypeptide binding]; other site 340100003639 substrate binding pocket [chemical binding]; other site 340100003640 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100003641 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 340100003642 C-terminal domain interface [polypeptide binding]; other site 340100003643 GSH binding site (G-site) [chemical binding]; other site 340100003644 dimer interface [polypeptide binding]; other site 340100003645 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 340100003646 N-terminal domain interface [polypeptide binding]; other site 340100003647 putative dimer interface [polypeptide binding]; other site 340100003648 active site 340100003649 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100003650 Helix-turn-helix domains; Region: HTH; cl00088 340100003651 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003652 NMT1-like family; Region: NMT1_2; cl15260 340100003653 acyl-CoA synthetase; Validated; Region: PRK06188 340100003654 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003655 AMP-binding enzyme; Region: AMP-binding; cl15778 340100003656 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 340100003657 active site 340100003658 oxalacetate binding site [chemical binding]; other site 340100003659 citrylCoA binding site [chemical binding]; other site 340100003660 coenzyme A binding site [chemical binding]; other site 340100003661 catalytic triad [active] 340100003662 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003663 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003664 NAD(P) binding site [chemical binding]; other site 340100003665 active site 340100003666 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003667 classical (c) SDRs; Region: SDR_c; cd05233 340100003668 NAD(P) binding site [chemical binding]; other site 340100003669 active site 340100003670 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100003671 Helix-turn-helix domains; Region: HTH; cl00088 340100003672 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100003673 dimerization interface [polypeptide binding]; other site 340100003674 substrate binding pocket [chemical binding]; other site 340100003675 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100003676 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100003677 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 340100003678 P-loop; other site 340100003679 Magnesium ion binding site [ion binding]; other site 340100003680 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 340100003681 Magnesium ion binding site [ion binding]; other site 340100003682 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100003683 ParB-like nuclease domain; Region: ParBc; cl02129 340100003684 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100003685 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 340100003686 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100003687 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003688 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 340100003689 ssDNA binding site [nucleotide binding]; other site 340100003690 dimer interface [polypeptide binding]; other site 340100003691 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100003692 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 340100003693 active site 340100003694 putative interdomain interaction site [polypeptide binding]; other site 340100003695 putative metal-binding site [ion binding]; other site 340100003696 putative nucleotide binding site [chemical binding]; other site 340100003697 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; cl11986 340100003698 domain I; other site 340100003699 DNA binding groove [nucleotide binding] 340100003700 phosphate binding site [ion binding]; other site 340100003701 domain III; other site 340100003702 nucleotide binding site [chemical binding]; other site 340100003703 catalytic site [active] 340100003704 Helix-turn-helix domains; Region: HTH; cl00088 340100003705 putative transposase OrfB; Reviewed; Region: PHA02517 340100003706 HTH-like domain; Region: HTH_21; pfam13276 340100003707 Integrase core domain; Region: rve; cl01316 340100003708 Integrase core domain; Region: rve_3; cl15866 340100003709 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; cl11986 340100003710 domain II; other site 340100003711 domain IV; other site 340100003712 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100003713 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; cl15754 340100003714 cofactor binding site; other site 340100003715 DNA binding site [nucleotide binding] 340100003716 substrate interaction site [chemical binding]; other site 340100003717 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 340100003718 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 340100003719 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 340100003720 DNA binding site [nucleotide binding] 340100003721 Int/Topo IB signature motif; other site 340100003722 active site 340100003723 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 340100003724 DNA binding site [nucleotide binding] 340100003725 Int/Topo IB signature motif; other site 340100003726 active site 340100003727 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100003728 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 340100003729 DNA binding site [nucleotide binding] 340100003730 Int/Topo IB signature motif; other site 340100003731 active site 340100003732 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; cl15754 340100003733 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100003734 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 340100003735 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 340100003736 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100003737 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100003738 Domain of unknown function (DUF932); Region: DUF932; cl12129 340100003739 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003740 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100003741 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 340100003742 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 340100003743 nucleotide binding region [chemical binding]; other site 340100003744 ATP-binding site [chemical binding]; other site 340100003745 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100003746 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 340100003747 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 340100003748 substrate-cofactor binding pocket; other site 340100003749 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100003750 catalytic residue [active] 340100003751 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 340100003752 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100003753 Coenzyme A binding pocket [chemical binding]; other site 340100003754 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 340100003755 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003756 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 340100003757 active site 340100003758 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 340100003759 dimer interface [polypeptide binding]; other site 340100003760 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 340100003761 Ligand Binding Site [chemical binding]; other site 340100003762 Molecular Tunnel; other site 340100003763 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 340100003764 putative substrate translocation pore; other site 340100003765 hypothetical protein; Provisional; Region: PRK06847 340100003766 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003767 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003768 FAD binding domain; Region: FAD_binding_3; pfam01494 340100003769 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003770 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 340100003771 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003772 Helix-turn-helix domains; Region: HTH; cl00088 340100003773 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 340100003774 putative substrate translocation pore; other site 340100003775 EamA-like transporter family; Region: EamA; cl01037 340100003776 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 340100003777 Biofilm formation and stress response factor; Region: BsmA; cl01794 340100003778 Helix-turn-helix domains; Region: HTH; cl00088 340100003779 putative transposase OrfB; Reviewed; Region: PHA02517 340100003780 HTH-like domain; Region: HTH_21; pfam13276 340100003781 Integrase core domain; Region: rve; cl01316 340100003782 Integrase core domain; Region: rve_3; cl15866 340100003783 Biofilm formation and stress response factor; Region: BsmA; cl01794 340100003784 LysE type translocator; Region: LysE; cl00565 340100003785 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100003786 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 340100003787 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100003788 Helix-turn-helix domains; Region: HTH; cl00088 340100003789 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 340100003790 putative effector binding pocket; other site 340100003791 dimerization interface [polypeptide binding]; other site 340100003792 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100003793 Mnd1 family; Region: Mnd1; pfam03962 340100003794 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100003795 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340100003796 Protein of unknown function (DUF2859); Region: DUF2859; cl12633 340100003797 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100003798 Domain of unknown function DUF87; Region: DUF87; pfam01935 340100003799 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100003800 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 340100003801 Global regulator protein family; Region: CsrA; cl00670 340100003802 HipA N-terminal domain; Region: Couple_hipA; cl11853 340100003803 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100003804 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100003805 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 340100003806 non-specific DNA binding site [nucleotide binding]; other site 340100003807 salt bridge; other site 340100003808 sequence-specific DNA binding site [nucleotide binding]; other site 340100003809 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100003810 Protein of unknown function (DUF3262); Region: DUF3262; cl13160 340100003811 Protein of unknown function (DUF2976); Region: DUF2976; cl12739 340100003812 Protein of unknown function (DUF3487); Region: DUF3487; cl13432 340100003813 Protein of unknown function (DUF2895); Region: DUF2895; cl12968 340100003814 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 340100003815 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100003816 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 340100003817 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100003818 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100003819 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 340100003820 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 340100003821 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 340100003822 metal binding site [ion binding]; metal-binding site 340100003823 active site 340100003824 I-site; other site 340100003825 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 340100003826 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100003827 DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a...; Region: DsbA_family; cd02972 340100003828 catalytic residues [active] 340100003829 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 340100003830 ParB-like nuclease domain; Region: ParBc; cl02129 340100003831 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 340100003832 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 340100003833 Active Sites [active] 340100003834 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 340100003835 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003836 Helix-turn-helix domains; Region: HTH; cl00088 340100003837 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 340100003838 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 340100003839 putative active site [active] 340100003840 heme pocket [chemical binding]; other site 340100003841 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 340100003842 putative active site [active] 340100003843 heme pocket [chemical binding]; other site 340100003844 GAF domain; Region: GAF; cl15785 340100003845 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 340100003846 metal binding site [ion binding]; metal-binding site 340100003847 active site 340100003848 I-site; other site 340100003849 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 340100003850 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 340100003851 PAS domain; Region: PAS_9; pfam13426 340100003852 putative active site [active] 340100003853 heme pocket [chemical binding]; other site 340100003854 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 340100003855 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100003856 dimer interface [polypeptide binding]; other site 340100003857 putative CheW interface [polypeptide binding]; other site 340100003858 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100003859 Helix-turn-helix domains; Region: HTH; cl00088 340100003860 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100003861 dimerization interface [polypeptide binding]; other site 340100003862 Biofilm formation and stress response factor; Region: BsmA; cl01794 340100003863 LysE type translocator; Region: LysE; cl00565 340100003864 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100003865 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 340100003866 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 340100003867 TraU protein; Region: TraU; cl06067 340100003868 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100003869 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100003870 PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, Archaeoglobus fulgidus AF0591 protein and homologs; Region: PIN_VapC-Smg6-like; cd09855 340100003871 putative active site [active] 340100003872 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100003873 Putative helicase; Region: TraI_2; pfam07514 340100003874 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100003875 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100003876 Dynamin family; Region: Dynamin_N; pfam00350 340100003877 G1 box; other site 340100003878 GTP/Mg2+ binding site [chemical binding]; other site 340100003879 G2 box; other site 340100003880 Switch I region; other site 340100003881 G3 box; other site 340100003882 Switch II region; other site 340100003883 G4 box; other site 340100003884 G5 box; other site 340100003885 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100003886 G1 box; other site 340100003887 GTP/Mg2+ binding site [chemical binding]; other site 340100003888 G2 box; other site 340100003889 Switch I region; other site 340100003890 G3 box; other site 340100003891 Switch II region; other site 340100003892 G4 box; other site 340100003893 G5 box; other site 340100003894 Benzoate membrane transport protein; Region: BenE; pfam03594 340100003895 benzoate transporter; Region: benE; TIGR00843 340100003896 benzoate transport; Region: 2A0115; TIGR00895 340100003897 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 340100003898 putative substrate translocation pore; other site 340100003899 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 340100003900 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 340100003901 catalytic Zn binding site [ion binding]; other site 340100003902 NAD binding site [chemical binding]; other site 340100003903 structural Zn binding site [ion binding]; other site 340100003904 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100003905 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 340100003906 NAD(P) binding site [chemical binding]; other site 340100003907 catalytic residues [active] 340100003908 NMT1-like family; Region: NMT1_2; cl15260 340100003909 Muconolactone delta-isomerase; Region: MIase; cl01992 340100003910 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 340100003911 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 340100003912 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 340100003913 active site 340100003914 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100003915 benzoate transport; Region: 2A0115; TIGR00895 340100003916 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 340100003917 putative substrate translocation pore; other site 340100003918 YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgH_like; cd02198 340100003919 homotrimer interaction site [polypeptide binding]; other site 340100003920 putative active site [active] 340100003921 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003922 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 340100003923 putative NAD(P) binding site [chemical binding]; other site 340100003924 active site 340100003925 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 340100003926 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 340100003927 catalytic loop [active] 340100003928 iron binding site [ion binding]; other site 340100003929 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 340100003930 FAD binding pocket [chemical binding]; other site 340100003931 FAD binding motif [chemical binding]; other site 340100003932 phosphate binding motif [ion binding]; other site 340100003933 beta-alpha-beta structure motif; other site 340100003934 NAD binding pocket [chemical binding]; other site 340100003935 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 340100003936 inter-subunit interface; other site 340100003937 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 340100003938 Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to...; Region: Rieske_RO_Alpha_HBDO; cd03542 340100003939 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 340100003940 putative alpha subunit interface [polypeptide binding]; other site 340100003941 putative active site [active] 340100003942 putative substrate binding site [chemical binding]; other site 340100003943 Fe binding site [ion binding]; other site 340100003944 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 340100003945 Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of...; Region: 1,2-CTD; cd03460 340100003946 dimer interface [polypeptide binding]; other site 340100003947 active site 340100003948 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100003949 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 340100003950 octamer interface [polypeptide binding]; other site 340100003951 active site 340100003952 Helix-turn-helix domains; Region: HTH; cl00088 340100003953 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; Region: PBP2_BenM_CatM_CatR; cd08445 340100003954 dimerizarion interface [polypeptide binding]; other site 340100003955 CrgA pocket; other site 340100003956 substrate binding pocket [chemical binding]; other site 340100003957 Transposase domain (DUF772); Region: DUF772; cl15789 340100003958 Transposase domain (DUF772); Region: DUF772; cl15789 340100003959 Helix-turn-helix domains; Region: HTH; cl00088 340100003960 Integrase core domain; Region: rve_3; cl15866 340100003961 Helix-turn-helix domains; Region: HTH; cl00088 340100003962 Winged helix-turn helix; Region: HTH_29; pfam13551 340100003963 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 340100003964 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 340100003965 catalytic residues [active] 340100003966 catalytic nucleophile [active] 340100003967 Recombinase; Region: Recombinase; pfam07508 340100003968 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 340100003969 HTH-like domain; Region: HTH_21; pfam13276 340100003970 Integrase core domain; Region: rve; cl01316 340100003971 Probable cobalt transporter subunit (CbtA); Region: CbtA; cl02266 340100003972 Probable cobalt transporter subunit (CbtB); Region: CbtB; cl09723 340100003973 nitrile hydratase, beta subunit; Region: nitrile_beta; cl03486 340100003974 Nitrile hydratase beta subunit; Region: NHase_beta; pfam02211 340100003975 nitrile hydratase, beta subunit; Region: nitrile_beta; cl03486 340100003976 Nitrile hydratase, alpha chain; Region: NHase_alpha; pfam02979 340100003977 NHLP leader peptide domain; Region: TOMM_pelo; cl15464 340100003978 NHLP leader peptide domain; Region: TOMM_pelo; cl15464 340100003979 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100003980 Amidase; Region: Amidase; cl11426 340100003981 Transposase domain (DUF772); Region: DUF772; cl15789 340100003982 PAS domain; Region: PAS_9; pfam13426 340100003983 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 340100003984 putative active site [active] 340100003985 heme pocket [chemical binding]; other site 340100003986 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 340100003987 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100003988 dimer interface [polypeptide binding]; other site 340100003989 putative CheW interface [polypeptide binding]; other site 340100003990 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100003991 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100003992 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100003993 Helix-turn-helix domains; Region: HTH; cl00088 340100003994 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100003995 salicylate hydroxylase; Provisional; Region: PRK08163 340100003996 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003997 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100003998 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 340100003999 Cupin domain; Region: Cupin_2; cl09118 340100004000 Cupin domain; Region: Cupin_2; cl09118 340100004001 benzoate transport; Region: 2A0115; TIGR00895 340100004002 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 340100004003 putative substrate translocation pore; other site 340100004004 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 340100004005 Presynaptic Site I dimer interface [polypeptide binding]; other site 340100004006 catalytic residues [active] 340100004007 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340100004008 Synaptic Flat tetramer interface [polypeptide binding]; other site 340100004009 Synaptic Site I dimer interface [polypeptide binding]; other site 340100004010 DNA binding site [nucleotide binding] 340100004011 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340100004012 DNA-binding interface [nucleotide binding]; DNA binding site 340100004013 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 340100004014 non-specific DNA binding site [nucleotide binding]; other site 340100004015 salt bridge; other site 340100004016 sequence-specific DNA binding site [nucleotide binding]; other site 340100004017 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100004018 dimerization interface [polypeptide binding]; other site 340100004019 substrate binding pocket [chemical binding]; other site 340100004020 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004021 Helix-turn-helix domains; Region: HTH; cl00088 340100004022 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 340100004023 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100004024 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 340100004025 integrase; Provisional; Region: PRK09692 340100004026 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 340100004027 active site 340100004028 Int/Topo IB signature motif; other site 340100004029 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100004030 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100004031 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 340100004032 Magnesium ion binding site [ion binding]; other site 340100004033 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100004034 ParB-like nuclease domain; Region: ParBc; cl02129 340100004035 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100004036 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 340100004037 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100004038 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 340100004039 ssDNA binding site [nucleotide binding]; other site 340100004040 dimer interface [polypeptide binding]; other site 340100004041 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100004042 DNA topoisomerase III; Provisional; Region: PRK07726 340100004043 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 340100004044 active site 340100004045 putative interdomain interaction site [polypeptide binding]; other site 340100004046 putative metal-binding site [ion binding]; other site 340100004047 putative nucleotide binding site [chemical binding]; other site 340100004048 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 340100004049 domain I; other site 340100004050 DNA binding groove [nucleotide binding] 340100004051 phosphate binding site [ion binding]; other site 340100004052 domain II; other site 340100004053 domain III; other site 340100004054 nucleotide binding site [chemical binding]; other site 340100004055 catalytic site [active] 340100004056 domain IV; other site 340100004057 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100004058 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; cl15754 340100004059 cofactor binding site; other site 340100004060 DNA binding site [nucleotide binding] 340100004061 substrate interaction site [chemical binding]; other site 340100004062 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 340100004063 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 340100004064 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 340100004065 DNA binding site [nucleotide binding] 340100004066 Int/Topo IB signature motif; other site 340100004067 active site 340100004068 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 340100004069 DNA binding site [nucleotide binding] 340100004070 Int/Topo IB signature motif; other site 340100004071 active site 340100004072 putative transposase OrfB; Reviewed; Region: PHA02517 340100004073 HTH-like domain; Region: HTH_21; pfam13276 340100004074 Integrase core domain; Region: rve; cl01316 340100004075 Integrase core domain; Region: rve_3; cl15866 340100004076 Helix-turn-helix domains; Region: HTH; cl00088 340100004077 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 340100004078 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 340100004079 DNA binding site [nucleotide binding] 340100004080 Int/Topo IB signature motif; other site 340100004081 active site 340100004082 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; cl15754 340100004083 putative transposase OrfB; Reviewed; Region: PHA02517 340100004084 HTH-like domain; Region: HTH_21; pfam13276 340100004085 Integrase core domain; Region: rve; cl01316 340100004086 Integrase core domain; Region: rve_3; cl15866 340100004087 Helix-turn-helix domains; Region: HTH; cl00088 340100004088 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 340100004089 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 340100004090 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 340100004091 Active Sites [active] 340100004092 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100004093 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100004094 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100004095 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004096 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100004097 putative active site [active] 340100004098 putative NTP binding site [chemical binding]; other site 340100004099 putative nucleic acid binding site [nucleotide binding]; other site 340100004100 Type II intron maturase; Region: Intron_maturas2; pfam01348 340100004101 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 340100004102 nucleotide binding region [chemical binding]; other site 340100004103 ATP-binding site [chemical binding]; other site 340100004104 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100004105 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100004106 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340100004107 Protein of unknown function (DUF2859); Region: DUF2859; cl12633 340100004108 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100004109 Domain of unknown function DUF87; Region: DUF87; pfam01935 340100004110 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100004111 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 340100004112 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100004113 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100004114 Protein of unknown function (DUF3262); Region: DUF3262; cl13160 340100004115 Protein of unknown function (DUF2976); Region: DUF2976; cl12739 340100004116 Protein of unknown function (DUF3487); Region: DUF3487; cl13432 340100004117 Protein of unknown function (DUF2895); Region: DUF2895; cl12968 340100004118 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 340100004119 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100004120 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100004121 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100004122 Helix-turn-helix domains; Region: HTH; cl00088 340100004123 putative transposase OrfB; Reviewed; Region: PHA02517 340100004124 HTH-like domain; Region: HTH_21; pfam13276 340100004125 Integrase core domain; Region: rve; cl01316 340100004126 Integrase core domain; Region: rve_3; cl15866 340100004127 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100004128 DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a...; Region: DsbA_family; cd02972 340100004129 catalytic residues [active] 340100004130 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100004131 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100004132 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 340100004133 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain. This CD includes various bacterial integrases, including the predicted integrase of the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus...; Region: INT_pAE1; cd01188 340100004134 Int/Topo IB signature motif; other site 340100004135 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 340100004136 DNA binding site [nucleotide binding] 340100004137 Int/Topo IB signature motif; other site 340100004138 active site 340100004139 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 340100004140 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases; Region: INT_SG5; cd01190 340100004141 Int/Topo IB signature motif; other site 340100004142 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 340100004143 TraU protein; Region: TraU; cl06067 340100004144 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100004145 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100004146 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 340100004147 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 340100004148 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340100004149 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100004150 Putative helicase; Region: TraI_2; pfam07514 340100004151 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100004152 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100004153 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100004154 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 340100004155 classical (c) SDRs; Region: SDR_c; cd05233 340100004156 NAD(P) binding site [chemical binding]; other site 340100004157 active site 340100004158 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 340100004159 inter-subunit interface; other site 340100004160 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 340100004161 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 340100004162 Putative transposase; Region: Y2_Tnp; pfam04986 340100004163 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 340100004164 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100004165 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100004166 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 340100004167 glutathione reductase; Validated; Region: PRK06116 340100004168 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100004169 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100004170 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100004171 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100004172 putative N-terminal domain interface [polypeptide binding]; other site 340100004173 putative dimer interface [polypeptide binding]; other site 340100004174 putative substrate binding pocket (H-site) [chemical binding]; other site 340100004175 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100004176 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 340100004177 C-terminal domain interface [polypeptide binding]; other site 340100004178 GSH binding site (G-site) [chemical binding]; other site 340100004179 dimer interface [polypeptide binding]; other site 340100004180 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100004181 N-terminal domain interface [polypeptide binding]; other site 340100004182 dimer interface [polypeptide binding]; other site 340100004183 substrate binding pocket (H-site) [chemical binding]; other site 340100004184 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_5; cd02148 340100004185 putative FMN binding site [chemical binding]; other site 340100004186 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 340100004187 YCII-related domain; Region: YCII; cl00999 340100004188 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 340100004189 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100004190 inhibitor-cofactor binding pocket; inhibition site 340100004191 catalytic residue [active] 340100004192 Putative transposase; Region: Y2_Tnp; pfam04986 340100004193 Organic solute transporter Ostalpha; Region: Solute_trans_a; pfam03619 340100004194 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 340100004195 Ligand binding site; other site 340100004196 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100004197 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 340100004198 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 340100004199 trimer interface [polypeptide binding]; other site 340100004200 active site 340100004201 substrate binding site [chemical binding]; other site 340100004202 CoA binding site [chemical binding]; other site 340100004203 Organic solute transporter Ostalpha; Region: Solute_trans_a; pfam03619 340100004204 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 340100004205 Putative transposase; Region: Y2_Tnp; pfam04986 340100004206 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 340100004207 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 340100004208 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 340100004209 LysE type translocator; Region: LysE; cl00565 340100004210 LysE type translocator; Region: LysE; cl00565 340100004211 Helix-turn-helix domains; Region: HTH; cl00088 340100004212 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100004213 The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold; Region: PBP2_ClcR; cd08485 340100004214 putative dimerization interface [polypeptide binding]; other site 340100004215 putative substrate binding pocket [chemical binding]; other site 340100004216 chlorocatechol 1,2-dioxygenases (1,2-CCDs) (type II enzymes) are homodimeric intradiol dioxygenases that degrade chlorocatechols via the addition of molecular oxygen and the subsequent cleavage between two adjacent hydroxyl groups. This reaction is part...; Region: 1,2-CCD; cd03462 340100004217 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 340100004218 dimer interface [polypeptide binding]; other site 340100004219 active site 340100004220 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 340100004221 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100004222 octamer interface [polypeptide binding]; other site 340100004223 active site 340100004224 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100004225 NMT1-like family; Region: NMT1_2; cl15260 340100004226 Dienelactone hydrolase family; Region: DLH; pfam01738 340100004227 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100004228 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100004229 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 340100004230 active site 340100004231 dimer interface [polypeptide binding]; other site 340100004232 metal binding site [ion binding]; metal-binding site 340100004233 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100004234 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 340100004235 iron-sulfur cluster [ion binding]; other site 340100004236 [2Fe-2S] cluster binding site [ion binding]; other site 340100004237 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 340100004238 putative alpha subunit interface [polypeptide binding]; other site 340100004239 putative active site [active] 340100004240 putative substrate binding site [chemical binding]; other site 340100004241 Fe binding site [ion binding]; other site 340100004242 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 340100004243 inter-subunit interface; other site 340100004244 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 340100004245 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 340100004246 FMN-binding pocket [chemical binding]; other site 340100004247 flavin binding motif; other site 340100004248 phosphate binding motif [ion binding]; other site 340100004249 beta-alpha-beta structure motif; other site 340100004250 NAD binding pocket [chemical binding]; other site 340100004251 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 340100004252 catalytic loop [active] 340100004253 iron binding site [ion binding]; other site 340100004254 benzoate transport; Region: 2A0115; TIGR00895 340100004255 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 340100004256 putative substrate translocation pore; other site 340100004257 YCII-related domain; Region: YCII; cl00999 340100004258 integrase; Provisional; Region: PRK09692 340100004259 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 340100004260 active site 340100004261 Int/Topo IB signature motif; other site 340100004262 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 340100004263 FAD binding domain; Region: FAD_binding_4; pfam01565 340100004264 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 340100004265 dihydrodipicolinate reductase; Provisional; Region: PRK00048 340100004266 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004267 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 340100004268 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 340100004269 Predicted membrane protein [Function unknown]; Region: COG5373 340100004270 ferric uptake regulator; Provisional; Region: fur; PRK09462 340100004271 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 340100004272 metal binding site 2 [ion binding]; metal-binding site 340100004273 putative DNA binding helix; other site 340100004274 metal binding site 1 [ion binding]; metal-binding site 340100004275 dimer interface [polypeptide binding]; other site 340100004276 structural Zn2+ binding site [ion binding]; other site 340100004277 recombination and repair protein; Provisional; Region: PRK10869 340100004278 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 340100004279 Walker A/P-loop; other site 340100004280 ATP binding site [chemical binding]; other site 340100004281 Q-loop/lid; other site 340100004282 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 340100004283 ABC transporter signature motif; other site 340100004284 Walker B; other site 340100004285 D-loop; other site 340100004286 H-loop/switch region; other site 340100004287 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 340100004288 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 340100004289 Helix-turn-helix domains; Region: HTH; cl00088 340100004290 HrcA protein C terminal domain; Region: HrcA; pfam01628 340100004291 ferrochelatase; Reviewed; Region: hemH; PRK00035 340100004292 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 340100004293 C-terminal domain interface [polypeptide binding]; other site 340100004294 active site 340100004295 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 340100004296 active site 340100004297 N-terminal domain interface [polypeptide binding]; other site 340100004298 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 340100004299 dimer interface [polypeptide binding]; other site 340100004300 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 340100004301 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 340100004302 catalytic residues [active] 340100004303 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 340100004304 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100004305 chaperone protein DnaJ; Provisional; Region: PRK10767 340100004306 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 340100004307 HSP70 interaction site [polypeptide binding]; other site 340100004308 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 340100004309 Zn binding sites [ion binding]; other site 340100004310 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 340100004311 dimer interface [polypeptide binding]; other site 340100004312 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100004313 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100004314 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 340100004315 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 340100004316 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 340100004317 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 340100004318 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 340100004319 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 340100004320 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100004321 Coenzyme A binding pocket [chemical binding]; other site 340100004322 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 340100004323 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 340100004324 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 340100004325 Walker A motif; other site 340100004326 ATP binding site [chemical binding]; other site 340100004327 Walker B motif; other site 340100004328 arginine finger; other site 340100004329 Cytochrome c; Region: Cytochrom_C; cl11414 340100004330 Cytochrome c; Region: Cytochrom_C; cl11414 340100004331 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 340100004332 isocitrate dehydrogenase; Validated; Region: PRK07362 340100004333 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 340100004334 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 340100004335 trimer interface [polypeptide binding]; other site 340100004336 eyelet of channel; other site 340100004337 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 340100004338 Sodium:solute symporter family; Region: SSF; cl00456 340100004339 AAA domain; Region: AAA_27; pfam13514 340100004340 Sodium:solute symporter family; Region: SSF; cl00456 340100004341 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100004342 Smr domain; Region: Smr; cl02619 340100004343 thioredoxin reductase; Provisional; Region: PRK10262 340100004344 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100004345 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 340100004346 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100004347 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 340100004348 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 340100004349 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional; Region: PRK14875 340100004350 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 340100004351 homotrimer interaction site [polypeptide binding]; other site 340100004352 putative active site [active] 340100004353 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100004354 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 340100004355 active site 340100004356 putative substrate binding pocket [chemical binding]; other site 340100004357 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 340100004358 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 340100004359 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 340100004360 putative active site [active] 340100004361 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100004362 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100004363 Walker A/P-loop; other site 340100004364 ATP binding site [chemical binding]; other site 340100004365 Q-loop/lid; other site 340100004366 ABC transporter signature motif; other site 340100004367 Walker B; other site 340100004368 D-loop; other site 340100004369 H-loop/switch region; other site 340100004370 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100004371 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100004372 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100004373 Walker A/P-loop; other site 340100004374 ATP binding site [chemical binding]; other site 340100004375 Q-loop/lid; other site 340100004376 ABC transporter signature motif; other site 340100004377 Walker B; other site 340100004378 D-loop; other site 340100004379 H-loop/switch region; other site 340100004380 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100004381 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100004382 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 340100004383 dimer interface [polypeptide binding]; other site 340100004384 conserved gate region; other site 340100004385 putative PBP binding loops; other site 340100004386 ABC-ATPase subunit interface; other site 340100004387 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100004388 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 340100004389 dimer interface [polypeptide binding]; other site 340100004390 conserved gate region; other site 340100004391 putative PBP binding loops; other site 340100004392 ABC-ATPase subunit interface; other site 340100004393 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_16; cd08502 340100004394 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100004395 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 340100004396 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase; Region: PLPDE_III_cryptic_DSD; cd06818 340100004397 dimer interface [polypeptide binding]; other site 340100004398 active site 340100004399 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100004400 substrate binding site [chemical binding]; other site 340100004401 catalytic residue [active] 340100004402 recombination factor protein RarA; Reviewed; Region: PRK13342 340100004403 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 340100004404 Walker A motif; other site 340100004405 ATP binding site [chemical binding]; other site 340100004406 Walker B motif; other site 340100004407 arginine finger; other site 340100004408 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 340100004409 seryl-tRNA synthetase; Provisional; Region: PRK05431 340100004410 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 340100004411 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 bound...; Region: SerRS_core; cd00770 340100004412 dimer interface [polypeptide binding]; other site 340100004413 active site 340100004414 motif 1; other site 340100004415 motif 2; other site 340100004416 motif 3; other site 340100004417 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100004418 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 340100004419 C-terminal domain interface [polypeptide binding]; other site 340100004420 GSH binding site (G-site) [chemical binding]; other site 340100004421 dimer interface [polypeptide binding]; other site 340100004422 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100004423 N-terminal domain interface [polypeptide binding]; other site 340100004424 dimer interface [polypeptide binding]; other site 340100004425 substrate binding pocket (H-site) [chemical binding]; other site 340100004426 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004427 Helix-turn-helix domains; Region: HTH; cl00088 340100004428 MarC family integral membrane protein; Region: MarC; cl00919 340100004429 Chromate transporter; Region: Chromate_transp; pfam02417 340100004430 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 340100004431 Chromate transporter; Region: Chromate_transp; pfam02417 340100004432 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 340100004433 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 340100004434 dimer interface [polypeptide binding]; other site 340100004435 phosphorylation site [posttranslational modification] 340100004436 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 340100004437 ATP binding site [chemical binding]; other site 340100004438 Mg2+ binding site [ion binding]; other site 340100004439 G-X-G motif; other site 340100004440 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100004441 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100004442 active site 340100004443 phosphorylation site [posttranslational modification] 340100004444 intermolecular recognition site; other site 340100004445 dimerization interface [polypeptide binding]; other site 340100004446 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 340100004447 DNA binding site [nucleotide binding] 340100004448 Helix-turn-helix domains; Region: HTH; cl00088 340100004449 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100004450 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 340100004451 active site 340100004452 metal binding site [ion binding]; metal-binding site 340100004453 Helix-turn-helix domains; Region: HTH; cl00088 340100004454 WYL domain; Region: WYL; cl14852 340100004455 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 340100004456 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 340100004457 NAD binding site [chemical binding]; other site 340100004458 homotetramer interface [polypeptide binding]; other site 340100004459 homodimer interface [polypeptide binding]; other site 340100004460 substrate binding site [chemical binding]; other site 340100004461 active site 340100004462 Protein of unknown function (DUF328); Region: DUF328; cl01143 340100004463 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 340100004464 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100004465 putative substrate translocation pore; other site 340100004466 Predicted membrane protein [Function unknown]; Region: COG1289 340100004467 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 340100004468 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 340100004469 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 340100004470 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100004471 PYR/PP interface [polypeptide binding]; other site 340100004472 dimer interface [polypeptide binding]; other site 340100004473 TPP binding site [chemical binding]; other site 340100004474 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100004475 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 340100004476 TPP-binding site [chemical binding]; other site 340100004477 dimer interface [polypeptide binding]; other site 340100004478 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 340100004479 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 340100004480 putative valine binding site [chemical binding]; other site 340100004481 dimer interface [polypeptide binding]; other site 340100004482 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 340100004483 ketol-acid reductoisomerase; Provisional; Region: PRK05479 340100004484 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004485 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 340100004486 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 340100004487 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 340100004488 16S/18S rRNA binding site [nucleotide binding]; other site 340100004489 S13e-L30e interaction site [polypeptide binding]; other site 340100004490 25S rRNA binding site [nucleotide binding]; other site 340100004491 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 340100004492 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 340100004493 RNase E interface [polypeptide binding]; other site 340100004494 trimer interface [polypeptide binding]; other site 340100004495 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 340100004496 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 340100004497 RNase E interface [polypeptide binding]; other site 340100004498 trimer interface [polypeptide binding]; other site 340100004499 active site 340100004500 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 340100004501 putative nucleic acid binding region [nucleotide binding]; other site 340100004502 G-X-X-G motif; other site 340100004503 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 340100004504 RNA binding site [nucleotide binding]; other site 340100004505 domain interface; other site 340100004506 threonine dehydratase; Provisional; Region: PRK07334 340100004507 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 340100004508 tetramer interface [polypeptide binding]; other site 340100004509 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100004510 catalytic residue [active] 340100004511 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 340100004512 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 340100004513 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 340100004514 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 340100004515 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340100004516 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 340100004517 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100004518 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004519 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004520 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004521 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100004522 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340100004523 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004524 PAAR motif; Region: PAAR_motif; cl15808 340100004525 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 340100004526 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340100004527 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100004528 dinuclear metal binding motif [ion binding]; other site 340100004529 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 340100004530 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 340100004531 NAD(P) binding site [chemical binding]; other site 340100004532 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 340100004533 substrate binding site [chemical binding]; other site 340100004534 dimer interface [polypeptide binding]; other site 340100004535 catalytic triad [active] 340100004536 Preprotein translocase SecG subunit; Region: SecG; cl09123 340100004537 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 340100004538 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 340100004539 motif II; other site 340100004540 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 340100004541 dinuclear metal binding motif [ion binding]; other site 340100004542 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_1; cd09319 340100004543 gating phenylalanine in ion channel; other site 340100004544 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 340100004545 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 340100004546 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 340100004547 catalytic residues [active] 340100004548 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100004549 NMT1-like family; Region: NMT1_2; cl15260 340100004550 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100004551 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 340100004552 active site 340100004553 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100004554 Helix-turn-helix domains; Region: HTH; cl00088 340100004555 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100004556 dimerization interface [polypeptide binding]; other site 340100004557 substrate binding pocket [chemical binding]; other site 340100004558 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100004559 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100004560 thiolase; Provisional; Region: PRK06158 340100004561 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100004562 active site 340100004563 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 340100004564 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100004565 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 340100004566 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 340100004567 dimanganese center [ion binding]; other site 340100004568 Protein of unknown function (DUF763); Region: DUF763; cl00620 340100004569 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 340100004570 Spore germination protein; Region: Spore_permease; cl15802 340100004571 Domain of unknown function (DUF305); Region: DUF305; cl15795 340100004572 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100004573 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004574 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004575 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 340100004576 NAD(P) binding site [chemical binding]; other site 340100004577 active site 340100004578 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100004579 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100004580 DNA-binding site [nucleotide binding]; DNA binding site 340100004581 FCD domain; Region: FCD; cl11656 340100004582 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100004583 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100004584 NMT1-like family; Region: NMT1_2; cl15260 340100004585 short chain dehydrogenase; Validated; Region: PRK08589 340100004586 classical (c) SDRs; Region: SDR_c; cd05233 340100004587 NAD(P) binding site [chemical binding]; other site 340100004588 active site 340100004589 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100004590 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 340100004591 TM-ABC transporter signature motif; other site 340100004592 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 340100004593 TM-ABC transporter signature motif; other site 340100004594 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100004595 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100004596 Walker A/P-loop; other site 340100004597 ATP binding site [chemical binding]; other site 340100004598 Q-loop/lid; other site 340100004599 ABC transporter signature motif; other site 340100004600 Walker B; other site 340100004601 D-loop; other site 340100004602 H-loop/switch region; other site 340100004603 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100004604 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100004605 Walker A/P-loop; other site 340100004606 ATP binding site [chemical binding]; other site 340100004607 Q-loop/lid; other site 340100004608 ABC transporter signature motif; other site 340100004609 Walker B; other site 340100004610 D-loop; other site 340100004611 H-loop/switch region; other site 340100004612 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100004613 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100004614 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100004615 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100004616 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004617 Cupin domain; Region: Cupin_2; cl09118 340100004618 NIPSNAP; Region: NIPSNAP; pfam07978 340100004619 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100004620 NMT1-like family; Region: NMT1_2; cl15260 340100004621 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100004622 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100004623 DNA-binding site [nucleotide binding]; DNA binding site 340100004624 UTRA domain; Region: UTRA; cl01230 340100004625 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 340100004626 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 340100004627 substrate binding site [chemical binding]; other site 340100004628 ligand binding site [chemical binding]; other site 340100004629 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 340100004630 substrate binding site [chemical binding]; other site 340100004631 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 340100004632 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 340100004633 tetramer interface [polypeptide binding]; other site 340100004634 active site 340100004635 Mg2+/Mn2+ binding site [ion binding]; other site 340100004636 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 340100004637 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100004638 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 340100004639 putative substrate translocation pore; other site 340100004640 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 340100004641 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 340100004642 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 340100004643 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100004644 active site 340100004645 metal binding site [ion binding]; metal-binding site 340100004646 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 340100004647 active site 340100004648 2,3-diaminopropionate biosynthesis protein SbnB; Region: dehyd_SbnB_fam; TIGR03944 340100004649 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 340100004650 CoenzymeA binding site [chemical binding]; other site 340100004651 subunit interaction site [polypeptide binding]; other site 340100004652 PHB binding site; other site 340100004653 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004654 Helix-turn-helix domains; Region: HTH; cl00088 340100004655 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 340100004656 trimer interface [polypeptide binding]; other site 340100004657 eyelet of channel; other site 340100004658 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 340100004659 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 340100004660 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 340100004661 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 340100004662 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 340100004663 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 340100004664 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 340100004665 putative dimer interface [polypeptide binding]; other site 340100004666 [2Fe-2S] cluster binding site [ion binding]; other site 340100004667 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 340100004668 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 340100004669 SLBB domain; Region: SLBB; pfam10531 340100004670 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 340100004671 NADH dehydrogenase subunit G; Validated; Region: PRK09129 340100004672 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 340100004673 catalytic loop [active] 340100004674 iron binding site [ion binding]; other site 340100004675 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 340100004676 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 340100004677 NADH dehydrogenase; Region: NADHdh; cl00469 340100004678 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 340100004679 4Fe-4S binding domain; Region: Fer4; cl02805 340100004680 4Fe-4S binding domain; Region: Fer4; cl02805 340100004681 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 340100004682 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 340100004683 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 340100004684 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 340100004685 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340100004686 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 340100004687 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340100004688 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 340100004689 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340100004690 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 340100004691 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 340100004692 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 340100004693 N-terminal plug; other site 340100004694 ligand-binding site [chemical binding]; other site 340100004695 phosphoserine phosphatase; Provisional; Region: serB; PRK11133 340100004696 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 340100004697 motif II; other site 340100004698 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 340100004699 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 340100004700 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 340100004701 ATP binding site [chemical binding]; other site 340100004702 putative Mg++ binding site [ion binding]; other site 340100004703 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 340100004704 nucleotide binding region [chemical binding]; other site 340100004705 ATP-binding site [chemical binding]; other site 340100004706 TRCF domain; Region: TRCF; cl04088 340100004707 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 340100004708 substrate binding site; other site 340100004709 dimer interface; other site 340100004710 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 340100004711 homotrimer interaction site [polypeptide binding]; other site 340100004712 zinc binding site [ion binding]; other site 340100004713 CDP-binding sites; other site 340100004714 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 340100004715 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100004716 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100004717 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 340100004718 dimer interface [polypeptide binding]; other site 340100004719 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340100004720 catalytic triad [active] 340100004721 peroxidatic and resolving cysteines [active] 340100004722 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 340100004723 dimerization interface [polypeptide binding]; other site 340100004724 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 340100004725 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 340100004726 dimer interface [polypeptide binding]; other site 340100004727 phosphorylation site [posttranslational modification] 340100004728 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 340100004729 ATP binding site [chemical binding]; other site 340100004730 Mg2+ binding site [ion binding]; other site 340100004731 G-X-G motif; other site 340100004732 osmolarity response regulator; Provisional; Region: ompR; PRK09468 340100004733 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100004734 active site 340100004735 phosphorylation site [posttranslational modification] 340100004736 intermolecular recognition site; other site 340100004737 dimerization interface [polypeptide binding]; other site 340100004738 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 340100004739 DNA binding site [nucleotide binding] 340100004740 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 340100004741 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 340100004742 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100004743 Coenzyme A binding pocket [chemical binding]; other site 340100004744 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 340100004745 Fe-S cluster binding site [ion binding]; other site 340100004746 active site 340100004747 lysophospholipid transporter LplT; Provisional; Region: PRK11195 340100004748 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340100004749 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 340100004750 Walker A/P-loop; other site 340100004751 ATP binding site [chemical binding]; other site 340100004752 Q-loop/lid; other site 340100004753 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 340100004754 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 340100004755 Q-loop/lid; other site 340100004756 ABC transporter signature motif; other site 340100004757 Walker B; other site 340100004758 D-loop; other site 340100004759 H-loop/switch region; other site 340100004760 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 340100004761 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 340100004762 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 340100004763 nucleotide binding pocket [chemical binding]; other site 340100004764 K-X-D-G motif; other site 340100004765 catalytic site [active] 340100004766 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 340100004767 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 340100004768 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 340100004769 Dimer interface [polypeptide binding]; other site 340100004770 BRCT sequence motif; other site 340100004771 SurA N-terminal domain; Region: SurA_N_3; cl07813 340100004772 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100004773 BolA-like protein; Region: BolA; cl00386 340100004774 Intracellular septation protein A; Region: IspA; cl01098 340100004775 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 340100004776 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 340100004777 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 340100004778 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 340100004779 Walker A/P-loop; other site 340100004780 ATP binding site [chemical binding]; other site 340100004781 Q-loop/lid; other site 340100004782 ABC transporter signature motif; other site 340100004783 Walker B; other site 340100004784 D-loop; other site 340100004785 H-loop/switch region; other site 340100004786 Cobalt transport protein; Region: CbiQ; cl00463 340100004787 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 340100004788 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100004789 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 340100004790 putative ligand binding site [chemical binding]; other site 340100004791 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 340100004792 TM-ABC transporter signature motif; other site 340100004793 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 340100004794 TM-ABC transporter signature motif; other site 340100004795 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100004796 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100004797 Walker A/P-loop; other site 340100004798 ATP binding site [chemical binding]; other site 340100004799 Q-loop/lid; other site 340100004800 ABC transporter signature motif; other site 340100004801 Walker B; other site 340100004802 D-loop; other site 340100004803 H-loop/switch region; other site 340100004804 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100004805 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100004806 Walker A/P-loop; other site 340100004807 ATP binding site [chemical binding]; other site 340100004808 Q-loop/lid; other site 340100004809 ABC transporter signature motif; other site 340100004810 Walker B; other site 340100004811 D-loop; other site 340100004812 H-loop/switch region; other site 340100004813 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 340100004814 homodimer interface [polypeptide binding]; other site 340100004815 substrate-cofactor binding pocket; other site 340100004816 catalytic residue [active] 340100004817 NMT1-like family; Region: NMT1_2; cl15260 340100004818 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 340100004819 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 340100004820 TM-ABC transporter signature motif; other site 340100004821 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 340100004822 TM-ABC transporter signature motif; other site 340100004823 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100004824 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 340100004825 putative ligand binding site [chemical binding]; other site 340100004826 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100004827 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100004828 Walker A/P-loop; other site 340100004829 ATP binding site [chemical binding]; other site 340100004830 Q-loop/lid; other site 340100004831 ABC transporter signature motif; other site 340100004832 Walker B; other site 340100004833 D-loop; other site 340100004834 H-loop/switch region; other site 340100004835 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100004836 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100004837 Walker A/P-loop; other site 340100004838 ATP binding site [chemical binding]; other site 340100004839 Q-loop/lid; other site 340100004840 ABC transporter signature motif; other site 340100004841 Walker B; other site 340100004842 D-loop; other site 340100004843 H-loop/switch region; other site 340100004844 endonuclease III; Provisional; Region: PRK10702 340100004845 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100004846 minor groove reading motif; other site 340100004847 helix-hairpin-helix signature motif; other site 340100004848 substrate binding pocket [chemical binding]; other site 340100004849 active site 340100004850 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 340100004851 ferredoxin; Provisional; Region: PRK06991 340100004852 Putative Fe-S cluster; Region: FeS; pfam04060 340100004853 4Fe-4S binding domain; Region: Fer4; cl02805 340100004854 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 340100004855 PHB de-polymerase C-terminus; Region: PHB_depo_C; cl14907 340100004856 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 340100004857 ferredoxin-NADP reductase; Provisional; Region: PRK10926 340100004858 FAD binding pocket [chemical binding]; other site 340100004859 FAD binding motif [chemical binding]; other site 340100004860 phosphate binding motif [ion binding]; other site 340100004861 beta-alpha-beta structure motif; other site 340100004862 NAD binding pocket [chemical binding]; other site 340100004863 Ferredoxin [Energy production and conversion]; Region: COG1146 340100004864 4Fe-4S binding domain; Region: Fer4; cl02805 340100004865 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 340100004866 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 340100004867 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 340100004868 active site 340100004869 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 340100004870 homotrimer interaction site [polypeptide binding]; other site 340100004871 putative active site [active] 340100004872 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 340100004873 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100004874 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 340100004875 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 340100004876 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340100004877 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 340100004878 synthetase active site [active] 340100004879 NTP binding site [chemical binding]; other site 340100004880 metal binding site [ion binding]; metal-binding site 340100004881 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 340100004882 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 340100004883 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 340100004884 acetylornithine deacetylase (ArgE); Region: AcOrn-deacetyl; TIGR01892 340100004885 metal binding site [ion binding]; metal-binding site 340100004886 putative dimer interface [polypeptide binding]; other site 340100004887 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 340100004888 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 340100004889 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100004890 catalytic residue [active] 340100004891 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 340100004892 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 340100004893 substrate binding site [chemical binding]; other site 340100004894 active site 340100004895 catalytic residues [active] 340100004896 heterodimer interface [polypeptide binding]; other site 340100004897 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 340100004898 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340100004899 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 340100004900 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 340100004901 active site 340100004902 ribonuclease E; Reviewed; Region: rne; PRK10811 340100004903 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 340100004904 homodimer interface [polypeptide binding]; other site 340100004905 oligonucleotide binding site [chemical binding]; other site 340100004906 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 340100004907 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 340100004908 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 340100004909 active site 340100004910 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 340100004911 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 340100004912 motif II; other site 340100004913 TMAO/DMSO reductase; Reviewed; Region: PRK05363 340100004914 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 340100004915 Moco binding site; other site 340100004916 metal coordination site [ion binding]; other site 340100004917 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 340100004918 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 340100004919 amidase catalytic site [active] 340100004920 Zn binding residues [ion binding]; other site 340100004921 substrate binding site [chemical binding]; other site 340100004922 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340100004923 Predicted methyltransferases [General function prediction only]; Region: COG0313 340100004924 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 340100004925 active site 340100004926 dimer interface [polypeptide binding]; other site 340100004927 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 340100004928 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 340100004929 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 340100004930 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 340100004931 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 340100004932 dimer interface [polypeptide binding]; other site 340100004933 active site 340100004934 CoA binding pocket [chemical binding]; other site 340100004935 Acyl transferase domain; Region: Acyl_transf_1; cl08282 340100004936 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 340100004937 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100004938 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340100004939 NAD(P) binding site [chemical binding]; other site 340100004940 homotetramer interface [polypeptide binding]; other site 340100004941 homodimer interface [polypeptide binding]; other site 340100004942 active site 340100004943 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340100004944 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 340100004945 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 340100004946 dimer interface [polypeptide binding]; other site 340100004947 active site 340100004948 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 340100004949 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100004950 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 340100004951 DNA binding residues [nucleotide binding] 340100004952 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 340100004953 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 340100004954 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 340100004955 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 340100004956 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 340100004957 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 340100004958 protein binding site [polypeptide binding]; other site 340100004959 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 340100004960 protein binding site [polypeptide binding]; other site 340100004961 GTP-binding protein LepA; Provisional; Region: PRK05433 340100004962 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 340100004963 G1 box; other site 340100004964 putative GEF interaction site [polypeptide binding]; other site 340100004965 GTP/Mg2+ binding site [chemical binding]; other site 340100004966 Switch I region; other site 340100004967 G2 box; other site 340100004968 G3 box; other site 340100004969 Switch II region; other site 340100004970 G4 box; other site 340100004971 G5 box; other site 340100004972 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 340100004973 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 340100004974 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 340100004975 signal peptidase I; Provisional; Region: PRK10861 340100004976 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 340100004977 Catalytic site [active] 340100004978 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 340100004979 ribonuclease III; Reviewed; Region: rnc; PRK00102 340100004980 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 340100004981 dimerization interface [polypeptide binding]; other site 340100004982 active site 340100004983 metal binding site [ion binding]; metal-binding site 340100004984 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 340100004985 GTPase Era; Reviewed; Region: era; PRK00089 340100004986 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 340100004987 G1 box; other site 340100004988 GTP/Mg2+ binding site [chemical binding]; other site 340100004989 Switch I region; other site 340100004990 G2 box; other site 340100004991 Switch II region; other site 340100004992 G3 box; other site 340100004993 G4 box; other site 340100004994 G5 box; other site 340100004995 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 340100004996 Recombination protein O N terminal; Region: RecO_N; cl15812 340100004997 Recombination protein O C terminal; Region: RecO_C; pfam02565 340100004998 Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins; Region: PliI_like; cd09632 340100004999 dimer interface [polypeptide binding]; other site 340100005000 putative inhibitory loop; other site 340100005001 YccA-like proteins; Region: YccA_like; cd10433 340100005002 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 340100005003 multifunctional aminopeptidase A; Provisional; Region: PRK00913 340100005004 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 340100005005 interface (dimer of trimers) [polypeptide binding]; other site 340100005006 Substrate-binding/catalytic site; other site 340100005007 Zn-binding sites [ion binding]; other site 340100005008 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 340100005009 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100005010 Helix-turn-helix domains; Region: HTH; cl00088 340100005011 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100005012 dimerization interface [polypeptide binding]; other site 340100005013 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100005014 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 340100005015 putative ligand binding site [chemical binding]; other site 340100005016 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 340100005017 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100005018 tetrameric interface [polypeptide binding]; other site 340100005019 NAD binding site [chemical binding]; other site 340100005020 catalytic residues [active] 340100005021 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 340100005022 Helix-turn-helix domains; Region: HTH; cl00088 340100005023 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 340100005024 substrate binding site [chemical binding]; other site 340100005025 dimerization interface [polypeptide binding]; other site 340100005026 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 340100005027 NlpC/P60 family; Region: NLPC_P60; cl11438 340100005028 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 340100005029 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 340100005030 AMP-binding enzyme; Region: AMP-binding; cl15778 340100005031 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005032 Domain of unknown function (DUF336); Region: DUF336; cl01249 340100005033 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 340100005034 acetyl-CoA synthetase; Provisional; Region: PRK00174 340100005035 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 340100005036 AMP-binding enzyme; Region: AMP-binding; cl15778 340100005037 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005038 EamA-like transporter family; Region: EamA; cl01037 340100005039 EamA-like transporter family; Region: EamA; cl01037 340100005040 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 340100005041 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 340100005042 tetramer interface [polypeptide binding]; other site 340100005043 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005044 catalytic residue [active] 340100005045 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005046 NAD(P) binding site [chemical binding]; other site 340100005047 active site 340100005048 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 340100005049 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 340100005050 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100005051 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 340100005052 active site 340100005053 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100005054 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100005055 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 340100005056 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 340100005057 putative active site [active] 340100005058 Ntn-hydrolase superfamily, L-Asparaginase type 2-like enzymes. This family includes Glycosylasparaginase, Taspase 1 and L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked...; Region: Ntn_Asparaginase_2_like; cd04512 340100005059 active site 340100005060 dimer interface [polypeptide binding]; other site 340100005061 catalytic nucleophile [active] 340100005062 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 340100005063 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100005064 Walker A/P-loop; other site 340100005065 ATP binding site [chemical binding]; other site 340100005066 Q-loop/lid; other site 340100005067 ABC transporter signature motif; other site 340100005068 Walker B; other site 340100005069 D-loop; other site 340100005070 H-loop/switch region; other site 340100005071 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100005072 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100005073 Walker A/P-loop; other site 340100005074 ATP binding site [chemical binding]; other site 340100005075 Q-loop/lid; other site 340100005076 ABC transporter signature motif; other site 340100005077 Walker B; other site 340100005078 D-loop; other site 340100005079 H-loop/switch region; other site 340100005080 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100005081 glutathione ABC transporter substrate-binding protein GsiB; Provisional; Region: PRK15413 340100005082 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 340100005083 glutathione ABC transporter permease GsiC; Provisional; Region: PRK15081 340100005084 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 340100005085 dimer interface [polypeptide binding]; other site 340100005086 conserved gate region; other site 340100005087 putative PBP binding loops; other site 340100005088 ABC-ATPase subunit interface; other site 340100005089 glutathione ABC transporter permease GsiD; Provisional; Region: PRK15082 340100005090 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340100005091 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 340100005092 dimer interface [polypeptide binding]; other site 340100005093 conserved gate region; other site 340100005094 putative PBP binding loops; other site 340100005095 ABC-ATPase subunit interface; other site 340100005096 L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active...; Region: DmpA; cd02253 340100005097 homodimer interface [polypeptide binding]; other site 340100005098 homotetramer interface [polypeptide binding]; other site 340100005099 active site pocket [active] 340100005100 cleavage site 340100005101 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA_1; cd08663 340100005102 SxDxEG motif; other site 340100005103 active site 340100005104 metal binding site [ion binding]; metal-binding site 340100005105 homopentamer interface [polypeptide binding]; other site 340100005106 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 340100005107 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 340100005108 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 340100005109 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 340100005110 active site 340100005111 CTP synthetase; Validated; Region: pyrG; PRK05380 340100005112 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 340100005113 Catalytic site [active] 340100005114 active site 340100005115 UTP binding site [chemical binding]; other site 340100005116 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 340100005117 active site 340100005118 putative oxyanion hole; other site 340100005119 catalytic triad [active] 340100005120 NeuB family; Region: NeuB; cl00496 340100005121 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340100005122 enolase; Provisional; Region: eno; PRK00077 340100005123 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 340100005124 dimer interface [polypeptide binding]; other site 340100005125 metal binding site [ion binding]; metal-binding site 340100005126 substrate binding pocket [chemical binding]; other site 340100005127 Septum formation initiator; Region: DivIC; cl11433 340100005128 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 340100005129 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 340100005130 dimerization interface [polypeptide binding]; other site 340100005131 domain crossover interface; other site 340100005132 redox-dependent activation switch; other site 340100005133 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 340100005134 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 340100005135 trimer interface [polypeptide binding]; other site 340100005136 putative metal binding site [ion binding]; other site 340100005137 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 340100005138 AMP-binding enzyme; Region: AMP-binding; cl15778 340100005139 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005140 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100005141 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 340100005142 putative active site [active] 340100005143 putative metal binding site [ion binding]; other site 340100005144 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 340100005145 THUMP domain; Region: THUMP; cl12076 340100005146 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005147 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 340100005148 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100005149 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100005150 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100005151 DNA-binding site [nucleotide binding]; DNA binding site 340100005152 FCD domain; Region: FCD; cl11656 340100005153 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 340100005154 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 340100005155 substrate binding site [chemical binding]; other site 340100005156 ligand binding site [chemical binding]; other site 340100005157 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 340100005158 substrate binding site [chemical binding]; other site 340100005159 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 340100005160 PrpF protein; Region: PrpF; pfam04303 340100005161 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 340100005162 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS)...; Region: Ec2MCS_like_1; cd06117 340100005163 dimer interface [polypeptide binding]; other site 340100005164 active site 340100005165 citrylCoA binding site [chemical binding]; other site 340100005166 oxalacetate/citrate binding site [chemical binding]; other site 340100005167 coenzyme A binding site [chemical binding]; other site 340100005168 catalytic triad [active] 340100005169 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 340100005170 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 340100005171 tetramer interface [polypeptide binding]; other site 340100005172 active site 340100005173 Mg2+/Mn2+ binding site [ion binding]; other site 340100005174 malate dehydrogenase; Provisional; Region: PRK05442 340100005175 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 340100005176 NAD(P) binding site [chemical binding]; other site 340100005177 dimer interface [polypeptide binding]; other site 340100005178 malate binding site [chemical binding]; other site 340100005179 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100005180 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100005181 DNA-binding site [nucleotide binding]; DNA binding site 340100005182 UTRA domain; Region: UTRA; cl01230 340100005183 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 340100005184 Iron-sulfur protein interface; other site 340100005185 proximal quinone binding site [chemical binding]; other site 340100005186 SdhD (CybS) interface [polypeptide binding]; other site 340100005187 proximal heme binding site [chemical binding]; other site 340100005188 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 340100005189 SdhC subunit interface [polypeptide binding]; other site 340100005190 proximal heme binding site [chemical binding]; other site 340100005191 cardiolipin binding site; other site 340100005192 Iron-sulfur protein interface; other site 340100005193 proximal quinone binding site [chemical binding]; other site 340100005194 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 340100005195 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005196 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340100005197 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 340100005198 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100005199 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 340100005200 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 340100005201 dimer interface [polypeptide binding]; other site 340100005202 Citrate synthase; Region: Citrate_synt; pfam00285 340100005203 active site 340100005204 citrylCoA binding site [chemical binding]; other site 340100005205 NADH binding [chemical binding]; other site 340100005206 cationic pore residues; other site 340100005207 oxalacetate/citrate binding site [chemical binding]; other site 340100005208 coenzyme A binding site [chemical binding]; other site 340100005209 catalytic triad [active] 340100005210 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 340100005211 proline/glycine betaine transporter; Provisional; Region: PRK10642 340100005212 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 340100005213 putative substrate translocation pore; other site 340100005214 Osmosensory transporter coiled coil; Region: Osmo_CC; pfam08946 340100005215 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 340100005216 Malic enzyme, N-terminal domain; Region: malic; pfam00390 340100005217 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 340100005218 putative NAD(P) binding site [chemical binding]; other site 340100005219 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 340100005220 2-oxoacid dehydrogenase subunit E1; Provisional; Region: PRK13012 340100005221 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 340100005222 dimer interface [polypeptide binding]; other site 340100005223 TPP-binding site [chemical binding]; other site 340100005224 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 340100005225 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100005226 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 340100005227 putative DNA binding site [nucleotide binding]; other site 340100005228 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100005229 putative Zn2+ binding site [ion binding]; other site 340100005230 Helix-turn-helix domains; Region: HTH; cl00088 340100005231 OPT oligopeptide transporter protein; Region: OPT; cl14607 340100005232 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 340100005233 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 340100005234 TPP-binding site [chemical binding]; other site 340100005235 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 340100005236 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 340100005237 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 340100005238 E3 interaction surface; other site 340100005239 lipoyl attachment site [posttranslational modification]; other site 340100005240 e3 binding domain; Region: E3_binding; pfam02817 340100005241 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 340100005242 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 340100005243 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100005244 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100005245 Predicted ATPase [General function prediction only]; Region: COG1485 340100005246 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 340100005247 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 340100005248 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 340100005249 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 340100005250 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 340100005251 active site 340100005252 HIGH motif; other site 340100005253 dimer interface [polypeptide binding]; other site 340100005254 KMSKS motif; other site 340100005255 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100005256 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 340100005257 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 340100005258 putative Zn2+ binding site [ion binding]; other site 340100005259 putative DNA binding site [nucleotide binding]; other site 340100005260 BON domain; Region: BON; cl02771 340100005261 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 340100005262 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 340100005263 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 340100005264 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 340100005265 RNA binding site [nucleotide binding]; other site 340100005266 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 340100005267 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100005268 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100005269 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 340100005270 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 340100005271 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 340100005272 RNA binding surface [nucleotide binding]; other site 340100005273 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 340100005274 active site 340100005275 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 340100005276 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 340100005277 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 340100005278 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 340100005279 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 340100005280 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340100005281 NAD(P) binding site [chemical binding]; other site 340100005282 homotetramer interface [polypeptide binding]; other site 340100005283 homodimer interface [polypeptide binding]; other site 340100005284 active site 340100005285 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 340100005286 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 340100005287 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 340100005288 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 340100005289 Fe2+ transport protein; Region: Iron_transport; cl01377 340100005290 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100005291 Iron permease FTR1 family; Region: FTR1; cl00475 340100005292 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 340100005293 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100005294 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 340100005295 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 340100005296 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 340100005297 CsbD-like; Region: CsbD; cl15799 340100005298 cyanophycin synthetase; Provisional; Region: PRK14016 340100005299 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100005300 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100005301 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100005302 cyanophycin synthetase; Provisional; Region: PRK14016 340100005303 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100005304 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100005305 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 340100005306 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100005307 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the...; Region: ABC_MTABC3_MDL1_MDL2; cd03249 340100005308 Walker A/P-loop; other site 340100005309 ATP binding site [chemical binding]; other site 340100005310 Q-loop/lid; other site 340100005311 ABC transporter signature motif; other site 340100005312 Walker B; other site 340100005313 D-loop; other site 340100005314 H-loop/switch region; other site 340100005315 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 340100005316 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100005317 Protein of unknown function, DUF482; Region: DUF482; pfam04339 340100005318 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 340100005319 dinuclear metal binding motif [ion binding]; other site 340100005320 Transglycosylase SLT domain; Region: SLT_2; pfam13406 340100005321 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100005322 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100005323 catalytic residue [active] 340100005324 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340100005325 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 340100005326 putative active site [active] 340100005327 metal binding site [ion binding]; metal-binding site 340100005328 Helix-turn-helix domains; Region: HTH; cl00088 340100005329 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100005330 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 340100005331 putative effector binding pocket; other site 340100005332 dimerization interface [polypeptide binding]; other site 340100005333 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 340100005334 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 340100005335 metal binding site [ion binding]; metal-binding site 340100005336 dimer interface [polypeptide binding]; other site 340100005337 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100005338 Helix-turn-helix domains; Region: HTH; cl00088 340100005339 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 340100005340 putative dimerization interface [polypeptide binding]; other site 340100005341 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100005342 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100005343 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100005344 Coenzyme A binding pocket [chemical binding]; other site 340100005345 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005346 HI0933-like protein; Region: HI0933_like; pfam03486 340100005347 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005348 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 340100005349 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 340100005350 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 340100005351 Protein of unknown function, DUF417; Region: DUF417; cl01162 340100005352 Helix-turn-helix domains; Region: HTH; cl00088 340100005353 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 340100005354 putative substrate translocation pore; other site 340100005355 phosphoglycolate phosphatase; Provisional; Region: PRK13222 340100005356 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 340100005357 motif II; other site 340100005358 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 340100005359 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 340100005360 S-adenosylmethionine binding site [chemical binding]; other site 340100005361 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100005362 ligand binding site [chemical binding]; other site 340100005363 DNA gyrase subunit A; Validated; Region: PRK05560 340100005364 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 340100005365 CAP-like domain; other site 340100005366 active site 340100005367 primary dimer interface [polypeptide binding]; other site 340100005368 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005369 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005370 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005371 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005372 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005373 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005374 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 340100005375 homodimer interface [polypeptide binding]; other site 340100005376 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 340100005377 substrate-cofactor binding pocket; other site 340100005378 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005379 catalytic residue [active] 340100005380 Chorismate mutase type II; Region: CM_2; cl00693 340100005381 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 340100005382 Prephenate dehydratase; Region: PDT; pfam00800 340100005383 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 340100005384 putative L-Phe binding site [chemical binding]; other site 340100005385 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 340100005386 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 340100005387 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005388 homodimer interface [polypeptide binding]; other site 340100005389 catalytic residue [active] 340100005390 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005391 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 340100005392 3-phosphoshikimate 1-carboxyvinyltransferase; Region: PLN02338 340100005393 hinge; other site 340100005394 active site 340100005395 cytidylate kinase; Provisional; Region: cmk; PRK00023 340100005396 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 340100005397 CMP-binding site; other site 340100005398 The sites determining sugar specificity; other site 340100005399 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 340100005400 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 consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 340100005401 RNA binding site [nucleotide binding]; other site 340100005402 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 340100005403 RNA binding site [nucleotide binding]; other site 340100005404 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 340100005405 RNA binding site [nucleotide binding]; other site 340100005406 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec4; cd05689 340100005407 RNA binding site [nucleotide binding]; other site 340100005408 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 340100005409 RNA binding site [nucleotide binding]; other site 340100005410 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 340100005411 RNA binding site [nucleotide binding]; other site 340100005412 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 340100005413 IHF dimer interface [polypeptide binding]; other site 340100005414 IHF - DNA interface [nucleotide binding]; other site 340100005415 tetratricopeptide repeat protein; Provisional; Region: PRK11788 340100005416 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 340100005417 binding surface 340100005418 TPR motif; other site 340100005419 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100005420 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 340100005421 putative ribose interaction site [chemical binding]; other site 340100005422 putative ADP binding site [chemical binding]; other site 340100005423 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 340100005424 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 340100005425 NADP binding site [chemical binding]; other site 340100005426 homopentamer interface [polypeptide binding]; other site 340100005427 substrate binding site [chemical binding]; other site 340100005428 active site 340100005429 Protein of unknown function, DUF655; Region: DUF655; pfam04919 340100005430 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 340100005431 cysteine synthase B; Region: cysM; TIGR01138 340100005432 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 340100005433 dimer interface [polypeptide binding]; other site 340100005434 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005435 catalytic residue [active] 340100005436 Transglycosylase SLT domain; Region: SLT_2; pfam13406 340100005437 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100005438 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100005439 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 340100005440 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 340100005441 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 340100005442 Ligand binding site [chemical binding]; other site 340100005443 Electron transfer flavoprotein domain; Region: ETF; pfam01012 340100005444 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 340100005445 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 340100005446 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 340100005447 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 340100005448 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005449 active site 340100005450 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 340100005451 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100005452 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 340100005453 dimer interface [polypeptide binding]; other site 340100005454 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340100005455 catalytic triad [active] 340100005456 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100005457 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100005458 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100005459 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 340100005460 dimer interface [polypeptide binding]; other site 340100005461 conserved gate region; other site 340100005462 putative PBP binding loops; other site 340100005463 ABC-ATPase subunit interface; other site 340100005464 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 340100005465 dimer interface [polypeptide binding]; other site 340100005466 conserved gate region; other site 340100005467 putative PBP binding loops; other site 340100005468 ABC-ATPase subunit interface; other site 340100005469 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 340100005470 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a...; Region: ABC_CysA_sulfate_importer; cd03296 340100005471 Walker A/P-loop; other site 340100005472 ATP binding site [chemical binding]; other site 340100005473 Q-loop/lid; other site 340100005474 ABC transporter signature motif; other site 340100005475 Walker B; other site 340100005476 D-loop; other site 340100005477 H-loop/switch region; other site 340100005478 TOBE-like domain; Region: TOBE_3; pfam12857 340100005479 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 340100005480 Active Sites [active] 340100005481 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 340100005482 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 340100005483 Active Sites [active] 340100005484 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 340100005485 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 340100005486 CysD dimerization site [polypeptide binding]; other site 340100005487 G1 box; other site 340100005488 putative GEF interaction site [polypeptide binding]; other site 340100005489 GTP/Mg2+ binding site [chemical binding]; other site 340100005490 Switch I region; other site 340100005491 G2 box; other site 340100005492 G3 box; other site 340100005493 Switch II region; other site 340100005494 G4 box; other site 340100005495 G5 box; other site 340100005496 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 340100005497 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 340100005498 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 340100005499 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 340100005500 FeS/SAM binding site; other site 340100005501 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 340100005502 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100005503 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 340100005504 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 340100005505 Helix-turn-helix domains; Region: HTH; cl00088 340100005506 putative transposase OrfB; Reviewed; Region: PHA02517 340100005507 HTH-like domain; Region: HTH_21; pfam13276 340100005508 Integrase core domain; Region: rve; cl01316 340100005509 Integrase core domain; Region: rve_3; cl15866 340100005510 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 340100005511 GTPase RsgA; Reviewed; Region: PRK00098 340100005512 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 340100005513 RNA binding site [nucleotide binding]; other site 340100005514 homodimer interface [polypeptide binding]; other site 340100005515 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 340100005516 GTPase/Zn-binding domain interface [polypeptide binding]; other site 340100005517 GTP/Mg2+ binding site [chemical binding]; other site 340100005518 G4 box; other site 340100005519 G5 box; other site 340100005520 G1 box; other site 340100005521 Switch I region; other site 340100005522 G2 box; other site 340100005523 G3 box; other site 340100005524 Switch II region; other site 340100005525 Peptidase family M48; Region: Peptidase_M48; cl12018 340100005526 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 340100005527 putative active site [active] 340100005528 putative substrate binding site [chemical binding]; other site 340100005529 catalytic site [active] 340100005530 dimer interface [polypeptide binding]; other site 340100005531 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 340100005532 PaaX-like protein; Region: PaaX; pfam07848 340100005533 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 340100005534 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 340100005535 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 340100005536 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 340100005537 Phenylacetic acid degradation B; Region: PaaB; cl01371 340100005538 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 340100005539 Domain of unknown function DUF59; Region: DUF59; cl00941 340100005540 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 340100005541 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 340100005542 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 340100005543 FAD binding pocket [chemical binding]; other site 340100005544 FAD binding motif [chemical binding]; other site 340100005545 phosphate binding motif [ion binding]; other site 340100005546 beta-alpha-beta structure motif; other site 340100005547 NAD(p) ribose binding residues [chemical binding]; other site 340100005548 NAD binding pocket [chemical binding]; other site 340100005549 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 340100005550 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 340100005551 catalytic loop [active] 340100005552 iron binding site [ion binding]; other site 340100005553 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 340100005554 NAD(P) binding site [chemical binding]; other site 340100005555 catalytic residues [active] 340100005556 putative transposase OrfB; Reviewed; Region: PHA02517 340100005557 HTH-like domain; Region: HTH_21; pfam13276 340100005558 Integrase core domain; Region: rve; cl01316 340100005559 Integrase core domain; Region: rve_3; cl15866 340100005560 Helix-turn-helix domains; Region: HTH; cl00088 340100005561 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 340100005562 enoyl-CoA hydratase; Provisional; Region: PRK08140 340100005563 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 340100005564 substrate binding site [chemical binding]; other site 340100005565 oxyanion hole (OAH) forming residues; other site 340100005566 trimer interface [polypeptide binding]; other site 340100005567 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 340100005568 CoenzymeA binding site [chemical binding]; other site 340100005569 subunit interaction site [polypeptide binding]; other site 340100005570 PHB binding site; other site 340100005571 AMP-binding enzyme; Region: AMP-binding; cl15778 340100005572 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 340100005573 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005574 active site 340100005575 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005576 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100005577 Helix-turn-helix domains; Region: HTH; cl00088 340100005578 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100005579 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100005580 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100005581 NMT1-like family; Region: NMT1_2; cl15260 340100005582 DctM-like transporters; Region: DctM; pfam06808 340100005583 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100005584 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100005585 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100005586 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100005587 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 340100005588 FtsX-like permease family; Region: FtsX; cl15850 340100005589 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 340100005590 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 340100005591 apolar tunnel; other site 340100005592 heme binding site [chemical binding]; other site 340100005593 dimerization interface [polypeptide binding]; other site 340100005594 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005595 ATP binding site [chemical binding]; other site 340100005596 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005597 activation loop (A-loop); other site 340100005598 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 340100005599 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100005600 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 340100005601 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100005602 Walker A/P-loop; other site 340100005603 ATP binding site [chemical binding]; other site 340100005604 Q-loop/lid; other site 340100005605 ABC transporter signature motif; other site 340100005606 Walker B; other site 340100005607 D-loop; other site 340100005608 H-loop/switch region; other site 340100005609 TOBE domain; Region: TOBE_2; cl01440 340100005610 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 340100005611 dimer interface [polypeptide binding]; other site 340100005612 conserved gate region; other site 340100005613 putative PBP binding loops; other site 340100005614 ABC-ATPase subunit interface; other site 340100005615 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 340100005616 dimer interface [polypeptide binding]; other site 340100005617 conserved gate region; other site 340100005618 putative PBP binding loops; other site 340100005619 ABC-ATPase subunit interface; other site 340100005620 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 340100005621 ArsC family; Region: ArsC; pfam03960 340100005622 putative catalytic residues [active] 340100005623 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 340100005624 active site 340100005625 DNA binding site [nucleotide binding] 340100005626 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005627 Apolipoprotein A1/A4/E domain; Region: Apolipoprotein; pfam01442 340100005628 RmuC family; Region: RmuC; pfam02646 340100005629 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005630 active site 340100005631 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 340100005632 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100005633 active site 340100005634 dimer interface [polypeptide binding]; other site 340100005635 transcriptional regulator PhoU; Provisional; Region: PRK11115 340100005636 PhoU domain; Region: PhoU; pfam01895 340100005637 PhoU domain; Region: PhoU; pfam01895 340100005638 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 340100005639 putative active site [active] 340100005640 putative catalytic site [active] 340100005641 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100005642 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100005643 NMT1-like family; Region: NMT1_2; cl15260 340100005644 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100005645 Helix-turn-helix domains; Region: HTH; cl00088 340100005646 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 340100005647 dimerization interface [polypeptide binding]; other site 340100005648 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 340100005649 N-acetylglutamate synthase; Validated; Region: PRK05279 340100005650 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 340100005651 putative feedback inhibition sensing region; other site 340100005652 putative nucleotide binding site [chemical binding]; other site 340100005653 putative substrate binding site [chemical binding]; other site 340100005654 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100005655 Coenzyme A binding pocket [chemical binding]; other site 340100005656 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100005657 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 340100005658 putative NAD(P) binding site [chemical binding]; other site 340100005659 putative active site [active] 340100005660 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 340100005661 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 340100005662 ATP binding site [chemical binding]; other site 340100005663 putative Mg++ binding site [ion binding]; other site 340100005664 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 340100005665 nucleotide binding region [chemical binding]; other site 340100005666 ATP-binding site [chemical binding]; other site 340100005667 Helicase associated domain (HA2); Region: HA2; cl04503 340100005668 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 340100005669 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 340100005670 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 340100005671 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 340100005672 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 340100005673 metal binding triad; other site 340100005674 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 340100005675 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 340100005676 metal binding triad; other site 340100005677 TIGR02099 family protein; Region: TIGR02099 340100005678 AsmA-like C-terminal region; Region: AsmA_2; cl15864 340100005679 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100005680 S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic...; Region: S15_NS1_EPRS_RNA-bind; cl00349 340100005681 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100005682 transcription termination factor Rho; Provisional; Region: rho; PRK09376 340100005683 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 340100005684 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 340100005685 RNA binding site [nucleotide binding]; other site 340100005686 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 340100005687 multimer interface [polypeptide binding]; other site 340100005688 Walker A motif; other site 340100005689 ATP binding site [chemical binding]; other site 340100005690 Walker B motif; other site 340100005691 thioredoxin 2; Provisional; Region: PRK10996 340100005692 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 340100005693 catalytic residues [active] 340100005694 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 340100005695 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 340100005696 ATP binding site [chemical binding]; other site 340100005697 Mg2+ binding site [ion binding]; other site 340100005698 G-X-G motif; other site 340100005699 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 340100005700 anchoring element; other site 340100005701 dimer interface [polypeptide binding]; other site 340100005702 ATP binding site [chemical binding]; other site 340100005703 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 340100005704 active site 340100005705 metal binding site [ion binding]; metal-binding site 340100005706 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 340100005707 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 340100005708 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 340100005709 CAP-like domain; other site 340100005710 active site 340100005711 primary dimer interface [polypeptide binding]; other site 340100005712 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100005713 DctM-like transporters; Region: DctM; pfam06808 340100005714 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100005715 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 340100005716 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 340100005717 NMT1-like family; Region: NMT1_2; cl15260 340100005718 hypothetical protein; Provisional; Region: PRK07483 340100005719 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 340100005720 inhibitor-cofactor binding pocket; inhibition site 340100005721 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005722 catalytic residue [active] 340100005723 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 340100005724 putative active site [active] 340100005725 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100005726 Helix-turn-helix domains; Region: HTH; cl00088 340100005727 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 340100005728 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100005729 Coenzyme A binding pocket [chemical binding]; other site 340100005730 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 340100005731 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 340100005732 inhibitor-cofactor binding pocket; inhibition site 340100005733 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005734 catalytic residue [active] 340100005735 Cupin domain; Region: Cupin_2; cl09118 340100005736 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100005737 2-keto-3-deoxygluconate permease; Region: KdgT; cl14653 340100005738 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 340100005739 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 340100005740 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 340100005741 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100005742 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100005743 DNA-binding site [nucleotide binding]; DNA binding site 340100005744 UTRA domain; Region: UTRA; cl01230 340100005745 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 340100005746 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 340100005747 MOSC domain; Region: MOSC; pfam03473 340100005748 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100005749 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 340100005750 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 340100005751 catalytic loop [active] 340100005752 iron binding site [ion binding]; other site 340100005753 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 340100005754 FAD binding pocket [chemical binding]; other site 340100005755 FAD binding motif [chemical binding]; other site 340100005756 phosphate binding motif [ion binding]; other site 340100005757 beta-alpha-beta structure motif; other site 340100005758 NAD binding pocket [chemical binding]; other site 340100005759 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100005760 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100005761 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100005762 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 340100005763 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100005764 VirB7 interaction site; other site 340100005765 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 340100005766 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 340100005767 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100005768 Type II/IV secretion system protein; Region: T2SE; pfam00437 340100005769 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100005770 Walker A motif; other site 340100005771 ATP binding site [chemical binding]; other site 340100005772 Walker B motif; other site 340100005773 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 340100005774 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 340100005775 motif 1; other site 340100005776 active site 340100005777 motif 2; other site 340100005778 motif 3; other site 340100005779 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 340100005780 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 340100005781 CPxP motif; other site 340100005782 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 340100005783 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 340100005784 RimM N-terminal domain; Region: RimM; pfam01782 340100005785 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 340100005786 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 340100005787 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 340100005788 non-specific DNA binding site [nucleotide binding]; other site 340100005789 salt bridge; other site 340100005790 sequence-specific DNA binding site [nucleotide binding]; other site 340100005791 Cupin domain; Region: Cupin_2; cl09118 340100005792 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 340100005793 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100005794 substrate binding pocket [chemical binding]; other site 340100005795 membrane-bound complex binding site; other site 340100005796 hinge residues; other site 340100005797 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100005798 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 340100005799 dimer interface [polypeptide binding]; other site 340100005800 conserved gate region; other site 340100005801 putative PBP binding loops; other site 340100005802 ABC-ATPase subunit interface; other site 340100005803 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100005804 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100005805 Walker A/P-loop; other site 340100005806 ATP binding site [chemical binding]; other site 340100005807 Q-loop/lid; other site 340100005808 ABC transporter signature motif; other site 340100005809 Walker B; other site 340100005810 D-loop; other site 340100005811 H-loop/switch region; other site 340100005812 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005813 FAD dependent oxidoreductase; Region: DAO; pfam01266 340100005814 sensor protein QseC; Provisional; Region: PRK10337 340100005815 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 340100005816 dimer interface [polypeptide binding]; other site 340100005817 phosphorylation site [posttranslational modification] 340100005818 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 340100005819 ATP binding site [chemical binding]; other site 340100005820 Mg2+ binding site [ion binding]; other site 340100005821 G-X-G motif; other site 340100005822 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 340100005823 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100005824 active site 340100005825 phosphorylation site [posttranslational modification] 340100005826 intermolecular recognition site; other site 340100005827 dimerization interface [polypeptide binding]; other site 340100005828 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 340100005829 DNA binding site [nucleotide binding] 340100005830 MltA-interacting protein MipA; Region: MipA; cl01504 340100005831 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 340100005832 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100005833 active site 340100005834 HIGH motif; other site 340100005835 nucleotide binding site [chemical binding]; other site 340100005836 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340100005837 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 340100005838 active site 340100005839 KMSKS motif; other site 340100005840 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 340100005841 tRNA binding surface [nucleotide binding]; other site 340100005842 anticodon binding site; other site 340100005843 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 340100005844 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 340100005845 active site 340100005846 multimer interface [polypeptide binding]; other site 340100005847 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 340100005848 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 340100005849 FeS/SAM binding site; other site 340100005850 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100005851 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 340100005852 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 340100005853 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 340100005854 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 340100005855 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 340100005856 dimer interface [polypeptide binding]; other site 340100005857 motif 1; other site 340100005858 active site 340100005859 motif 2; other site 340100005860 motif 3; other site 340100005861 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 340100005862 anticodon binding site; other site 340100005863 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 340100005864 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 340100005865 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 340100005866 Trp docking motif [polypeptide binding]; other site 340100005867 active site 340100005868 GTP-binding protein Der; Reviewed; Region: PRK00093 340100005869 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 340100005870 G1 box; other site 340100005871 GTP/Mg2+ binding site [chemical binding]; other site 340100005872 Switch I region; other site 340100005873 G2 box; other site 340100005874 Switch II region; other site 340100005875 G3 box; other site 340100005876 G4 box; other site 340100005877 G5 box; other site 340100005878 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 340100005879 G1 box; other site 340100005880 GTP/Mg2+ binding site [chemical binding]; other site 340100005881 Switch I region; other site 340100005882 G2 box; other site 340100005883 G3 box; other site 340100005884 Switch II region; other site 340100005885 G4 box; other site 340100005886 G5 box; other site 340100005887 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 340100005888 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 340100005889 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005890 homodimer interface [polypeptide binding]; other site 340100005891 catalytic residue [active] 340100005892 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 340100005893 Sm1 motif; other site 340100005894 intra - hexamer interaction site; other site 340100005895 inter - hexamer interaction site [polypeptide binding]; other site 340100005896 nucleotide binding pocket [chemical binding]; other site 340100005897 Sm2 motif; other site 340100005898 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 340100005899 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 340100005900 HflX GTPase family; Region: HflX; cd01878 340100005901 G1 box; other site 340100005902 GTP/Mg2+ binding site [chemical binding]; other site 340100005903 Switch I region; other site 340100005904 G2 box; other site 340100005905 G3 box; other site 340100005906 Switch II region; other site 340100005907 G4 box; other site 340100005908 G5 box; other site 340100005909 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 340100005910 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 340100005911 HflK protein; Region: hflK; TIGR01933 340100005912 HflC protein; Region: hflC; TIGR01932 340100005913 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 340100005914 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100005915 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 340100005916 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100005917 putative active site [active] 340100005918 putative NTP binding site [chemical binding]; other site 340100005919 putative nucleic acid binding site [nucleotide binding]; other site 340100005920 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100005921 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 340100005922 active site 340100005923 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 340100005924 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 340100005925 dimer interface [polypeptide binding]; other site 340100005926 motif 1; other site 340100005927 active site 340100005928 motif 2; other site 340100005929 motif 3; other site 340100005930 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 340100005931 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 340100005932 GDP-binding site [chemical binding]; other site 340100005933 ACT binding site; other site 340100005934 IMP binding site; other site 340100005935 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100005936 active site 340100005937 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 340100005938 DNA primase, catalytic core; Region: dnaG; TIGR01391 340100005939 CHC2 zinc finger; Region: zf-CHC2; cl15369 340100005940 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 340100005941 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 340100005942 active site 340100005943 metal binding site [ion binding]; metal-binding site 340100005944 interdomain interaction site; other site 340100005945 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 340100005946 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 340100005947 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 340100005948 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 340100005949 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 340100005950 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 340100005951 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100005952 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 340100005953 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 340100005954 DNA binding residues [nucleotide binding] 340100005955 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100005956 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100005957 Helix-turn-helix domains; Region: HTH; cl00088 340100005958 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100005959 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 340100005960 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005961 Family of unknown function (DUF500); Region: DUF500; cl01109 340100005962 Helix-turn-helix domains; Region: HTH; cl00088 340100005963 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100005964 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100005965 DNA-binding site [nucleotide binding]; DNA binding site 340100005966 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 340100005967 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005968 homodimer interface [polypeptide binding]; other site 340100005969 catalytic residue [active] 340100005970 aspartate carbamoyltransferase; Provisional; Region: PRK11891 340100005971 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 340100005972 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005973 Putative exonuclease, RdgC; Region: RdgC; cl01122 340100005974 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 340100005975 putative substrate translocation pore; other site 340100005976 metabolite-proton symporter; Region: 2A0106; TIGR00883 340100005977 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 340100005978 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100005979 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 340100005980 dimer interface [polypeptide binding]; other site 340100005981 phosphorylation site [posttranslational modification] 340100005982 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 340100005983 ATP binding site [chemical binding]; other site 340100005984 Mg2+ binding site [ion binding]; other site 340100005985 G-X-G motif; other site 340100005986 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 340100005987 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100005988 active site 340100005989 phosphorylation site [posttranslational modification] 340100005990 intermolecular recognition site; other site 340100005991 dimerization interface [polypeptide binding]; other site 340100005992 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 340100005993 DNA binding site [nucleotide binding] 340100005994 recombinase A; Provisional; Region: recA; PRK09354 340100005995 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 340100005996 hexamer interface [polypeptide binding]; other site 340100005997 Walker A motif; other site 340100005998 ATP binding site [chemical binding]; other site 340100005999 Walker B motif; other site 340100006000 RecX family; Region: RecX; cl00936 340100006001 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 340100006002 Helix-turn-helix domains; Region: HTH; cl00088 340100006003 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 340100006004 putative dimerization interface [polypeptide binding]; other site 340100006005 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 340100006006 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 340100006007 THF binding site; other site 340100006008 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 340100006009 substrate binding site [chemical binding]; other site 340100006010 THF binding site; other site 340100006011 zinc-binding site [ion binding]; other site 340100006012 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 340100006013 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 340100006014 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100006015 CoA-ligase; Region: Ligase_CoA; cl02894 340100006016 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 340100006017 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006018 CoA-ligase; Region: Ligase_CoA; cl02894 340100006019 Integral membrane protein TerC family; Region: TerC; cl10468 340100006020 Integral membrane protein TerC family; Region: TerC; cl10468 340100006021 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 340100006022 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 340100006023 domain interfaces; other site 340100006024 active site 340100006025 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 340100006026 active site 340100006027 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed; Region: PRK06975 340100006028 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 340100006029 HemY protein N-terminus; Region: HemY_N; pfam07219 340100006030 translocon at the inner envelope of chloroplast subunit 62; Provisional; Region: PLN03209 340100006031 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 340100006032 dimer interface [polypeptide binding]; other site 340100006033 substrate binding site [chemical binding]; other site 340100006034 metal binding sites [ion binding]; metal-binding site 340100006035 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100006036 Entericidin EcnA/B family; Region: Entericidin; cl02322 340100006037 SAF domain; Region: SAF; cl00555 340100006038 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 340100006039 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100006040 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 340100006041 phosphopeptide binding site; other site 340100006042 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 340100006043 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 340100006044 ATP binding site [chemical binding]; other site 340100006045 Walker A motif; other site 340100006046 hexamer interface [polypeptide binding]; other site 340100006047 Walker B motif; other site 340100006048 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340100006049 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340100006050 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 340100006051 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006052 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; cl01461 340100006053 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 340100006054 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340100006055 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 340100006056 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 340100006057 active site 340100006058 GMP synthase; Reviewed; Region: guaA; PRK00074 340100006059 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 340100006060 AMP/PPi binding site [chemical binding]; other site 340100006061 candidate oxyanion hole; other site 340100006062 catalytic triad [active] 340100006063 potential glutamine specificity residues [chemical binding]; other site 340100006064 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 340100006065 ATP Binding subdomain [chemical binding]; other site 340100006066 Ligand Binding sites [chemical binding]; other site 340100006067 Dimerization subdomain; other site 340100006068 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 340100006069 Domain of unknown function (DUF3817); Region: DUF3817; cl14844 340100006070 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100006071 conserved cys residue [active] 340100006072 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006073 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100006074 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006075 transcriptional regulator; Provisional; Region: PRK10632 340100006076 Helix-turn-helix domains; Region: HTH; cl00088 340100006077 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_6; cd08475 340100006078 putative effector binding pocket; other site 340100006079 putative dimerization interface [polypeptide binding]; other site 340100006080 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR2; cd08268 340100006081 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 340100006082 putative NAD(P) binding site [chemical binding]; other site 340100006083 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006084 Helix-turn-helix domains; Region: HTH; cl00088 340100006085 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100006086 dimerization interface [polypeptide binding]; other site 340100006087 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100006088 putative transposase OrfB; Reviewed; Region: PHA02517 340100006089 HTH-like domain; Region: HTH_21; pfam13276 340100006090 Integrase core domain; Region: rve; cl01316 340100006091 Integrase core domain; Region: rve_3; cl15866 340100006092 Helix-turn-helix domains; Region: HTH; cl00088 340100006093 flagellin; Validated; Region: PRK08026 340100006094 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 340100006095 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 340100006096 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 340100006097 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100006098 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 340100006099 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 340100006100 DNA binding residues [nucleotide binding] 340100006101 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 340100006102 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 340100006103 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 340100006104 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340100006105 flagellar motor protein MotB; Validated; Region: motB; PRK09041 340100006106 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 340100006107 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100006108 ligand binding site [chemical binding]; other site 340100006109 Response regulator receiver domain; Region: Response_reg; pfam00072 340100006110 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006111 active site 340100006112 phosphorylation site [posttranslational modification] 340100006113 intermolecular recognition site; other site 340100006114 dimerization interface [polypeptide binding]; other site 340100006115 chemotaxis protein CheA; Provisional; Region: PRK10547 340100006116 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 340100006117 putative binding surface; other site 340100006118 active site 340100006119 CheY binding; Region: CheY-binding; pfam09078 340100006120 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 340100006121 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 340100006122 ATP binding site [chemical binding]; other site 340100006123 Mg2+ binding site [ion binding]; other site 340100006124 G-X-G motif; other site 340100006125 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 340100006126 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 340100006127 putative CheA interaction surface; other site 340100006128 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cd00181 340100006129 dimer interface [polypeptide binding]; other site 340100006130 ligand binding site [chemical binding]; other site 340100006131 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 340100006132 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 340100006133 dimerization interface [polypeptide binding]; other site 340100006134 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006135 dimer interface [polypeptide binding]; other site 340100006136 putative CheW interface [polypeptide binding]; other site 340100006137 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 340100006138 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 340100006139 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006140 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 340100006141 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006142 active site 340100006143 phosphorylation site [posttranslational modification] 340100006144 intermolecular recognition site; other site 340100006145 dimerization interface [polypeptide binding]; other site 340100006146 CheB methylesterase; Region: CheB_methylest; pfam01339 340100006147 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 340100006148 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006149 active site 340100006150 phosphorylation site [posttranslational modification] 340100006151 intermolecular recognition site; other site 340100006152 dimerization interface [polypeptide binding]; other site 340100006153 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 340100006154 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006155 dimer interface [polypeptide binding]; other site 340100006156 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 340100006157 putative CheW interface [polypeptide binding]; other site 340100006158 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 340100006159 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 340100006160 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 340100006161 putative transposase OrfB; Reviewed; Region: PHA02517 340100006162 HTH-like domain; Region: HTH_21; pfam13276 340100006163 Integrase core domain; Region: rve; cl01316 340100006164 Integrase core domain; Region: rve_3; cl15866 340100006165 Helix-turn-helix domains; Region: HTH; cl00088 340100006166 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 340100006167 flagellar biosynthesis regulator FlhF; Provisional; Region: flhF; PRK14723 340100006168 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100006169 flagellar biosynthesis regulator FlhF; Provisional; Region: flhF; PRK14723 340100006170 FlgN protein; Region: FlgN; cl09176 340100006171 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 340100006172 Helix-turn-helix domains; Region: HTH; cl00088 340100006173 putative transposase OrfB; Reviewed; Region: PHA02517 340100006174 HTH-like domain; Region: HTH_21; pfam13276 340100006175 Integrase core domain; Region: rve; cl01316 340100006176 Integrase core domain; Region: rve_3; cl15866 340100006177 SAF domain; Region: SAF; cl00555 340100006178 SAF-like; Region: SAF_2; pfam13144 340100006179 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 340100006180 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 340100006181 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 340100006182 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 340100006183 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006184 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006185 flagellar basal body rod modification protein; Provisional; Region: flgD; PRK12633 340100006186 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 340100006187 FlgD Ig-like domain; Region: FlgD_ig; cl15790 340100006188 flagellar hook protein FlgE; Provisional; Region: flgE; PRK12637 340100006189 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 340100006190 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 340100006191 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006192 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 340100006193 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 340100006194 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006195 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12694 340100006196 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 340100006197 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006198 Flagellar L-ring protein; Region: FlgH; cl00905 340100006199 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 340100006200 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 340100006201 flagellar rod assembly protein/muramidase FlgJ; Provisional; Region: flgJ; PRK12713 340100006202 Rod binding protein; Region: Rod-binding; cl01626 340100006203 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340100006204 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08147 340100006205 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006206 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 340100006207 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 340100006208 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 340100006209 dimerization interface [polypeptide binding]; other site 340100006210 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006211 dimer interface [polypeptide binding]; other site 340100006212 putative CheW interface [polypeptide binding]; other site 340100006213 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 340100006214 dimerization interface [polypeptide binding]; other site 340100006215 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006216 dimer interface [polypeptide binding]; other site 340100006217 putative CheW interface [polypeptide binding]; other site 340100006218 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 340100006219 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 340100006220 FliP family; Region: FliP; cl00593 340100006221 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 340100006222 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 340100006223 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 340100006224 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 340100006225 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 340100006226 flagellar biosynthesis chaperone; Validated; Region: fliJ; cl09161 340100006227 Flagellar FliJ protein; Region: FliJ; pfam02050 340100006228 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 340100006229 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 340100006230 Walker A motif/ATP binding site; other site 340100006231 Walker B motif; other site 340100006232 flagellar assembly protein H; Validated; Region: fliH; PRK05687 340100006233 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 340100006234 Flagellar assembly protein FliH; Region: FliH; pfam02108 340100006235 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 340100006236 FliG C-terminal domain; Region: FliG_C; pfam01706 340100006237 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 340100006238 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 340100006239 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 340100006240 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 340100006241 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 340100006242 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 340100006243 Flagellar protein FliT; Region: FliT; cl05125 340100006244 Flagellar protein FliS; Region: FliS; cl00654 340100006245 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 340100006246 flagellar capping protein; Reviewed; Region: fliD; PRK08032 340100006247 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 340100006248 FlaG protein; Region: FlaG; cl00591 340100006249 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100006250 Helix-turn-helix domains; Region: HTH; cl00088 340100006251 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100006252 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100006253 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100006254 active site 340100006255 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100006256 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100006257 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100006258 NMT1-like family; Region: NMT1_2; cl15260 340100006259 Cupin domain; Region: Cupin_2; cl09118 340100006260 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 340100006261 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100006262 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100006263 Sporulation related domain; Region: SPOR; cl10051 340100006264 Colicin V production protein; Region: Colicin_V; cl00567 340100006265 amidophosphoribosyltransferase; Provisional; Region: PRK09246 340100006266 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 340100006267 active site 340100006268 tetramer interface [polypeptide binding]; other site 340100006269 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100006270 active site 340100006271 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 340100006272 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 340100006273 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 340100006274 Int/Topo IB signature motif; other site 340100006275 active site 340100006276 DNA binding site [nucleotide binding] 340100006277 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 340100006278 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100006279 Predicted ATPase [General function prediction only]; Region: COG5293 340100006280 Uncharacterized protein conserved in bacteria (DUF2326); Region: DUF2326; pfam10088 340100006281 hypothetical protein; Reviewed; Region: PRK00024 340100006282 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100006283 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 340100006284 Domain of unknown function (DUF932); Region: DUF932; cl12129 340100006285 ParB-like nuclease domain; Region: ParBc; cl02129 340100006286 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 340100006287 Protein of unknown function DUF86; Region: DUF86; cl01031 340100006288 Protein of unknown function (DUF736); Region: DUF736; cl02303 340100006289 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 340100006290 non-specific DNA binding site [nucleotide binding]; other site 340100006291 salt bridge; other site 340100006292 sequence-specific DNA binding site [nucleotide binding]; other site 340100006293 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 340100006294 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 340100006295 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100006296 Replication initiator protein A; Region: RPA; cl02339 340100006297 ParA-like protein; Provisional; Region: PHA02518 340100006298 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 340100006299 P-loop; other site 340100006300 Magnesium ion binding site [ion binding]; other site 340100006301 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 340100006302 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 340100006303 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 340100006304 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 340100006305 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 340100006306 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 340100006307 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 340100006308 dimer interface [polypeptide binding]; other site 340100006309 active site 340100006310 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 340100006311 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 340100006312 active site 340100006313 catalytic tetrad [active] 340100006314 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 340100006315 putative active site [active] 340100006316 putative catalytic site [active] 340100006317 putative acyltransferase; Provisional; Region: PRK05790 340100006318 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 340100006319 dimer interface [polypeptide binding]; other site 340100006320 active site 340100006321 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 340100006322 CoenzymeA binding site [chemical binding]; other site 340100006323 subunit interaction site [polypeptide binding]; other site 340100006324 PHB binding site; other site 340100006325 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100006326 Helix-turn-helix domains; Region: HTH; cl00088 340100006327 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 340100006328 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100006329 putative substrate translocation pore; other site 340100006330 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340100006331 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 340100006332 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100006333 Helix-turn-helix domains; Region: HTH; cl00088 340100006334 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 340100006335 dimerization interface [polypeptide binding]; other site 340100006336 substrate binding pocket [chemical binding]; other site 340100006337 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 340100006338 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 340100006339 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100006340 catalytic residue [active] 340100006341 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100006342 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100006343 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 340100006344 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100006345 putative substrate translocation pore; other site 340100006346 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 340100006347 Helix-turn-helix domains; Region: HTH; cl00088 340100006348 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100006349 dimerization interface [polypeptide binding]; other site 340100006350 substrate binding pocket [chemical binding]; other site 340100006351 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 340100006352 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 340100006353 Walker A motif; other site 340100006354 ATP binding site [chemical binding]; other site 340100006355 Walker B motif; other site 340100006356 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 340100006357 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 340100006358 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 340100006359 ATP binding site [chemical binding]; other site 340100006360 Walker A motif; other site 340100006361 hexamer interface [polypeptide binding]; other site 340100006362 Walker B motif; other site 340100006363 TrbC/VIRB2 family; Region: TrbC; cl01583 340100006364 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 340100006365 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 340100006366 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 340100006367 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100006368 Walker A motif; other site 340100006369 ATP binding site [chemical binding]; other site 340100006370 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100006371 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 340100006372 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340100006373 VirB8 protein; Region: VirB8; cl01500 340100006374 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100006375 VirB7 interaction site; other site 340100006376 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 340100006377 Protein of unknown function (DUF2274); Region: DUF2274; cl02406 340100006378 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 340100006379 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 340100006380 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 340100006381 putative active site [active] 340100006382 catalytic site [active] 340100006383 putative metal binding site [ion binding]; other site 340100006384 SurA N-terminal domain; Region: SurA_N_3; cl07813 340100006385 periplasmic folding chaperone; Provisional; Region: PRK10788 340100006386 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100006387 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 340100006388 active site 340100006389 catalytic triad [active] 340100006390 oxyanion hole [active] 340100006391 switch loop; other site 340100006392 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 340100006393 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 340100006394 Walker A/P-loop; other site 340100006395 ATP binding site [chemical binding]; other site 340100006396 Q-loop/lid; other site 340100006397 ABC transporter signature motif; other site 340100006398 Walker B; other site 340100006399 D-loop; other site 340100006400 H-loop/switch region; other site 340100006401 Isochorismatase family; Region: Isochorismatase; pfam00857 340100006402 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 340100006403 catalytic triad [active] 340100006404 conserved cis-peptide bond; other site 340100006405 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 340100006406 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100006407 conserved cys residue [active] 340100006408 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006409 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 340100006410 EamA-like transporter family; Region: EamA; cl01037 340100006411 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006412 Helix-turn-helix domains; Region: HTH; cl00088 340100006413 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 340100006414 dimerization interface [polypeptide binding]; other site 340100006415 Cupin domain; Region: Cupin_2; cl09118 340100006416 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100006417 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006418 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006419 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100006420 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100006421 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 340100006422 amidase; Provisional; Region: PRK07056 340100006423 Amidase; Region: Amidase; cl11426 340100006424 Protein of unknown function (DUF1445); Region: DUF1445; cl01790 340100006425 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 340100006426 trimer interface [polypeptide binding]; other site 340100006427 eyelet of channel; other site 340100006428 DctM-like transporters; Region: DctM; pfam06808 340100006429 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100006430 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100006431 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100006432 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006433 Helix-turn-helix domains; Region: HTH; cl00088 340100006434 5-oxoprolinase; Region: PLN02666 340100006435 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340100006436 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 340100006437 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 340100006438 glutamine ABC transporter periplasmic protein; Reviewed; Region: glnH; PRK09495 340100006439 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 340100006440 substrate binding pocket [chemical binding]; other site 340100006441 membrane-bound complex binding site; other site 340100006442 hinge residues; other site 340100006443 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 340100006444 dimer interface [polypeptide binding]; other site 340100006445 conserved gate region; other site 340100006446 putative PBP binding loops; other site 340100006447 ABC-ATPase subunit interface; other site 340100006448 glutamine ABC transporter ATP-binding protein; Reviewed; Region: glnQ; PRK09493 340100006449 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100006450 Walker A/P-loop; other site 340100006451 ATP binding site [chemical binding]; other site 340100006452 Q-loop/lid; other site 340100006453 ABC transporter signature motif; other site 340100006454 Walker B; other site 340100006455 D-loop; other site 340100006456 H-loop/switch region; other site 340100006457 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100006458 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100006459 DNA-binding site [nucleotide binding]; DNA binding site 340100006460 FCD domain; Region: FCD; cl11656 340100006461 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100006462 NMT1-like family; Region: NMT1_2; cl15260 340100006463 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 340100006464 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340100006465 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 340100006466 synthetase active site [active] 340100006467 NTP binding site [chemical binding]; other site 340100006468 metal binding site [ion binding]; metal-binding site 340100006469 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 340100006470 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 340100006471 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 340100006472 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 340100006473 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 340100006474 catalytic site [active] 340100006475 G-X2-G-X-G-K; other site 340100006476 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 340100006477 classical (c) SDRs; Region: SDR_c; cd05233 340100006478 NAD(P) binding site [chemical binding]; other site 340100006479 active site 340100006480 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100006481 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 340100006482 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 340100006483 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100006484 Helix-turn-helix domains; Region: HTH; cl00088 340100006485 NlpC/P60 family; Region: NLPC_P60; cl11438 340100006486 AMP nucleosidase; Provisional; Region: PRK08292 340100006487 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 340100006488 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 340100006489 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 340100006490 non-specific DNA binding site [nucleotide binding]; other site 340100006491 salt bridge; other site 340100006492 sequence-specific DNA binding site [nucleotide binding]; other site 340100006493 HipA N-terminal domain; Region: Couple_hipA; cl11853 340100006494 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100006495 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100006496 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 340100006497 Helix-turn-helix domains; Region: HTH; cl00088 340100006498 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100006499 putative dimerization interface [polypeptide binding]; other site 340100006500 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100006501 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006502 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100006503 NMT1-like family; Region: NMT1_2; cl15260 340100006504 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 340100006505 active site 340100006506 tetramer interface; other site 340100006507 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 340100006508 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 340100006509 Low affinity iron permease; Region: Iron_permease; cl12096 340100006510 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 340100006511 GAF domain; Region: GAF; cl15785 340100006512 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 340100006513 Walker A motif; other site 340100006514 ATP binding site [chemical binding]; other site 340100006515 Walker B motif; other site 340100006516 arginine finger; other site 340100006517 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 340100006518 hypothetical protein; Provisional; Region: PRK11820 340100006519 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 340100006520 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 340100006521 ribonuclease PH; Reviewed; Region: rph; PRK00173 340100006522 Ribonuclease PH; Region: RNase_PH_bact; cd11362 340100006523 hexamer interface [polypeptide binding]; other site 340100006524 active site 340100006525 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100006526 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100006527 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100006528 active site 340100006529 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006530 Helix-turn-helix domains; Region: HTH; cl00088 340100006531 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 340100006532 putative dimerization interface [polypeptide binding]; other site 340100006533 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 340100006534 active site 340100006535 dimerization interface [polypeptide binding]; other site 340100006536 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 340100006537 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 340100006538 FeS/SAM binding site; other site 340100006539 HemN C-terminal domain; Region: HemN_C; pfam06969 340100006540 glutamine synthetase; Provisional; Region: glnA; PRK09469 340100006541 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 340100006542 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 340100006543 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 340100006544 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 340100006545 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 340100006546 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 340100006547 ATP binding site [chemical binding]; other site 340100006548 Mg2+ binding site [ion binding]; other site 340100006549 G-X-G motif; other site 340100006550 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 340100006551 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006552 active site 340100006553 phosphorylation site [posttranslational modification] 340100006554 intermolecular recognition site; other site 340100006555 dimerization interface [polypeptide binding]; other site 340100006556 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 340100006557 Walker A motif; other site 340100006558 ATP binding site [chemical binding]; other site 340100006559 Walker B motif; other site 340100006560 arginine finger; other site 340100006561 Helix-turn-helix domains; Region: HTH; cl00088 340100006562 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 340100006563 Helix-turn-helix domains; Region: HTH; cl00088 340100006564 The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; Region: PBP2_HupR; cd08431 340100006565 putative dimerization interface [polypeptide binding]; other site 340100006566 Cupin domain; Region: Cupin_2; cl09118 340100006567 Pirin-related protein [General function prediction only]; Region: COG1741 340100006568 Cupin domain; Region: Cupin_2; cl09118 340100006569 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 340100006570 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 340100006571 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 340100006572 Walker A/P-loop; other site 340100006573 ATP binding site [chemical binding]; other site 340100006574 Q-loop/lid; other site 340100006575 ABC transporter signature motif; other site 340100006576 Walker B; other site 340100006577 D-loop; other site 340100006578 H-loop/switch region; other site 340100006579 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 340100006580 dimer interface [polypeptide binding]; other site 340100006581 conserved gate region; other site 340100006582 putative PBP binding loops; other site 340100006583 ABC-ATPase subunit interface; other site 340100006584 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 340100006585 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100006586 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100006587 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 340100006588 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 340100006589 FAD binding pocket [chemical binding]; other site 340100006590 FAD binding motif [chemical binding]; other site 340100006591 phosphate binding motif [ion binding]; other site 340100006592 beta-alpha-beta structure motif; other site 340100006593 NAD binding pocket [chemical binding]; other site 340100006594 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006595 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 340100006596 TPP-binding site [chemical binding]; other site 340100006597 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100006598 NMT1-like family; Region: NMT1_2; cl15260 340100006599 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100006600 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 340100006601 Helix-turn-helix domains; Region: HTH; cl00088 340100006602 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 340100006603 putative dimerization interface [polypeptide binding]; other site 340100006604 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 340100006605 homotrimer interaction site [polypeptide binding]; other site 340100006606 putative active site [active] 340100006607 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 340100006608 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 340100006609 generic binding surface II; other site 340100006610 ssDNA binding site; other site 340100006611 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 340100006612 ATP binding site [chemical binding]; other site 340100006613 putative Mg++ binding site [ion binding]; other site 340100006614 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 340100006615 nucleotide binding region [chemical binding]; other site 340100006616 ATP-binding site [chemical binding]; other site 340100006617 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 340100006618 Helix-turn-helix domains; Region: HTH; cl00088 340100006619 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 340100006620 dimerization interface [polypeptide binding]; other site 340100006621 Ferritin-like domain; Region: Ferritin; pfam00210 340100006622 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 340100006623 dimerization interface [polypeptide binding]; other site 340100006624 DPS ferroxidase diiron center [ion binding]; other site 340100006625 ion pore; other site 340100006626 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100006627 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 340100006628 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006629 NAD(P) binding site [chemical binding]; other site 340100006630 active site 340100006631 Sulfatase; Region: Sulfatase; cl10460 340100006632 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 340100006633 Chain length determinant protein; Region: Wzz; cl15801 340100006634 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 340100006635 polysaccharide export protein Wza; Provisional; Region: PRK15078 340100006636 SLBB domain; Region: SLBB; pfam10531 340100006637 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100006638 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 340100006639 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 340100006640 Walker A/P-loop; other site 340100006641 ATP binding site [chemical binding]; other site 340100006642 Q-loop/lid; other site 340100006643 ABC transporter signature motif; other site 340100006644 Walker B; other site 340100006645 D-loop; other site 340100006646 H-loop/switch region; other site 340100006647 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsC; COG3563 340100006648 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 340100006649 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 340100006650 NAD(P) binding site [chemical binding]; other site 340100006651 homodimer interface [polypeptide binding]; other site 340100006652 substrate binding site [chemical binding]; other site 340100006653 active site 340100006654 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 340100006655 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 340100006656 inhibitor-cofactor binding pocket; inhibition site 340100006657 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006658 catalytic residue [active] 340100006659 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 340100006660 ligand binding site; other site 340100006661 tetramer interface; other site 340100006662 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 340100006663 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 340100006664 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 340100006665 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100006666 pseudaminic acid synthase; Region: PseI; TIGR03586 340100006667 NeuB family; Region: NeuB; cl00496 340100006668 SAF domain; Region: SAF; cl00555 340100006669 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsC; COG3563 340100006670 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 340100006671 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 340100006672 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 340100006673 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 340100006674 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 340100006675 substrate-cofactor binding pocket; other site 340100006676 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006677 catalytic residue [active] 340100006678 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 340100006679 Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3321 340100006680 active site 340100006681 Acyl transferase domain; Region: Acyl_transf_1; cl08282 340100006682 Dehydratase domain in polyketide synthase (PKS) enzymes; Region: PKS_DH; smart00826 340100006683 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006684 enoyl reductase of polyketide synthase; Region: enoyl_red; cd05195 340100006685 Enoylreductase; Region: PKS_ER; smart00829 340100006686 NAD(P) binding site [chemical binding]; other site 340100006687 beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x); Region: KR_2_FAS_SDR_x; cd08955 340100006688 short chain dehydrogenase; Provisional; Region: PRK06123 340100006689 putative NADP binding site [chemical binding]; other site 340100006690 active site 340100006691 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340100006692 leucine ABC transporter subunit substrate-binding protein LivK; Provisional; Region: PRK15404 340100006693 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 340100006694 dimerization interface [polypeptide binding]; other site 340100006695 ligand binding site [chemical binding]; other site 340100006696 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100006697 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 340100006698 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 340100006699 Walker A/P-loop; other site 340100006700 ATP binding site [chemical binding]; other site 340100006701 Q-loop/lid; other site 340100006702 ABC transporter signature motif; other site 340100006703 Walker B; other site 340100006704 D-loop; other site 340100006705 H-loop/switch region; other site 340100006706 TOBE domain; Region: TOBE_2; cl01440 340100006707 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 340100006708 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 340100006709 dimer interface [polypeptide binding]; other site 340100006710 conserved gate region; other site 340100006711 putative PBP binding loops; other site 340100006712 ABC-ATPase subunit interface; other site 340100006713 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 340100006714 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 340100006715 dimer interface [polypeptide binding]; other site 340100006716 conserved gate region; other site 340100006717 putative PBP binding loops; other site 340100006718 ABC-ATPase subunit interface; other site 340100006719 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100006720 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100006721 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 340100006722 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006723 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 340100006724 leucine ABC transporter subunit substrate-binding protein LivK; Provisional; Region: PRK15404 340100006725 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 340100006726 dimerization interface [polypeptide binding]; other site 340100006727 ligand binding site [chemical binding]; other site 340100006728 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 340100006729 TM-ABC transporter signature motif; other site 340100006730 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 340100006731 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 340100006732 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 340100006733 TM-ABC transporter signature motif; other site 340100006734 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 340100006735 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100006736 Walker A/P-loop; other site 340100006737 ATP binding site [chemical binding]; other site 340100006738 Q-loop/lid; other site 340100006739 ABC transporter signature motif; other site 340100006740 Walker B; other site 340100006741 D-loop; other site 340100006742 H-loop/switch region; other site 340100006743 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livF; PRK11614 340100006744 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100006745 Walker A/P-loop; other site 340100006746 ATP binding site [chemical binding]; other site 340100006747 Q-loop/lid; other site 340100006748 ABC transporter signature motif; other site 340100006749 Walker B; other site 340100006750 D-loop; other site 340100006751 H-loop/switch region; other site 340100006752 aspartate racemase; Region: asp_race; TIGR00035 340100006753 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 340100006754 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100006755 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 340100006756 active site 340100006757 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 340100006758 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100006759 NMT1-like family; Region: NMT1_2; cl15260 340100006760 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006761 Helix-turn-helix domains; Region: HTH; cl00088 340100006762 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100006763 dimerization interface [polypeptide binding]; other site 340100006764 N-carbamyl-D-amino acid amidohydrolase (DCase, class 6 nitrilases); Region: DCase; cd07569 340100006765 tetramer interface [polypeptide binding]; other site 340100006766 Predicted amidohydrolase [General function prediction only]; Region: COG0388 340100006767 active site 340100006768 catalytic triad [active] 340100006769 dimer interface [polypeptide binding]; other site 340100006770 glutathionine S-transferase; Provisional; Region: PRK10542 340100006771 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 340100006772 C-terminal domain interface [polypeptide binding]; other site 340100006773 GSH binding site (G-site) [chemical binding]; other site 340100006774 dimer interface [polypeptide binding]; other site 340100006775 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100006776 N-terminal domain interface [polypeptide binding]; other site 340100006777 dimer interface [polypeptide binding]; other site 340100006778 substrate binding pocket (H-site) [chemical binding]; other site 340100006779 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 340100006780 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 340100006781 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 340100006782 C-terminal domain interface [polypeptide binding]; other site 340100006783 GSH binding site (G-site) [chemical binding]; other site 340100006784 dimer interface [polypeptide binding]; other site 340100006785 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100006786 N-terminal domain interface [polypeptide binding]; other site 340100006787 dimer interface [polypeptide binding]; other site 340100006788 substrate binding pocket (H-site) [chemical binding]; other site 340100006789 Protein of unknown function (DUF423); Region: DUF423; cl01008 340100006790 Arginase family; Region: Arginase; cl00306 340100006791 NMT1-like family; Region: NMT1_2; cl15260 340100006792 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 340100006793 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 340100006794 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 340100006795 NAD(P) binding site [chemical binding]; other site 340100006796 catalytic residues [active] 340100006797 allantoate amidohydrolase; Reviewed; Region: PRK12893 340100006798 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 340100006799 active site 340100006800 metal binding site [ion binding]; metal-binding site 340100006801 dimer interface [polypeptide binding]; other site 340100006802 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100006803 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100006804 PYR/PP interface [polypeptide binding]; other site 340100006805 dimer interface [polypeptide binding]; other site 340100006806 TPP binding site [chemical binding]; other site 340100006807 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100006808 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 340100006809 TPP-binding site [chemical binding]; other site 340100006810 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; cl09155 340100006811 DctM-like transporters; Region: DctM; pfam06808 340100006812 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100006813 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100006814 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100006815 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006816 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100006817 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100006818 DNA-binding site [nucleotide binding]; DNA binding site 340100006819 FCD domain; Region: FCD; cl11656 340100006820 short chain dehydrogenase; Provisional; Region: PRK06701 340100006821 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 340100006822 NAD binding site [chemical binding]; other site 340100006823 metal binding site [ion binding]; metal-binding site 340100006824 active site 340100006825 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 340100006826 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 340100006827 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 340100006828 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 340100006829 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 340100006830 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 340100006831 putative ADP-binding pocket [chemical binding]; other site 340100006832 Protein of unknown function (DUF421); Region: DUF421; cl00990 340100006833 Domain of unknown function (DUF305); Region: DUF305; cl15795 340100006834 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 340100006835 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 340100006836 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 340100006837 dimer interface [polypeptide binding]; other site 340100006838 active site residues [active] 340100006839 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 340100006840 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100006841 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006842 short chain dehydrogenase; Provisional; Region: PRK07109 340100006843 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 340100006844 putative NAD(P) binding site [chemical binding]; other site 340100006845 active site 340100006846 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 340100006847 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100006848 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 340100006849 Subunit I/III interface [polypeptide binding]; other site 340100006850 D-pathway; other site 340100006851 Subunit I/VIIc interface [polypeptide binding]; other site 340100006852 Subunit I/IV interface [polypeptide binding]; other site 340100006853 Subunit I/II interface [polypeptide binding]; other site 340100006854 Low-spin heme (heme a) binding site [chemical binding]; other site 340100006855 Subunit I/VIIa interface [polypeptide binding]; other site 340100006856 Subunit I/VIa interface [polypeptide binding]; other site 340100006857 Dimer interface; other site 340100006858 Putative water exit pathway; other site 340100006859 Binuclear center (heme a3/CuB) [ion binding]; other site 340100006860 K-pathway; other site 340100006861 Subunit I/Vb interface [polypeptide binding]; other site 340100006862 Putative proton exit pathway; other site 340100006863 Subunit I/VIb interface; other site 340100006864 Subunit I/VIc interface [polypeptide binding]; other site 340100006865 Electron transfer pathway; other site 340100006866 Subunit I/VIIIb interface [polypeptide binding]; other site 340100006867 Subunit I/VIIb interface [polypeptide binding]; other site 340100006868 Predicted integral membrane protein [Function unknown]; Region: COG0392 340100006869 cardiolipin synthase 2; Provisional; Region: PRK11263 340100006870 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 340100006871 putative active site [active] 340100006872 catalytic site [active] 340100006873 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 340100006874 putative active site [active] 340100006875 catalytic site [active] 340100006876 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 340100006877 putative catalytic site [active] 340100006878 putative metal binding site [ion binding]; other site 340100006879 putative phosphate binding site [ion binding]; other site 340100006880 GAF domain; Region: GAF; cl15785 340100006881 GAF domain; Region: GAF_2; pfam13185 340100006882 PAS domain S-box; Region: sensory_box; TIGR00229 340100006883 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 340100006884 PAS domain S-box; Region: sensory_box; TIGR00229 340100006885 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 340100006886 putative active site [active] 340100006887 heme pocket [chemical binding]; other site 340100006888 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 340100006889 dimer interface [polypeptide binding]; other site 340100006890 phosphorylation site [posttranslational modification] 340100006891 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 340100006892 ATP binding site [chemical binding]; other site 340100006893 Mg2+ binding site [ion binding]; other site 340100006894 G-X-G motif; other site 340100006895 Response regulator receiver domain; Region: Response_reg; pfam00072 340100006896 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006897 active site 340100006898 phosphorylation site [posttranslational modification] 340100006899 intermolecular recognition site; other site 340100006900 dimerization interface [polypeptide binding]; other site 340100006901 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 340100006902 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 340100006903 active site 340100006904 catalytic site [active] 340100006905 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 340100006906 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 340100006907 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 340100006908 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 340100006909 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 340100006910 catalytic site [active] 340100006911 active site 340100006912 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 340100006913 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 340100006914 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 340100006915 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 340100006916 active site 340100006917 catalytic site [active] 340100006918 glycogen branching enzyme; Provisional; Region: PRK05402 340100006919 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 340100006920 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 340100006921 active site 340100006922 catalytic site [active] 340100006923 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 340100006924 trehalose synthase; Region: treS_nterm; TIGR02456 340100006925 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 340100006926 active site 340100006927 catalytic site [active] 340100006928 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; cl01286 340100006929 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 340100006930 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 340100006931 active site 340100006932 homodimer interface [polypeptide binding]; other site 340100006933 catalytic site [active] 340100006934 acceptor binding site [chemical binding]; other site 340100006935 glycogen synthase; Provisional; Region: glgA; PRK00654 340100006936 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 340100006937 ADP-binding pocket [chemical binding]; other site 340100006938 homodimer interface [polypeptide binding]; other site 340100006939 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100006940 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 340100006941 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 340100006942 Walker A motif; other site 340100006943 ATP binding site [chemical binding]; other site 340100006944 Walker B motif; other site 340100006945 Helix-turn-helix domains; Region: HTH; cl00088 340100006946 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 340100006947 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006948 active site 340100006949 phosphorylation site [posttranslational modification] 340100006950 intermolecular recognition site; other site 340100006951 dimerization interface [polypeptide binding]; other site 340100006952 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 340100006953 Walker A motif; other site 340100006954 ATP binding site [chemical binding]; other site 340100006955 Walker B motif; other site 340100006956 arginine finger; other site 340100006957 Helix-turn-helix domains; Region: HTH; cl00088 340100006958 thiamine pyrophosphate protein; Provisional; Region: PRK08273 340100006959 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 340100006960 PYR/PP interface [polypeptide binding]; other site 340100006961 tetramer interface [polypeptide binding]; other site 340100006962 dimer interface [polypeptide binding]; other site 340100006963 TPP binding site [chemical binding]; other site 340100006964 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100006965 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 340100006966 TPP-binding site [chemical binding]; other site 340100006967 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 340100006968 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 340100006969 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100006970 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100006971 Walker A/P-loop; other site 340100006972 ATP binding site [chemical binding]; other site 340100006973 Q-loop/lid; other site 340100006974 ABC transporter signature motif; other site 340100006975 Walker B; other site 340100006976 D-loop; other site 340100006977 H-loop/switch region; other site 340100006978 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 340100006979 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 340100006980 Response regulator receiver domain; Region: Response_reg; pfam00072 340100006981 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100006982 active site 340100006983 phosphorylation site [posttranslational modification] 340100006984 intermolecular recognition site; other site 340100006985 dimerization interface [polypeptide binding]; other site 340100006986 BON domain; Region: BON; cl02771 340100006987 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 340100006988 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 340100006989 classical (c) SDRs; Region: SDR_c; cd05233 340100006990 NAD(P) binding site [chemical binding]; other site 340100006991 active site 340100006992 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 340100006993 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 340100006994 active site 340100006995 motif I; other site 340100006996 motif II; other site 340100006997 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340100006998 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 340100006999 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 340100007000 putative active site [active] 340100007001 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 340100007002 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 340100007003 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 340100007004 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340100007005 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 340100007006 active site 340100007007 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340100007008 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 340100007009 putative active site [active] 340100007010 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 340100007011 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340100007012 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 340100007013 NAD binding site [chemical binding]; other site 340100007014 putative substrate binding site 2 [chemical binding]; other site 340100007015 putative substrate binding site 1 [chemical binding]; other site 340100007016 active site 340100007017 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 340100007018 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340100007019 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 340100007020 Probable Catalytic site; other site 340100007021 metal-binding site 340100007022 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 340100007023 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 340100007024 DNA binding site [nucleotide binding] 340100007025 active site 340100007026 Int/Topo IB signature motif; other site 340100007027 catalytic residues [active] 340100007028 Competence-damaged protein; Region: CinA; cl00666 340100007029 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 340100007030 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100007031 Protein of unknown function (DUF3182); Region: DUF3182; pfam11379 340100007032 Integral membrane protein TerC family; Region: TerC; cl10468 340100007033 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100007034 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100007035 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 340100007036 substrate binding pocket [chemical binding]; other site 340100007037 membrane-bound complex binding site; other site 340100007038 hinge residues; other site 340100007039 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 340100007040 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 340100007041 active site 340100007042 dimer interface [polypeptide binding]; other site 340100007043 non-prolyl cis peptide bond; other site 340100007044 insertion regions; other site 340100007045 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 340100007046 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 340100007047 ABC-ATPase subunit interface; other site 340100007048 putative PBP binding loops; other site 340100007049 putative mechanosensitive channel protein; Provisional; Region: PRK11465 340100007050 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100007051 Protein of unknown function, DUF; Region: DUF411; cl01142 340100007052 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_2; cd05679 340100007053 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 340100007054 metal binding site [ion binding]; metal-binding site 340100007055 putative dimer interface [polypeptide binding]; other site 340100007056 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100007057 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100007058 Walker A/P-loop; other site 340100007059 ATP binding site [chemical binding]; other site 340100007060 Q-loop/lid; other site 340100007061 ABC transporter signature motif; other site 340100007062 Walker B; other site 340100007063 D-loop; other site 340100007064 H-loop/switch region; other site 340100007065 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100007066 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100007067 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100007068 Walker A/P-loop; other site 340100007069 ATP binding site [chemical binding]; other site 340100007070 Q-loop/lid; other site 340100007071 ABC transporter signature motif; other site 340100007072 Walker B; other site 340100007073 D-loop; other site 340100007074 H-loop/switch region; other site 340100007075 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100007076 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340100007077 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100007078 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 340100007079 dimer interface [polypeptide binding]; other site 340100007080 conserved gate region; other site 340100007081 putative PBP binding loops; other site 340100007082 ABC-ATPase subunit interface; other site 340100007083 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 340100007084 dimer interface [polypeptide binding]; other site 340100007085 conserved gate region; other site 340100007086 putative PBP binding loops; other site 340100007087 ABC-ATPase subunit interface; other site 340100007088 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_10; cd08515 340100007089 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100007090 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100007091 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 340100007092 active site 340100007093 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 340100007094 Ligand Binding Site [chemical binding]; other site 340100007095 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100007096 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 340100007097 substrate binding pocket [chemical binding]; other site 340100007098 membrane-bound complex binding site; other site 340100007099 hinge residues; other site 340100007100 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 340100007101 dimer interface [polypeptide binding]; other site 340100007102 conserved gate region; other site 340100007103 putative PBP binding loops; other site 340100007104 ABC-ATPase subunit interface; other site 340100007105 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 340100007106 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100007107 Walker A/P-loop; other site 340100007108 ATP binding site [chemical binding]; other site 340100007109 Q-loop/lid; other site 340100007110 ABC transporter signature motif; other site 340100007111 Walker B; other site 340100007112 D-loop; other site 340100007113 H-loop/switch region; other site 340100007114 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 340100007115 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 340100007116 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 340100007117 active site 340100007118 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 340100007119 LysE type translocator; Region: LysE; cl00565 340100007120 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 340100007121 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 340100007122 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 340100007123 arginine/ornithine antiporter; Region: arg_ornith_anti; TIGR03810 340100007124 Amidinotransferase; Region: Amidinotransf; cl12043 340100007125 arginine/ornithine antiporter; Region: arg_ornith_anti; TIGR03810 340100007126 Spore germination protein; Region: Spore_permease; cl15802 340100007127 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 340100007128 Family of unknown function (DUF500); Region: DUF500; cl01109 340100007129 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 340100007130 Helix-turn-helix domains; Region: HTH; cl00088 340100007131 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100007132 putative dimerization interface [polypeptide binding]; other site 340100007133 Sulfatase; Region: Sulfatase; cl10460 340100007134 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 340100007135 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100007136 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100007137 tetramerization interface [polypeptide binding]; other site 340100007138 NAD(P) binding site [chemical binding]; other site 340100007139 catalytic residues [active] 340100007140 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100007141 NMT1-like family; Region: NMT1_2; cl15260 340100007142 Integrase core domain; Region: rve_3; cl15866 340100007143 HTH-like domain; Region: HTH_21; pfam13276 340100007144 Integrase core domain; Region: rve; cl01316 340100007145 Helix-turn-helix domains; Region: HTH; cl00088 340100007146 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 340100007147 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100007148 C-terminal domain interface [polypeptide binding]; other site 340100007149 GSH binding site (G-site) [chemical binding]; other site 340100007150 dimer interface [polypeptide binding]; other site 340100007151 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100007152 dimer interface [polypeptide binding]; other site 340100007153 N-terminal domain interface [polypeptide binding]; other site 340100007154 substrate binding pocket (H-site) [chemical binding]; other site 340100007155 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100007156 Helix-turn-helix domains; Region: HTH; cl00088 340100007157 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 340100007158 dimerization interface [polypeptide binding]; other site 340100007159 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase; Region: DapE-ArgE; TIGR01910 340100007160 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like2; cd03895 340100007161 metal binding site [ion binding]; metal-binding site 340100007162 dimer interface [polypeptide binding]; other site 340100007163 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 340100007164 TOMM system kinase/cyclase multidomain protein; Region: TOMM_kin_cyc; TIGR03903 340100007165 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100007166 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 340100007167 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 340100007168 Protein of unknown function (DUF770); Region: DUF770; cl01402 340100007169 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 340100007170 Protein of unknown function (DUF877); Region: DUF877; pfam05943 340100007171 Protein of unknown function (DUF796); Region: DUF796; cl01226 340100007172 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 340100007173 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 340100007174 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 340100007175 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 340100007176 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 340100007177 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 340100007178 Clp amino terminal domain; Region: Clp_N; pfam02861 340100007179 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 340100007180 Walker A motif; other site 340100007181 ATP binding site [chemical binding]; other site 340100007182 Walker B motif; other site 340100007183 arginine finger; other site 340100007184 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 340100007185 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 340100007186 Walker A motif; other site 340100007187 ATP binding site [chemical binding]; other site 340100007188 Walker B motif; other site 340100007189 arginine finger; other site 340100007190 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340100007191 Rhs element Vgr protein; Region: vgr_GE; TIGR01646 340100007192 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 340100007193 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340100007194 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 340100007195 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100007196 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100007197 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100007198 secreted effector protein PipB2; Provisional; Region: PRK15196 340100007199 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100007200 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100007201 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100007202 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 340100007203 PAAR motif; Region: PAAR_motif; cl15808 340100007204 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 340100007205 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 340100007206 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 340100007207 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 340100007208 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 340100007209 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 340100007210 Protein of unknown function DUF72; Region: DUF72; cl00777 340100007211 sensory histidine kinase CreC; Provisional; Region: PRK11100 340100007212 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 340100007213 dimer interface [polypeptide binding]; other site 340100007214 phosphorylation site [posttranslational modification] 340100007215 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 340100007216 ATP binding site [chemical binding]; other site 340100007217 Mg2+ binding site [ion binding]; other site 340100007218 G-X-G motif; other site 340100007219 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100007220 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100007221 active site 340100007222 phosphorylation site [posttranslational modification] 340100007223 intermolecular recognition site; other site 340100007224 dimerization interface [polypeptide binding]; other site 340100007225 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 340100007226 DNA binding site [nucleotide binding] 340100007227 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 340100007228 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 340100007229 Moco binding site; other site 340100007230 metal coordination site [ion binding]; other site 340100007231 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 340100007232 SelR domain; Region: SelR; pfam01641 340100007233 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 340100007234 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 340100007235 metal-binding site 340100007236 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 340100007237 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 340100007238 XdhC Rossmann domain; Region: XdhC_C; pfam13478 340100007239 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100007240 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100007241 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100007242 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100007243 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100007244 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100007245 Cytochrome c; Region: Cytochrom_C; cl11414 340100007246 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 340100007247 Ligand Binding Site [chemical binding]; other site 340100007248 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 340100007249 active site 340100007250 Zn binding site [ion binding]; other site 340100007251 DoxX; Region: DoxX; cl00976 340100007252 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 340100007253 catalytic triad [active] 340100007254 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 340100007255 ArsC family; Region: ArsC; pfam03960 340100007256 catalytic residues [active] 340100007257 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100007258 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 340100007259 TPR repeat; Region: TPR_11; pfam13414 340100007260 binding surface 340100007261 TPR motif; other site 340100007262 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 340100007263 catalytic residues [active] 340100007264 dimer interface [polypeptide binding]; other site 340100007265 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100007266 Helix-turn-helix domains; Region: HTH; cl00088 340100007267 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100007268 EamA-like transporter family; Region: EamA; cl01037 340100007269 EamA-like transporter family; Region: EamA; cl01037 340100007270 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100007271 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 340100007272 C-terminal domain interface [polypeptide binding]; other site 340100007273 GSH binding site (G-site) [chemical binding]; other site 340100007274 dimer interface [polypeptide binding]; other site 340100007275 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 340100007276 N-terminal domain interface [polypeptide binding]; other site 340100007277 putative dimer interface [polypeptide binding]; other site 340100007278 active site 340100007279 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100007280 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 340100007281 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 340100007282 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 340100007283 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 340100007284 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 340100007285 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 340100007286 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 340100007287 NAD(P) binding site [chemical binding]; other site 340100007288 Arginase family; Region: Arginase; cl00306 340100007289 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100007290 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100007291 Walker A/P-loop; other site 340100007292 ATP binding site [chemical binding]; other site 340100007293 Q-loop/lid; other site 340100007294 ABC transporter signature motif; other site 340100007295 Walker B; other site 340100007296 D-loop; other site 340100007297 H-loop/switch region; other site 340100007298 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100007299 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 340100007300 dimer interface [polypeptide binding]; other site 340100007301 conserved gate region; other site 340100007302 putative PBP binding loops; other site 340100007303 ABC-ATPase subunit interface; other site 340100007304 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 340100007305 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100007306 substrate binding pocket [chemical binding]; other site 340100007307 membrane-bound complex binding site; other site 340100007308 hinge residues; other site 340100007309 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100007310 Helix-turn-helix domains; Region: HTH; cl00088 340100007311 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100007312 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 340100007313 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 340100007314 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 340100007315 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 340100007316 active site 340100007317 DNA polymerase III subunit delta'; Validated; Region: PRK06964 340100007318 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100007319 thymidylate kinase; Validated; Region: tmk; PRK00698 340100007320 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 340100007321 TMP-binding site; other site 340100007322 ATP-binding site [chemical binding]; other site 340100007323 YceG-like family; Region: YceG; pfam02618 340100007324 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 340100007325 dimerization interface [polypeptide binding]; other site 340100007326 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 340100007327 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 340100007328 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 340100007329 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 340100007330 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 340100007331 CoenzymeA binding site [chemical binding]; other site 340100007332 subunit interaction site [polypeptide binding]; other site 340100007333 PHB binding site; other site 340100007334 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007335 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 340100007336 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 340100007337 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 340100007338 substrate binding site [chemical binding]; other site 340100007339 oxyanion hole (OAH) forming residues; other site 340100007340 trimer interface [polypeptide binding]; other site 340100007341 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 340100007342 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100007343 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100007344 active site 340100007345 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl15768 340100007346 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 340100007347 putative coenzyme Q binding site [chemical binding]; other site 340100007348 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 340100007349 SmpB-tmRNA interface; other site 340100007350 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 340100007351 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 340100007352 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 340100007353 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 340100007354 catalytic triad [active] 340100007355 phosphoenolpyruvate synthase; Validated; Region: PRK06464 340100007356 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 340100007357 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 340100007358 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; cl09155 340100007359 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 340100007360 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 340100007361 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340100007362 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 340100007363 RNA/DNA hybrid binding site [nucleotide binding]; other site 340100007364 active site 340100007365 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 340100007366 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 340100007367 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 340100007368 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 340100007369 active site 340100007370 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 340100007371 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 340100007372 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 340100007373 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 340100007374 trimer interface [polypeptide binding]; other site 340100007375 active site 340100007376 UDP-GlcNAc binding site [chemical binding]; other site 340100007377 lipid binding site [chemical binding]; lipid-binding site 340100007378 periplasmic chaperone; Provisional; Region: PRK10780 340100007379 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 340100007380 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 340100007381 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340100007382 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340100007383 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340100007384 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340100007385 Surface antigen; Region: Bac_surface_Ag; cl03097 340100007386 zinc metallopeptidase RseP; Provisional; Region: PRK10779 340100007387 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 340100007388 active site 340100007389 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 340100007390 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 340100007391 putative substrate binding region [chemical binding]; other site 340100007392 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 340100007393 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 340100007394 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 340100007395 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 340100007396 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 340100007397 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 340100007398 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 340100007399 catalytic residue [active] 340100007400 putative FPP diphosphate binding site; other site 340100007401 putative FPP binding hydrophobic cleft; other site 340100007402 dimer interface [polypeptide binding]; other site 340100007403 putative IPP diphosphate binding site; other site 340100007404 ribosome recycling factor; Reviewed; Region: frr; PRK00083 340100007405 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 340100007406 hinge region; other site 340100007407 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 340100007408 putative nucleotide binding site [chemical binding]; other site 340100007409 uridine monophosphate binding site [chemical binding]; other site 340100007410 homohexameric interface [polypeptide binding]; other site 340100007411 elongation factor Ts; Provisional; Region: tsf; PRK09377 340100007412 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 340100007413 Elongation factor TS; Region: EF_TS; pfam00889 340100007414 Elongation factor TS; Region: EF_TS; pfam00889 340100007415 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 340100007416 rRNA interaction site [nucleotide binding]; other site 340100007417 S8 interaction site; other site 340100007418 putative laminin-1 binding site; other site 340100007419 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 340100007420 active site 340100007421 PII uridylyl-transferase; Provisional; Region: PRK03059 340100007422 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 340100007423 metal binding triad; other site 340100007424 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 340100007425 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340100007426 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 340100007427 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 340100007428 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 340100007429 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100007430 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 340100007431 catalytic triad [active] 340100007432 dimer interface [polypeptide binding]; other site 340100007433 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100007434 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 340100007435 metal-binding site [ion binding] 340100007436 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 340100007437 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 340100007438 metal-binding site [ion binding] 340100007439 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340100007440 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100007441 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 340100007442 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 340100007443 DNA binding residues [nucleotide binding] 340100007444 dimer interface [polypeptide binding]; other site 340100007445 copper binding site [ion binding]; other site 340100007446 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 340100007447 TRAM domain; Region: TRAM; cl01282 340100007448 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; cl15754 340100007449 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 340100007450 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 340100007451 active site 340100007452 catalytic site [active] 340100007453 substrate binding site [chemical binding]; other site 340100007454 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 340100007455 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340100007456 putative peptidoglycan binding site; other site 340100007457 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 340100007458 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007459 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 340100007460 Survival protein SurE; Region: SurE; cl00448 340100007461 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 340100007462 UGMP family protein; Validated; Region: PRK09604 340100007463 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 340100007464 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 340100007465 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 340100007466 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100007467 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 340100007468 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 340100007469 catalytic residues [active] 340100007470 Uncharacterized conserved protein [Function unknown]; Region: COG1739 340100007471 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 340100007472 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 340100007473 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 340100007474 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 340100007475 substrate binding pocket [chemical binding]; other site 340100007476 membrane-bound complex binding site; other site 340100007477 hinge residues; other site 340100007478 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 340100007479 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100007480 NMT1-like family; Region: NMT1_2; cl15260 340100007481 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100007482 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 340100007483 Walker A/P-loop; other site 340100007484 ATP binding site [chemical binding]; other site 340100007485 Q-loop/lid; other site 340100007486 ABC transporter signature motif; other site 340100007487 Walker B; other site 340100007488 D-loop; other site 340100007489 H-loop/switch region; other site 340100007490 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 340100007491 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100007492 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100007493 ABC transporter; Region: ABC_tran_2; pfam12848 340100007494 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100007495 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100007496 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100007497 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100007498 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100007499 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100007500 enoyl-CoA hydratase; Provisional; Region: PRK05995 340100007501 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 340100007502 substrate binding site [chemical binding]; other site 340100007503 oxyanion hole (OAH) forming residues; other site 340100007504 trimer interface [polypeptide binding]; other site 340100007505 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 340100007506 dimer interface [polypeptide binding]; other site 340100007507 catalytic triad [active] 340100007508 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 340100007509 nucleoside/Zn binding site; other site 340100007510 dimer interface [polypeptide binding]; other site 340100007511 catalytic motif [active] 340100007512 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 340100007513 motif II; other site 340100007514 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 340100007515 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 340100007516 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 340100007517 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 340100007518 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340100007519 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 340100007520 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 340100007521 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340100007522 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 340100007523 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 340100007524 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100007525 NMT1-like family; Region: NMT1_2; cl15260 340100007526 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100007527 Walker A/P-loop; other site 340100007528 ATP binding site [chemical binding]; other site 340100007529 Q-loop/lid; other site 340100007530 AAA domain; Region: AAA_27; pfam13514 340100007531 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 340100007532 active site 340100007533 metal binding site [ion binding]; metal-binding site 340100007534 DNA binding site [nucleotide binding] 340100007535 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100007536 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100007537 Helix-turn-helix domains; Region: HTH; cl00088 340100007538 Protein of unknown function (DUF502); Region: DUF502; cl01107 340100007539 transglutaminase; Provisional; Region: tgl; PRK03187 340100007540 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100007541 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100007542 Predicted small integral membrane protein (DUF2160); Region: DUF2160; cl02294 340100007543 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 340100007544 dimer interface [polypeptide binding]; other site 340100007545 conserved gate region; other site 340100007546 putative PBP binding loops; other site 340100007547 ABC-ATPase subunit interface; other site 340100007548 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 340100007549 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 340100007550 dimer interface [polypeptide binding]; other site 340100007551 putative PBP binding loops; other site 340100007552 ABC-ATPase subunit interface; other site 340100007553 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 340100007554 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 340100007555 Walker A/P-loop; other site 340100007556 ATP binding site [chemical binding]; other site 340100007557 Q-loop/lid; other site 340100007558 ABC transporter signature motif; other site 340100007559 Walker B; other site 340100007560 D-loop; other site 340100007561 H-loop/switch region; other site 340100007562 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 340100007563 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100007564 Walker A/P-loop; other site 340100007565 ATP binding site [chemical binding]; other site 340100007566 Q-loop/lid; other site 340100007567 ABC transporter signature motif; other site 340100007568 Walker B; other site 340100007569 D-loop; other site 340100007570 H-loop/switch region; other site 340100007571 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 340100007572 Helix-turn-helix domains; Region: HTH; cl00088 340100007573 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100007574 glycerol-3-phosphate dehydrogenase; Region: PLN02464 340100007575 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007576 Helix-turn-helix domains; Region: HTH; cl00088 340100007577 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 340100007578 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 340100007579 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 340100007580 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340100007581 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 340100007582 Walker A/P-loop; other site 340100007583 ATP binding site [chemical binding]; other site 340100007584 Q-loop/lid; other site 340100007585 ABC transporter signature motif; other site 340100007586 Walker B; other site 340100007587 D-loop; other site 340100007588 H-loop/switch region; other site 340100007589 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 340100007590 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100007591 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100007592 YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting...; Region: YeaK; cd04336 340100007593 putative deacylase active site [active] 340100007594 NRDE protein; Region: NRDE; cl01315 340100007595 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 340100007596 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 340100007597 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 340100007598 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340100007599 active site 340100007600 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100007601 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100007602 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 340100007603 intersubunit interface [polypeptide binding]; other site 340100007604 active site 340100007605 Zn2+ binding site [ion binding]; other site 340100007606 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100007607 sequence-specific DNA binding site [nucleotide binding]; other site 340100007608 salt bridge; other site 340100007609 Cupin domain; Region: Cupin_2; cl09118 340100007610 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100007611 Helix-turn-helix domains; Region: HTH; cl00088 340100007612 Fusaric acid resistance protein family; Region: FUSC; pfam04632 340100007613 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 340100007614 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 340100007615 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 340100007616 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 340100007617 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 340100007618 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100007619 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100007620 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 340100007621 Cell division inhibitor SulA; Region: SulA; cl01880 340100007622 DNA Polymerase Y-family; Region: PolY_like; cd03468 340100007623 active site 340100007624 DNA binding site [nucleotide binding] 340100007625 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 340100007626 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 340100007627 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 340100007628 generic binding surface II; other site 340100007629 generic binding surface I; other site 340100007630 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100007631 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007632 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 340100007633 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100007634 Helix-turn-helix domains; Region: HTH; cl00088 340100007635 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 340100007636 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 340100007637 heme-binding site [chemical binding]; other site 340100007638 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 340100007639 FAD binding pocket [chemical binding]; other site 340100007640 FAD binding motif [chemical binding]; other site 340100007641 phosphate binding motif [ion binding]; other site 340100007642 beta-alpha-beta structure motif; other site 340100007643 NAD binding pocket [chemical binding]; other site 340100007644 Heme binding pocket [chemical binding]; other site 340100007645 GatB domain; Region: GatB_Yqey; cl11497 340100007646 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 340100007647 active site 340100007648 DNA polymerase IV; Validated; Region: PRK02406 340100007649 DNA binding site [nucleotide binding] 340100007650 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 340100007651 CoenzymeA binding site [chemical binding]; other site 340100007652 subunit interaction site [polypeptide binding]; other site 340100007653 PHB binding site; other site 340100007654 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 340100007655 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100007656 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 340100007657 Transglycosylase; Region: Transgly; cl07896 340100007658 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100007659 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 340100007660 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 340100007661 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 340100007662 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 340100007663 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100007664 active site 340100007665 catalytic tetrad [active] 340100007666 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100007667 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 340100007668 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 340100007669 Walker A/P-loop; other site 340100007670 ATP binding site [chemical binding]; other site 340100007671 Q-loop/lid; other site 340100007672 ABC transporter signature motif; other site 340100007673 Walker B; other site 340100007674 D-loop; other site 340100007675 H-loop/switch region; other site 340100007676 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 340100007677 iron-sulfur cluster [ion binding]; other site 340100007678 [2Fe-2S] cluster binding site [ion binding]; other site 340100007679 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 340100007680 N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism]; Region: COG2942 340100007681 dimerization interface [polypeptide binding]; other site 340100007682 putative active cleft [active] 340100007683 coproporphyrinogen III oxidase; Validated; Region: PRK05628 340100007684 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100007685 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 340100007686 dimer interface [polypeptide binding]; other site 340100007687 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100007688 metal binding site [ion binding]; metal-binding site 340100007689 Helix-turn-helix domains; Region: HTH; cl00088 340100007690 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100007691 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 340100007692 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; cl09155 340100007693 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 340100007694 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 340100007695 tetramer interface [polypeptide binding]; other site 340100007696 catalytic Zn binding site [ion binding]; other site 340100007697 NADP binding site [chemical binding]; other site 340100007698 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 340100007699 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 340100007700 DNA binding residues [nucleotide binding] 340100007701 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 340100007702 IHF - DNA interface [nucleotide binding]; other site 340100007703 IHF dimer interface [polypeptide binding]; other site 340100007704 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 340100007705 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 340100007706 putative tRNA-binding site [nucleotide binding]; other site 340100007707 B3/4 domain; Region: B3_4; cl11458 340100007708 tRNA synthetase B5 domain; Region: B5; cl08394 340100007709 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 340100007710 dimer interface [polypeptide binding]; other site 340100007711 motif 1; other site 340100007712 motif 3; other site 340100007713 motif 2; other site 340100007714 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 340100007715 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 340100007716 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 340100007717 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 340100007718 dimer interface [polypeptide binding]; other site 340100007719 motif 1; other site 340100007720 active site 340100007721 motif 2; other site 340100007722 motif 3; other site 340100007723 ribosomal protein L20; Region: rpl20; CHL00068 340100007724 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 340100007725 23S rRNA binding site [nucleotide binding]; other site 340100007726 L21 binding site [polypeptide binding]; other site 340100007727 L13 binding site [polypeptide binding]; other site 340100007728 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 340100007729 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 340100007730 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340100007731 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100007732 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 340100007733 Membrane fusogenic activity; Region: BMFP; cl01115 340100007734 Nitrogen regulatory protein P-II; Region: P-II; cl00412 340100007735 Nitrogen regulatory protein P-II; Region: P-II; smart00938 340100007736 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 340100007737 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100007738 Helix-turn-helix domains; Region: HTH; cl00088 340100007739 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 340100007740 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100007741 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 340100007742 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100007743 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100007744 Walker A/P-loop; other site 340100007745 ATP binding site [chemical binding]; other site 340100007746 Q-loop/lid; other site 340100007747 ABC transporter signature motif; other site 340100007748 Walker B; other site 340100007749 D-loop; other site 340100007750 H-loop/switch region; other site 340100007751 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100007752 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100007753 Walker A/P-loop; other site 340100007754 ATP binding site [chemical binding]; other site 340100007755 Q-loop/lid; other site 340100007756 ABC transporter signature motif; other site 340100007757 Walker B; other site 340100007758 D-loop; other site 340100007759 H-loop/switch region; other site 340100007760 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 340100007761 TM-ABC transporter signature motif; other site 340100007762 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 340100007763 TM-ABC transporter signature motif; other site 340100007764 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100007765 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 340100007766 dimerization interface [polypeptide binding]; other site 340100007767 ligand binding site [chemical binding]; other site 340100007768 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 340100007769 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 340100007770 Proline dehydrogenase; Region: Pro_dh; cl03282 340100007771 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 340100007772 Glutamate binding site [chemical binding]; other site 340100007773 NAD binding site [chemical binding]; other site 340100007774 catalytic residues [active] 340100007775 Protein of unknown function (DUF330); Region: DUF330; cl01135 340100007776 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 340100007777 mce related protein; Region: MCE; pfam02470 340100007778 mce related protein; Region: MCE; pfam02470 340100007779 mce related protein; Region: MCE; pfam02470 340100007780 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 340100007781 Paraquat-inducible protein A; Region: PqiA; pfam04403 340100007782 Paraquat-inducible protein A; Region: PqiA; pfam04403 340100007783 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 340100007784 Clp amino terminal domain; Region: Clp_N; pfam02861 340100007785 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 340100007786 Walker A motif; other site 340100007787 ATP binding site [chemical binding]; other site 340100007788 Walker B motif; other site 340100007789 arginine finger; other site 340100007790 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 340100007791 Walker A motif; other site 340100007792 ATP binding site [chemical binding]; other site 340100007793 Walker B motif; other site 340100007794 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340100007795 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 340100007796 Transglycosylase; Region: Transgly; cl07896 340100007797 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100007798 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 340100007799 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 340100007800 MG2 domain; Region: A2M_N; pfam01835 340100007801 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 340100007802 Alpha-2-macroglobulin family; Region: A2M; pfam00207 340100007803 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 340100007804 surface patch; other site 340100007805 thioester region; other site 340100007806 specificity defining residues; other site 340100007807 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 340100007808 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 340100007809 DNA-binding site [nucleotide binding]; DNA binding site 340100007810 RNA-binding motif; other site 340100007811 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 340100007812 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 340100007813 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 340100007814 dimer interface [polypeptide binding]; other site 340100007815 active site 340100007816 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 340100007817 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 340100007818 putative ion selectivity filter; other site 340100007819 putative pore gating glutamate residue; other site 340100007820 putative H+/Cl- coupling transport residue; other site 340100007821 superoxide dismutase; Provisional; Region: PRK10543 340100007822 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 340100007823 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 340100007824 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 340100007825 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 340100007826 generic binding surface II; other site 340100007827 generic binding surface I; other site 340100007828 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340100007829 tetraacyldisaccharide 4'-kinase; Provisional; Region: PRK01906 340100007830 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 340100007831 Trm112p-like protein; Region: Trm112p; cl01066 340100007832 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 340100007833 Ligand binding site; other site 340100007834 oligomer interface; other site 340100007835 adenylate kinase; Reviewed; Region: adk; PRK00279 340100007836 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 340100007837 AMP-binding site [chemical binding]; other site 340100007838 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 340100007839 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100007840 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 340100007841 NAD binding site [chemical binding]; other site 340100007842 homotetramer interface [polypeptide binding]; other site 340100007843 homodimer interface [polypeptide binding]; other site 340100007844 active site 340100007845 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 340100007846 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 340100007847 FecR protein; Region: FecR; pfam04773 340100007848 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 340100007849 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; cl09155 340100007850 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 340100007851 Dehydratase family; Region: ILVD_EDD; cl00340 340100007852 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100007853 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100007854 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100007855 DNA-binding site [nucleotide binding]; DNA binding site 340100007856 FCD domain; Region: FCD; cl11656 340100007857 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 340100007858 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 340100007859 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100007860 inhibitor site; inhibition site 340100007861 active site 340100007862 dimer interface [polypeptide binding]; other site 340100007863 catalytic residue [active] 340100007864 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100007865 NMT1-like family; Region: NMT1_2; cl15260 340100007866 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100007867 NMT1-like family; Region: NMT1_2; cl15260 340100007868 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 340100007869 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007870 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 340100007871 ornithine carbamoyltransferase; Provisional; Region: PRK00779 340100007872 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 340100007873 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007874 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 340100007875 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 340100007876 Ligand Binding Site [chemical binding]; other site 340100007877 K+ potassium transporter; Region: K_trans; cl15781 340100007878 potassium uptake protein; Region: kup; TIGR00794 340100007879 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100007880 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 340100007881 dimer interface [polypeptide binding]; other site 340100007882 phosphorylation site [posttranslational modification] 340100007883 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 340100007884 ATP binding site [chemical binding]; other site 340100007885 G-X-G motif; other site 340100007886 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100007887 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100007888 active site 340100007889 phosphorylation site [posttranslational modification] 340100007890 intermolecular recognition site; other site 340100007891 dimerization interface [polypeptide binding]; other site 340100007892 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 340100007893 DNA binding site [nucleotide binding] 340100007894 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 340100007895 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340100007896 Gram-negative bacterial tonB protein; Region: TonB; cl10048 340100007897 Rdx family; Region: Rdx; cl01407 340100007898 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100007899 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 340100007900 ATP binding site [chemical binding]; other site 340100007901 G-X-G motif; other site 340100007902 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 340100007903 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100007904 active site 340100007905 phosphorylation site [posttranslational modification] 340100007906 intermolecular recognition site; other site 340100007907 dimerization interface [polypeptide binding]; other site 340100007908 Helix-turn-helix domains; Region: HTH; cl00088 340100007909 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 340100007910 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100007911 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 340100007912 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100007913 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 340100007914 D-pathway; other site 340100007915 Putative ubiquinol binding site [chemical binding]; other site 340100007916 Low-spin heme (heme b) binding site [chemical binding]; other site 340100007917 Putative water exit pathway; other site 340100007918 Binuclear center (heme o3/CuB) [ion binding]; other site 340100007919 K-pathway; other site 340100007920 Putative proton exit pathway; other site 340100007921 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 340100007922 Subunit I/III interface [polypeptide binding]; other site 340100007923 Subunit III/IV interface [polypeptide binding]; other site 340100007924 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 340100007925 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 340100007926 IHF dimer interface [polypeptide binding]; other site 340100007927 IHF - DNA interface [nucleotide binding]; other site 340100007928 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100007929 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 340100007930 hypothetical protein; Provisional; Region: PRK05939 340100007931 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 340100007932 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100007933 catalytic residue [active] 340100007934 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 340100007935 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 340100007936 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340100007937 ribonuclease R; Region: RNase_R; TIGR02063 340100007938 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 340100007939 RNB domain; Region: RNB; pfam00773 340100007940 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 340100007941 RNA binding site [nucleotide binding]; other site 340100007942 DTW domain; Region: DTW; cl01221 340100007943 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100007944 Membrane transport protein; Region: Mem_trans; cl09117 340100007945 arsenical pump membrane protein; Provisional; Region: PRK15445 340100007946 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 340100007947 transmembrane helices; other site 340100007948 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 340100007949 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 340100007950 active site 340100007951 FMN binding site [chemical binding]; other site 340100007952 substrate binding site [chemical binding]; other site 340100007953 3Fe-4S cluster binding site [ion binding]; other site 340100007954 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 340100007955 putative active site [active] 340100007956 catalytic site [active] 340100007957 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 340100007958 PLD-like domain; Region: PLDc_2; pfam13091 340100007959 putative active site [active] 340100007960 catalytic site [active] 340100007961 probable methyltransferase; Region: TIGR03438 340100007962 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 340100007963 TIGR03440 family protein; Region: unchr_TIGR03440 340100007964 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 340100007965 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 340100007966 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 340100007967 Protein of unknown function (DUF3053); Region: DUF3053; pfam11254 340100007968 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 340100007969 Cytochrome C'; Region: Cytochrom_C_2; cl01610 340100007970 adenylosuccinate lyase; Provisional; Region: PRK09285 340100007971 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 340100007972 tetramer interface [polypeptide binding]; other site 340100007973 active site 340100007974 putative glutathione S-transferase; Provisional; Region: PRK10357 340100007975 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 340100007976 putative C-terminal domain interface [polypeptide binding]; other site 340100007977 putative GSH binding site (G-site) [chemical binding]; other site 340100007978 putative dimer interface [polypeptide binding]; other site 340100007979 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 340100007980 dimer interface [polypeptide binding]; other site 340100007981 N-terminal domain interface [polypeptide binding]; other site 340100007982 putative substrate binding pocket (H-site) [chemical binding]; other site 340100007983 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 340100007984 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 340100007985 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 340100007986 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100007987 Helix-turn-helix domains; Region: HTH; cl00088 340100007988 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 340100007989 dimerization interface [polypeptide binding]; other site 340100007990 substrate binding pocket [chemical binding]; other site 340100007991 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100007992 NMT1-like family; Region: NMT1_2; cl15260 340100007993 N-formylglutamate amidohydrolase; Region: FGase; cl01522 340100007994 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 340100007995 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 340100007996 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007997 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 340100007998 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 340100007999 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 340100008000 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 340100008001 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 340100008002 Cysteine-rich domain; Region: CCG; pfam02754 340100008003 Cysteine-rich domain; Region: CCG; pfam02754 340100008004 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 340100008005 FAD binding domain; Region: FAD_binding_4; pfam01565 340100008006 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 340100008007 FAD binding domain; Region: FAD_binding_4; pfam01565 340100008008 D-lactate dehydrogenase [cytochrome]; Region: PLN02805 340100008009 FAD binding domain; Region: FAD_binding_4; pfam01565 340100008010 NeuB family; Region: NeuB; cl00496 340100008011 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340100008012 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 340100008013 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 340100008014 Predicted amidohydrolase [General function prediction only]; Region: COG0388 340100008015 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 340100008016 putative active site [active] 340100008017 catalytic triad [active] 340100008018 dimer interface [polypeptide binding]; other site 340100008019 H-NS histone family; Region: Histone_HNS; pfam00816 340100008020 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 340100008021 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 340100008022 aminopeptidase N; Provisional; Region: pepN; PRK14015 340100008023 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 340100008024 active site 340100008025 Zn binding site [ion binding]; other site 340100008026 fructose-1,6-bisphosphatase family protein; Region: PLN02628 340100008027 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 340100008028 AMP binding site [chemical binding]; other site 340100008029 metal binding site [ion binding]; metal-binding site 340100008030 active site 340100008031 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 340100008032 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 340100008033 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 340100008034 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008035 catalytic residue [active] 340100008036 homoserine dehydrogenase; Provisional; Region: PRK06349 340100008037 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008038 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 340100008039 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 340100008040 aminotransferase; Validated; Region: PRK08175 340100008041 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 340100008042 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008043 homodimer interface [polypeptide binding]; other site 340100008044 catalytic residue [active] 340100008045 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 340100008046 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 340100008047 catalytic triad [active] 340100008048 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 340100008049 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 340100008050 putative active site [active] 340100008051 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100008052 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 340100008053 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 340100008054 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 340100008055 Membrane transport protein; Region: Mem_trans; cl09117 340100008056 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 340100008057 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 340100008058 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 340100008059 metal binding site [ion binding]; metal-binding site 340100008060 putative dimer interface [polypeptide binding]; other site 340100008061 NMT1-like family; Region: NMT1_2; cl15260 340100008062 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 340100008063 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 340100008064 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 340100008065 dimerization interface [polypeptide binding]; other site 340100008066 ATP binding site [chemical binding]; other site 340100008067 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 340100008068 dimerization interface [polypeptide binding]; other site 340100008069 ATP binding site [chemical binding]; other site 340100008070 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 340100008071 putative active site [active] 340100008072 catalytic triad [active] 340100008073 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 340100008074 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 340100008075 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 340100008076 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 340100008077 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100008078 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100008079 ComEC family competence protein; Provisional; Region: PRK11539 340100008080 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 340100008081 Competence protein; Region: Competence; cl00471 340100008082 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100008083 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 340100008084 active site 340100008085 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 340100008086 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 340100008087 Walker A/P-loop; other site 340100008088 ATP binding site [chemical binding]; other site 340100008089 Q-loop/lid; other site 340100008090 ABC transporter signature motif; other site 340100008091 Walker B; other site 340100008092 D-loop; other site 340100008093 H-loop/switch region; other site 340100008094 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 340100008095 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 340100008096 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 340100008097 DHH family; Region: DHH; pfam01368 340100008098 DHHA1 domain; Region: DHHA1; pfam02272 340100008099 peptide chain release factor 2; Validated; Region: prfB; PRK00578 340100008100 RF-1 domain; Region: RF-1; cl02875 340100008101 RF-1 domain; Region: RF-1; cl02875 340100008102 short chain dehydrogenase; Provisional; Region: PRK07023 340100008103 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008104 NAD(P) binding site [chemical binding]; other site 340100008105 active site 340100008106 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 340100008107 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 340100008108 dimer interface [polypeptide binding]; other site 340100008109 putative anticodon binding site; other site 340100008110 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 340100008111 motif 1; other site 340100008112 active site 340100008113 motif 2; other site 340100008114 motif 3; other site 340100008115 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 340100008116 substrate binding site [chemical binding]; other site 340100008117 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 340100008118 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100008119 chaperone protein HscA; Provisional; Region: hscA; PRK05183 340100008120 co-chaperone HscB; Provisional; Region: hscB; PRK03578 340100008121 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; cl02542 340100008122 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 340100008123 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 340100008124 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 340100008125 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 340100008126 trimerization site [polypeptide binding]; other site 340100008127 active site 340100008128 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 340100008129 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 340100008130 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100008131 catalytic residue [active] 340100008132 Helix-turn-helix domains; Region: HTH; cl00088 340100008133 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100008134 Low molecular weight phosphatase family; Region: LMWPc; cd00115 340100008135 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 340100008136 active site 340100008137 excinuclease ABC subunit B; Provisional; Region: PRK05298 340100008138 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 340100008139 ATP binding site [chemical binding]; other site 340100008140 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 340100008141 nucleotide binding region [chemical binding]; other site 340100008142 ATP-binding site [chemical binding]; other site 340100008143 Ultra-violet resistance protein B; Region: UvrB; pfam12344 340100008144 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 340100008145 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 340100008146 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008147 homodimer interface [polypeptide binding]; other site 340100008148 catalytic residue [active] 340100008149 LexA repressor; Validated; Region: PRK00215 340100008150 Helix-turn-helix domains; Region: HTH; cl00088 340100008151 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 340100008152 Catalytic site [active] 340100008153 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100008154 active site 340100008155 catalytic residues [active] 340100008156 metal binding site [ion binding]; metal-binding site 340100008157 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100008158 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008159 DNA-binding site [nucleotide binding]; DNA binding site 340100008160 FCD domain; Region: FCD; cl11656 340100008161 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100008162 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100008163 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100008164 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100008165 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100008166 DctM-like transporters; Region: DctM; pfam06808 340100008167 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100008168 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 340100008169 Found in ATP-dependent protease La (LON); Region: LON; smart00464 340100008170 Found in ATP-dependent protease La (LON); Region: LON; smart00464 340100008171 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 340100008172 Walker A motif; other site 340100008173 ATP binding site [chemical binding]; other site 340100008174 Walker B motif; other site 340100008175 arginine finger; other site 340100008176 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340100008177 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 340100008178 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 340100008179 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100008180 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 340100008181 Walker A motif; other site 340100008182 ATP binding site [chemical binding]; other site 340100008183 Walker B motif; other site 340100008184 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340100008185 Clp protease; Region: CLP_protease; pfam00574 340100008186 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 340100008187 oligomer interface [polypeptide binding]; other site 340100008188 active site residues [active] 340100008189 trigger factor; Provisional; Region: tig; PRK01490 340100008190 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 340100008191 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 340100008192 Peptidase family M48; Region: Peptidase_M48; cl12018 340100008193 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 340100008194 DNA-binding site [nucleotide binding]; DNA binding site 340100008195 RNA-binding motif; other site 340100008196 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 340100008197 DNA-binding site [nucleotide binding]; DNA binding site 340100008198 RNA-binding motif; other site 340100008199 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 340100008200 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 340100008201 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008202 homodimer interface [polypeptide binding]; other site 340100008203 catalytic residue [active] 340100008204 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 340100008205 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 340100008206 trimer interface [polypeptide binding]; other site 340100008207 active site 340100008208 substrate binding site [chemical binding]; other site 340100008209 CoA binding site [chemical binding]; other site 340100008210 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 340100008211 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 340100008212 metal binding site [ion binding]; metal-binding site 340100008213 dimer interface [polypeptide binding]; other site 340100008214 HemK family putative methylases; Region: hemK_fam; TIGR00536 340100008215 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 340100008216 S-adenosylmethionine binding site [chemical binding]; other site 340100008217 nodulation factor exporter subunit NodI; Provisional; Region: PRK13536 340100008218 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100008219 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 340100008220 Walker A/P-loop; other site 340100008221 ATP binding site [chemical binding]; other site 340100008222 Q-loop/lid; other site 340100008223 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100008224 ABC transporter; Region: ABC_tran_2; pfam12848 340100008225 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340100008226 Helix-turn-helix domains; Region: HTH; cl00088 340100008227 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 340100008228 substrate binding pocket [chemical binding]; other site 340100008229 dimerization interface [polypeptide binding]; other site 340100008230 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100008231 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 340100008232 iron-sulfur cluster [ion binding]; other site 340100008233 [2Fe-2S] cluster binding site [ion binding]; other site 340100008234 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 340100008235 putative alpha subunit interface [polypeptide binding]; other site 340100008236 putative active site [active] 340100008237 putative substrate binding site [chemical binding]; other site 340100008238 Fe binding site [ion binding]; other site 340100008239 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 340100008240 inter-subunit interface; other site 340100008241 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 340100008242 [2Fe-2S] cluster binding site [ion binding]; other site 340100008243 Chorismate mutase type II; Region: CM_2; cl00693 340100008244 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 340100008245 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100008246 Family description; Region: UvrD_C_2; cl15862 340100008247 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 340100008248 Di-iron ligands [ion binding]; other site 340100008249 Transposase; Region: DDE_Tnp_ISL3; pfam01610 340100008250 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 340100008251 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; cl15754 340100008252 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 340100008253 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 340100008254 active site 340100008255 substrate binding site [chemical binding]; other site 340100008256 cosubstrate binding site; other site 340100008257 catalytic site [active] 340100008258 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 340100008259 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 340100008260 active site 340100008261 Riboflavin kinase; Region: Flavokinase; cl03312 340100008262 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 340100008263 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100008264 active site 340100008265 HIGH motif; other site 340100008266 nucleotide binding site [chemical binding]; other site 340100008267 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340100008268 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 340100008269 active site 340100008270 KMSKS motif; other site 340100008271 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 340100008272 tRNA binding surface [nucleotide binding]; other site 340100008273 anticodon binding site; other site 340100008274 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 340100008275 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 340100008276 lipoprotein signal peptidase; Provisional; Region: PRK14787 340100008277 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 340100008278 Flavoprotein; Region: Flavoprotein; cl08021 340100008279 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 340100008280 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100008281 Helix-turn-helix domains; Region: HTH; cl00088 340100008282 Helix-turn-helix domains; Region: HTH; cl00088 340100008283 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 340100008284 dUTPase; Region: dUTPase_2; pfam08761 340100008285 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100008286 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100008287 Walker A/P-loop; other site 340100008288 ATP binding site [chemical binding]; other site 340100008289 Q-loop/lid; other site 340100008290 ABC transporter signature motif; other site 340100008291 Walker B; other site 340100008292 D-loop; other site 340100008293 H-loop/switch region; other site 340100008294 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 340100008295 dimer interface [polypeptide binding]; other site 340100008296 conserved gate region; other site 340100008297 putative PBP binding loops; other site 340100008298 ABC-ATPase subunit interface; other site 340100008299 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 340100008300 dimer interface [polypeptide binding]; other site 340100008301 conserved gate region; other site 340100008302 putative PBP binding loops; other site 340100008303 ABC-ATPase subunit interface; other site 340100008304 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100008305 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 340100008306 substrate binding pocket [chemical binding]; other site 340100008307 membrane-bound complex binding site; other site 340100008308 hinge residues; other site 340100008309 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100008310 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 340100008311 putative ligand binding site [chemical binding]; other site 340100008312 ornithine cyclodeaminase; Validated; Region: PRK06141 340100008313 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008314 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 340100008315 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 340100008316 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 340100008317 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; cl09155 340100008318 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 340100008319 dimerization domain swap beta strand [polypeptide binding]; other site 340100008320 regulatory protein interface [polypeptide binding]; other site 340100008321 active site 340100008322 regulatory phosphorylation site [posttranslational modification]; other site 340100008323 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 340100008324 active pocket/dimerization site; other site 340100008325 active site 340100008326 phosphorylation site [posttranslational modification] 340100008327 glutathione synthetase; Provisional; Region: PRK05246 340100008328 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 340100008329 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100008330 translation initiation factor IF-3; Region: infC; TIGR00168 340100008331 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 340100008332 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 340100008333 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 340100008334 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 340100008335 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 340100008336 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 340100008337 active site 340100008338 dimer interface [polypeptide binding]; other site 340100008339 motif 1; other site 340100008340 motif 2; other site 340100008341 motif 3; other site 340100008342 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 340100008343 anticodon binding site; other site 340100008344 Response regulator receiver domain; Region: Response_reg; pfam00072 340100008345 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100008346 active site 340100008347 phosphorylation site [posttranslational modification] 340100008348 intermolecular recognition site; other site 340100008349 dimerization interface [polypeptide binding]; other site 340100008350 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 340100008351 DNA binding residues [nucleotide binding] 340100008352 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008353 Helix-turn-helix domains; Region: HTH; cl00088 340100008354 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 340100008355 putative effector binding pocket; other site 340100008356 putative dimerization interface [polypeptide binding]; other site 340100008357 short chain dehydrogenase; Provisional; Region: PRK12744 340100008358 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008359 NAD(P) binding site [chemical binding]; other site 340100008360 active site 340100008361 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 340100008362 O-Antigen ligase; Region: Wzy_C; cl04850 340100008363 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 340100008364 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 340100008365 DNA-binding site [nucleotide binding]; DNA binding site 340100008366 RNA-binding motif; other site 340100008367 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 340100008368 active site 340100008369 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100008370 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100008371 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100008372 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100008373 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 340100008374 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 340100008375 dimerization interface 3.5A [polypeptide binding]; other site 340100008376 active site 340100008377 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 340100008378 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 340100008379 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 340100008380 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008381 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 340100008382 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 340100008383 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100008384 Walker A/P-loop; other site 340100008385 ATP binding site [chemical binding]; other site 340100008386 Q-loop/lid; other site 340100008387 ABC transporter signature motif; other site 340100008388 Walker B; other site 340100008389 D-loop; other site 340100008390 H-loop/switch region; other site 340100008391 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100008392 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100008393 Walker A/P-loop; other site 340100008394 ATP binding site [chemical binding]; other site 340100008395 Q-loop/lid; other site 340100008396 ABC transporter signature motif; other site 340100008397 Walker B; other site 340100008398 D-loop; other site 340100008399 H-loop/switch region; other site 340100008400 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100008401 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100008402 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 340100008403 dimer interface [polypeptide binding]; other site 340100008404 conserved gate region; other site 340100008405 putative PBP binding loops; other site 340100008406 ABC-ATPase subunit interface; other site 340100008407 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100008408 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 340100008409 dimer interface [polypeptide binding]; other site 340100008410 conserved gate region; other site 340100008411 putative PBP binding loops; other site 340100008412 ABC-ATPase subunit interface; other site 340100008413 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100008414 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_5; cd08511 340100008415 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100008416 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100008417 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008418 Helix-turn-helix domains; Region: HTH; cl00088 340100008419 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100008420 dimerization interface [polypeptide binding]; other site 340100008421 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 340100008422 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 340100008423 general secretion pathway protein H; Region: typeII_sec_gspH; TIGR01708 340100008424 Type II transport protein GspH; Region: GspH; pfam12019 340100008425 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 340100008426 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 340100008427 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 340100008428 general secretion pathway protein J; Region: gspJ; TIGR01711 340100008429 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 340100008430 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 340100008431 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 340100008432 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 340100008433 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 340100008434 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 340100008435 Walker A motif; other site 340100008436 ATP binding site [chemical binding]; other site 340100008437 Walker B motif; other site 340100008438 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 340100008439 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340100008440 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340100008441 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340100008442 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100008443 general secretion pathway protein F; Region: GspF; TIGR02120 340100008444 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340100008445 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340100008446 Nitrogen regulatory protein P-II; Region: P-II; cl00412 340100008447 Nitrogen regulatory protein P-II; Region: P-II; smart00938 340100008448 NAD synthetase; Provisional; Region: PRK13981 340100008449 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 340100008450 multimer interface [polypeptide binding]; other site 340100008451 active site 340100008452 catalytic triad [active] 340100008453 protein interface 1 [polypeptide binding]; other site 340100008454 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 340100008455 homodimer interface [polypeptide binding]; other site 340100008456 NAD binding pocket [chemical binding]; other site 340100008457 ATP binding pocket [chemical binding]; other site 340100008458 Mg binding site [ion binding]; other site 340100008459 active-site loop [active] 340100008460 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 340100008461 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100008462 argininosuccinate lyase; Provisional; Region: PRK00855 340100008463 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 340100008464 active sites [active] 340100008465 tetramer interface [polypeptide binding]; other site 340100008466 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 340100008467 putative FMN binding site [chemical binding]; other site 340100008468 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 340100008469 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 340100008470 DNA binding residues [nucleotide binding] 340100008471 dimer interface [polypeptide binding]; other site 340100008472 putative metal binding site [ion binding]; other site 340100008473 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 340100008474 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 340100008475 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340100008476 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100008477 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100008478 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 340100008479 substrate binding pocket [chemical binding]; other site 340100008480 membrane-bound complex binding site; other site 340100008481 hinge residues; other site 340100008482 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100008483 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 340100008484 dimer interface [polypeptide binding]; other site 340100008485 conserved gate region; other site 340100008486 putative PBP binding loops; other site 340100008487 ABC-ATPase subunit interface; other site 340100008488 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100008489 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100008490 Walker A/P-loop; other site 340100008491 ATP binding site [chemical binding]; other site 340100008492 Q-loop/lid; other site 340100008493 ABC transporter signature motif; other site 340100008494 Walker B; other site 340100008495 D-loop; other site 340100008496 H-loop/switch region; other site 340100008497 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100008498 NMT1-like family; Region: NMT1_2; cl15260 340100008499 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 340100008500 active site 340100008501 citrylCoA binding site [chemical binding]; other site 340100008502 oxalacetate binding site [chemical binding]; other site 340100008503 coenzyme A binding site [chemical binding]; other site 340100008504 catalytic triad [active] 340100008505 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100008506 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100008507 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 340100008508 Helix-turn-helix domains; Region: HTH; cl00088 340100008509 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 340100008510 dimerization interface [polypeptide binding]; other site 340100008511 integrase; Provisional; Region: PRK09692 340100008512 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 340100008513 active site 340100008514 Int/Topo IB signature motif; other site 340100008515 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100008516 Uncharacterized conserved protein [Function unknown]; Region: COG4983 340100008517 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 340100008518 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 340100008519 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 340100008520 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 340100008521 putative phosphate binding site [ion binding]; other site 340100008522 putative catalytic site [active] 340100008523 active site 340100008524 metal binding site A [ion binding]; metal-binding site 340100008525 DNA binding site [nucleotide binding] 340100008526 putative AP binding site [nucleotide binding]; other site 340100008527 putative metal binding site B [ion binding]; other site 340100008528 putative inner membrane protein; Provisional; Region: PRK11099 340100008529 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 340100008530 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 340100008531 active site residue [active] 340100008532 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 340100008533 active site residue [active] 340100008534 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100008535 Predicted transcriptional regulator [Transcription]; Region: COG1959 340100008536 Helix-turn-helix domains; Region: HTH; cl00088 340100008537 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100008538 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 340100008539 putative substrate translocation pore; other site 340100008540 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 340100008541 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100008542 catalytic residue [active] 340100008543 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 340100008544 dimer interface [polypeptide binding]; other site 340100008545 pyridoxamine kinase; Validated; Region: PRK05756 340100008546 pyridoxal binding site [chemical binding]; other site 340100008547 ATP binding site [chemical binding]; other site 340100008548 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 340100008549 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 340100008550 Walker A/P-loop; other site 340100008551 ATP binding site [chemical binding]; other site 340100008552 Q-loop/lid; other site 340100008553 ABC transporter signature motif; other site 340100008554 Walker B; other site 340100008555 D-loop; other site 340100008556 H-loop/switch region; other site 340100008557 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_11; cd07261 340100008558 putative dimer interface [polypeptide binding]; other site 340100008559 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100008560 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100008561 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 340100008562 putative substrate translocation pore; other site 340100008563 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 340100008564 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 340100008565 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100008566 Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues; Region: MR_like; cd03316 340100008567 active site pocket [active] 340100008568 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100008569 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008570 DNA-binding site [nucleotide binding]; DNA binding site 340100008571 UTRA domain; Region: UTRA; cl01230 340100008572 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 340100008573 dimer interface [polypeptide binding]; other site 340100008574 conserved gate region; other site 340100008575 putative PBP binding loops; other site 340100008576 ABC-ATPase subunit interface; other site 340100008577 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100008578 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 340100008579 Walker A/P-loop; other site 340100008580 ATP binding site [chemical binding]; other site 340100008581 Q-loop/lid; other site 340100008582 ABC transporter signature motif; other site 340100008583 Walker B; other site 340100008584 D-loop; other site 340100008585 H-loop/switch region; other site 340100008586 NMT1-like family; Region: NMT1_2; cl15260 340100008587 choline dehydrogenase; Validated; Region: PRK02106 340100008588 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 340100008589 NMT1-like family; Region: NMT1_2; cl15260 340100008590 Dehydratase family; Region: ILVD_EDD; cl00340 340100008591 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008592 Helix-turn-helix domains; Region: HTH; cl00088 340100008593 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 340100008594 putative dimerization interface [polypeptide binding]; other site 340100008595 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008596 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 340100008597 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100008598 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 340100008599 putative active site [active] 340100008600 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 340100008601 S-adenosylmethionine binding site [chemical binding]; other site 340100008602 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 340100008603 Phosphoenolpyruvate carboxykinase; Region: PEPCK; pfam00821 340100008604 active site 340100008605 substrate-binding site [chemical binding]; other site 340100008606 metal-binding site [ion binding] 340100008607 GTP binding site [chemical binding]; other site 340100008608 putative efflux protein, MATE family; Region: matE; TIGR00797 340100008609 MatE; Region: MatE; cl10513 340100008610 MatE; Region: MatE; cl10513 340100008611 allantoate amidohydrolase; Reviewed; Region: PRK12890 340100008612 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 340100008613 active site 340100008614 metal binding site [ion binding]; metal-binding site 340100008615 dimer interface [polypeptide binding]; other site 340100008616 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 340100008617 catalytic residues [active] 340100008618 EamA-like transporter family; Region: EamA; cl01037 340100008619 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 340100008620 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100008621 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100008622 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100008623 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008624 DNA-binding site [nucleotide binding]; DNA binding site 340100008625 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 340100008626 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008627 homodimer interface [polypeptide binding]; other site 340100008628 catalytic residue [active] 340100008629 glutathione reductase; Validated; Region: PRK06116 340100008630 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100008631 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100008632 LysE type translocator; Region: LysE; cl00565 340100008633 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100008634 S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic...; Region: S15_NS1_EPRS_RNA-bind; cl00349 340100008635 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100008636 NeuB family; Region: NeuB; cl00496 340100008637 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340100008638 4-hydroxybenzoyl-CoA reductase, gamma subunit; Region: 4hydroxCoAred; TIGR03193 340100008639 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100008640 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100008641 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100008642 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100008643 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 340100008644 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100008645 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100008646 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 340100008647 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100008648 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100008649 Potato inhibitor I family; Region: potato_inhibit; cl15459 340100008650 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100008651 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100008652 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 340100008653 dimer interface [polypeptide binding]; other site 340100008654 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100008655 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 340100008656 putative substrate translocation pore; other site 340100008657 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 340100008658 putative transporter; Provisional; Region: PRK11660 340100008659 Sulfate transporter family; Region: Sulfate_transp; cl15842 340100008660 Sulfate transporter family; Region: Sulfate_transp; cl15842 340100008661 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 340100008662 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 340100008663 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100008664 Uncharacterized conserved protein [Function unknown]; Region: COG1432 340100008665 LabA_like proteins; Region: LabA_like; cd06167 340100008666 putative metal binding site [ion binding]; other site 340100008667 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 340100008668 YCII-related domain; Region: YCII; cl00999 340100008669 YCII-related domain; Region: YCII; cl00999 340100008670 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 340100008671 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100008672 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 340100008673 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100008674 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100008675 Domain of unknown function (DUF4168); Region: DUF4168; pfam13767 340100008676 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 340100008677 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340100008678 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100008679 ligand binding site [chemical binding]; other site 340100008680 Domain of unknown function (DUF4281); Region: DUF4281; pfam14108 340100008681 Helix-turn-helix domains; Region: HTH; cl00088 340100008682 WHG domain; Region: WHG; pfam13305 340100008683 Cupin domain; Region: Cupin_2; cl09118 340100008684 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100008685 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100008686 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 340100008687 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100008688 Walker A/P-loop; other site 340100008689 ATP binding site [chemical binding]; other site 340100008690 Q-loop/lid; other site 340100008691 ABC transporter signature motif; other site 340100008692 Walker B; other site 340100008693 D-loop; other site 340100008694 H-loop/switch region; other site 340100008695 SlyX; Region: SlyX; cl01090 340100008696 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 340100008697 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100008698 galactarate dehydratase; Region: galactar-dH20; TIGR03248 340100008699 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 340100008700 enterobactin exporter EntS; Provisional; Region: PRK10489 340100008701 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 340100008702 allantoate amidohydrolase; Reviewed; Region: PRK09290 340100008703 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 340100008704 active site 340100008705 metal binding site [ion binding]; metal-binding site 340100008706 dimer interface [polypeptide binding]; other site 340100008707 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008708 Helix-turn-helix domains; Region: HTH; cl00088 340100008709 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 340100008710 putative effector binding pocket; other site 340100008711 dimerization interface [polypeptide binding]; other site 340100008712 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 340100008713 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 340100008714 substrate binding site [chemical binding]; other site 340100008715 oxyanion hole (OAH) forming residues; other site 340100008716 trimer interface [polypeptide binding]; other site 340100008717 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008718 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100008719 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100008720 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 340100008721 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 340100008722 dimer interface [polypeptide binding]; other site 340100008723 active site 340100008724 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100008725 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100008726 active site 340100008727 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 340100008728 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 340100008729 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 340100008730 active site 340100008731 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100008732 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100008733 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100008734 NMT1-like family; Region: NMT1_2; cl15260 340100008735 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100008736 NMT1-like family; Region: NMT1_2; cl15260 340100008737 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100008738 NMT1-like family; Region: NMT1_2; cl15260 340100008739 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100008740 EamA-like transporter family; Region: EamA; cl01037 340100008741 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100008742 EamA-like transporter family; Region: EamA; cl01037 340100008743 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 340100008744 putative substrate translocation pore; other site 340100008745 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100008746 Helix-turn-helix domains; Region: HTH; cl00088 340100008747 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 340100008748 Fe-S cluster binding site [ion binding]; other site 340100008749 active site 340100008750 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100008751 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 340100008752 C-terminal domain interface [polypeptide binding]; other site 340100008753 GSH binding site (G-site) [chemical binding]; other site 340100008754 dimer interface [polypeptide binding]; other site 340100008755 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 340100008756 dimer interface [polypeptide binding]; other site 340100008757 N-terminal domain interface [polypeptide binding]; other site 340100008758 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100008759 Helix-turn-helix domains; Region: HTH; cl00088 340100008760 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 340100008761 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100008762 C-terminal domain interface [polypeptide binding]; other site 340100008763 GSH binding site (G-site) [chemical binding]; other site 340100008764 dimer interface [polypeptide binding]; other site 340100008765 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100008766 N-terminal domain interface [polypeptide binding]; other site 340100008767 dimer interface [polypeptide binding]; other site 340100008768 substrate binding pocket (H-site) [chemical binding]; other site 340100008769 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100008770 Protein of unknown function (DUF454); Region: DUF454; cl01063 340100008771 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 340100008772 dimerization interface [polypeptide binding]; other site 340100008773 putative DNA binding site [nucleotide binding]; other site 340100008774 putative Zn2+ binding site [ion binding]; other site 340100008775 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 340100008776 putative hydrophobic ligand binding site [chemical binding]; other site 340100008777 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 340100008778 putative C-terminal domain interface [polypeptide binding]; other site 340100008779 putative GSH binding site (G-site) [chemical binding]; other site 340100008780 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100008781 putative dimer interface [polypeptide binding]; other site 340100008782 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 340100008783 dimer interface [polypeptide binding]; other site 340100008784 N-terminal domain interface [polypeptide binding]; other site 340100008785 putative substrate binding pocket (H-site) [chemical binding]; other site 340100008786 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 340100008787 Helix-turn-helix domains; Region: HTH; cl00088 340100008788 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100008789 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100008790 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008791 CoA-ligase; Region: Ligase_CoA; cl02894 340100008792 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100008793 Uncharacterized conserved protein [Function unknown]; Region: COG5361 340100008794 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 340100008795 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 340100008796 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008797 Helix-turn-helix domains; Region: HTH; cl00088 340100008798 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 340100008799 putative dimerization interface [polypeptide binding]; other site 340100008800 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100008801 NMT1-like family; Region: NMT1_2; cl15260 340100008802 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 340100008803 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100008804 Helix-turn-helix domains; Region: HTH; cl00088 340100008805 Protein of unknown function (DUF1348); Region: DUF1348; pfam07080 340100008806 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 340100008807 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100008808 NMT1-like family; Region: NMT1_2; cl15260 340100008809 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100008810 Helix-turn-helix domains; Region: HTH; cl00088 340100008811 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100008812 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100008813 DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: CbpA; COG2214 340100008814 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 340100008815 HSP70 interaction site [polypeptide binding]; other site 340100008816 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 340100008817 substrate binding site [polypeptide binding]; other site 340100008818 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 340100008819 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100008820 Helix-turn-helix domains; Region: HTH; cl00088 340100008821 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100008822 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008823 DNA-binding site [nucleotide binding]; DNA binding site 340100008824 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 340100008825 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008826 homodimer interface [polypeptide binding]; other site 340100008827 catalytic residue [active] 340100008828 Cupin domain; Region: Cupin_2; cl09118 340100008829 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100008830 Uncharacterized conserved protein [Function unknown]; Region: COG2128 340100008831 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340100008832 Helix-turn-helix domains; Region: HTH; cl00088 340100008833 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 340100008834 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 340100008835 CoenzymeA binding site [chemical binding]; other site 340100008836 subunit interaction site [polypeptide binding]; other site 340100008837 PHB binding site; other site 340100008838 Helix-turn-helix domains; Region: HTH; cl00088 340100008839 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100008840 dimerization interface [polypeptide binding]; other site 340100008841 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100008842 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100008843 active site 1 [active] 340100008844 dimer interface [polypeptide binding]; other site 340100008845 hexamer interface [polypeptide binding]; other site 340100008846 active site 2 [active] 340100008847 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100008848 active site 1 [active] 340100008849 dimer interface [polypeptide binding]; other site 340100008850 hexamer interface [polypeptide binding]; other site 340100008851 active site 2 [active] 340100008852 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100008853 classical (c) SDRs; Region: SDR_c; cd05233 340100008854 NAD(P) binding site [chemical binding]; other site 340100008855 active site 340100008856 Helix-turn-helix domains; Region: HTH; cl00088 340100008857 Helix-turn-helix domains; Region: HTH; cl00088 340100008858 putative transposase OrfB; Reviewed; Region: PHA02517 340100008859 HTH-like domain; Region: HTH_21; pfam13276 340100008860 Integrase core domain; Region: rve; cl01316 340100008861 Integrase core domain; Region: rve_3; cl15866 340100008862 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 340100008863 binding surface 340100008864 TPR repeat; Region: TPR_11; pfam13414 340100008865 TPR motif; other site 340100008866 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 340100008867 binding surface 340100008868 TPR motif; other site 340100008869 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 340100008870 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 340100008871 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 340100008872 E3 interaction surface; other site 340100008873 lipoyl attachment site [posttranslational modification]; other site 340100008874 glycerol-3-phosphate dehydrogenase; Region: PLN02464 340100008875 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 340100008876 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008877 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100008878 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100008879 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 340100008880 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 340100008881 E3 interaction surface; other site 340100008882 lipoyl attachment site [posttranslational modification]; other site 340100008883 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 340100008884 E3 interaction surface; other site 340100008885 lipoyl attachment site [posttranslational modification]; other site 340100008886 e3 binding domain; Region: E3_binding; pfam02817 340100008887 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 340100008888 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 340100008889 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 340100008890 dimer interface [polypeptide binding]; other site 340100008891 TPP-binding site [chemical binding]; other site 340100008892 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 340100008893 PAS domain S-box; Region: sensory_box; TIGR00229 340100008894 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 340100008895 putative active site [active] 340100008896 heme pocket [chemical binding]; other site 340100008897 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 340100008898 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 340100008899 dimer interface [polypeptide binding]; other site 340100008900 phosphorylation site [posttranslational modification] 340100008901 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 340100008902 ATP binding site [chemical binding]; other site 340100008903 Mg2+ binding site [ion binding]; other site 340100008904 G-X-G motif; other site 340100008905 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100008906 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100008907 active site 340100008908 phosphorylation site [posttranslational modification] 340100008909 intermolecular recognition site; other site 340100008910 dimerization interface [polypeptide binding]; other site 340100008911 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 340100008912 DNA binding residues [nucleotide binding] 340100008913 dimerization interface [polypeptide binding]; other site 340100008914 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 340100008915 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 340100008916 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 340100008917 homodimer interface [polypeptide binding]; other site 340100008918 NADP binding site [chemical binding]; other site 340100008919 substrate binding site [chemical binding]; other site 340100008920 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 340100008921 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 340100008922 active site 340100008923 Zn binding site [ion binding]; other site 340100008924 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 340100008925 Cu(I) binding site [ion binding]; other site 340100008926 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 340100008927 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100008928 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100008929 Protein export membrane protein; Region: SecD_SecF; cl14618 340100008930 Protein export membrane protein; Region: SecD_SecF; cl14618 340100008931 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 340100008932 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 340100008933 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 340100008934 transcriptional regulator; Provisional; Region: PRK10632 340100008935 Helix-turn-helix domains; Region: HTH; cl00088 340100008936 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 340100008937 putative effector binding pocket; other site 340100008938 dimerization interface [polypeptide binding]; other site 340100008939 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 340100008940 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 340100008941 RNA binding surface [nucleotide binding]; other site 340100008942 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 340100008943 active site 340100008944 UTRA domain; Region: UTRA; cl01230 340100008945 YaeQ protein; Region: YaeQ; cl01913 340100008946 LysE type translocator; Region: LysE; cl00565 340100008947 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 340100008948 tartrate dehydrogenase; Provisional; Region: PRK08194 340100008949 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 340100008950 substrate binding site [chemical binding]; other site 340100008951 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 340100008952 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 340100008953 substrate binding site [chemical binding]; other site 340100008954 ligand binding site [chemical binding]; other site 340100008955 Peptidase family M48; Region: Peptidase_M48; cl12018 340100008956 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 340100008957 Tetramer interface [polypeptide binding]; other site 340100008958 active site 340100008959 FMN-binding site [chemical binding]; other site 340100008960 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 340100008961 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 340100008962 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 340100008963 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 340100008964 FOG: CBS domain [General function prediction only]; Region: COG0517 340100008965 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_12; cd04625 340100008966 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 340100008967 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 340100008968 FMN binding site [chemical binding]; other site 340100008969 active site 340100008970 catalytic residues [active] 340100008971 substrate binding site [chemical binding]; other site 340100008972 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 340100008973 Phosphotransferase enzyme family; Region: APH; pfam01636 340100008974 putative active site [active] 340100008975 putative substrate binding site [chemical binding]; other site 340100008976 ATP binding site [chemical binding]; other site 340100008977 Helix-turn-helix domains; Region: HTH; cl00088 340100008978 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100008979 dimerization interface [polypeptide binding]; other site 340100008980 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 340100008981 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100008982 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 340100008983 FAD binding pocket [chemical binding]; other site 340100008984 FAD binding motif [chemical binding]; other site 340100008985 catalytic residues [active] 340100008986 NAD binding pocket [chemical binding]; other site 340100008987 phosphate binding motif [ion binding]; other site 340100008988 beta-alpha-beta structure motif; other site 340100008989 sulfite reductase subunit beta; Provisional; Region: PRK13504 340100008990 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100008991 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100008992 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 340100008993 dimer interface [polypeptide binding]; other site 340100008994 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100008995 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340100008996 catalytic triad [active] 340100008997 replicative DNA helicase; Provisional; Region: PRK07004 340100008998 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 340100008999 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 340100009000 Walker A motif; other site 340100009001 ATP binding site [chemical binding]; other site 340100009002 Walker B motif; other site 340100009003 DNA binding loops [nucleotide binding] 340100009004 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 340100009005 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 340100009006 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 340100009007 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 340100009008 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 340100009009 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 340100009010 Protein of unknown function (DUF817); Region: DUF817; cl01520 340100009011 Type I GTP cyclohydrolase folE2; Region: GCHY-1; cl00642 340100009012 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 340100009013 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 340100009014 TPP-binding site; other site 340100009015 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 340100009016 PYR/PP interface [polypeptide binding]; other site 340100009017 dimer interface [polypeptide binding]; other site 340100009018 TPP binding site [chemical binding]; other site 340100009019 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100009020 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340100009021 substrate binding pocket [chemical binding]; other site 340100009022 chain length determination region; other site 340100009023 substrate-Mg2+ binding site; other site 340100009024 catalytic residues [active] 340100009025 aspartate-rich region 1; other site 340100009026 active site lid residues [active] 340100009027 aspartate-rich region 2; other site 340100009028 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 340100009029 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100009030 Helix-turn-helix domains; Region: HTH; cl00088 340100009031 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100009032 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009033 NMT1-like family; Region: NMT1_2; cl15260 340100009034 OpgC protein; Region: OpgC_C; cl00792 340100009035 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100009036 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 340100009037 [2Fe-2S] cluster binding site [ion binding]; other site 340100009038 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 340100009039 alpha subunit interface [polypeptide binding]; other site 340100009040 active site 340100009041 substrate binding site [chemical binding]; other site 340100009042 Fe binding site [ion binding]; other site 340100009043 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 340100009044 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 340100009045 active site residue [active] 340100009046 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 340100009047 active site residue [active] 340100009048 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 340100009049 Peptidase family M48; Region: Peptidase_M48; cl12018 340100009050 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 340100009051 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 340100009052 NADP binding site [chemical binding]; other site 340100009053 dimer interface [polypeptide binding]; other site 340100009054 EamA-like transporter family; Region: EamA; cl01037 340100009055 EamA-like transporter family; Region: EamA; cl01037 340100009056 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100009057 Helix-turn-helix domains; Region: HTH; cl00088 340100009058 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100009059 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100009060 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 340100009061 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 340100009062 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 340100009063 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100009064 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 340100009065 putative substrate translocation pore; other site 340100009066 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 340100009067 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 340100009068 tartrate dehydrogenase; Provisional; Region: PRK08194 340100009069 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100009070 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009071 DNA-binding site [nucleotide binding]; DNA binding site 340100009072 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 340100009073 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009074 homodimer interface [polypeptide binding]; other site 340100009075 catalytic residue [active] 340100009076 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100009077 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_13; cd08517 340100009078 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100009079 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 340100009080 dimer interface [polypeptide binding]; other site 340100009081 conserved gate region; other site 340100009082 putative PBP binding loops; other site 340100009083 ABC-ATPase subunit interface; other site 340100009084 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 340100009085 dimer interface [polypeptide binding]; other site 340100009086 conserved gate region; other site 340100009087 putative PBP binding loops; other site 340100009088 ABC-ATPase subunit interface; other site 340100009089 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100009090 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100009091 Walker A/P-loop; other site 340100009092 ATP binding site [chemical binding]; other site 340100009093 Q-loop/lid; other site 340100009094 ABC transporter signature motif; other site 340100009095 Walker B; other site 340100009096 D-loop; other site 340100009097 H-loop/switch region; other site 340100009098 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100009099 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100009100 Walker A/P-loop; other site 340100009101 ATP binding site [chemical binding]; other site 340100009102 Q-loop/lid; other site 340100009103 ABC transporter signature motif; other site 340100009104 Walker B; other site 340100009105 D-loop; other site 340100009106 H-loop/switch region; other site 340100009107 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100009108 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 340100009109 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 340100009110 inhibitor-cofactor binding pocket; inhibition site 340100009111 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009112 catalytic residue [active] 340100009113 Cupin domain; Region: Cupin_2; cl09118 340100009114 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 340100009115 EamA-like transporter family; Region: EamA; cl01037 340100009116 EamA-like transporter family; Region: EamA; cl01037 340100009117 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 340100009118 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 340100009119 FeS/SAM binding site; other site 340100009120 HemN C-terminal domain; Region: HemN_C; pfam06969 340100009121 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 340100009122 ATP cone domain; Region: ATP-cone; pfam03477 340100009123 Class III ribonucleotide reductase; Region: RNR_III; cd01675 340100009124 effector binding site; other site 340100009125 active site 340100009126 Zn binding site [ion binding]; other site 340100009127 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 340100009128 [benzylsuccinate synthase]-activating enzyme; Region: rSAM_BssD; TIGR04003 340100009129 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 340100009130 FeS/SAM binding site; other site 340100009131 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100009132 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100009133 FMN binding site [chemical binding]; other site 340100009134 substrate binding site [chemical binding]; other site 340100009135 putative catalytic residue [active] 340100009136 DGC domain; Region: DGC; cl01742 340100009137 SCP-2 sterol transfer family; Region: SCP2; cl01225 340100009138 Peptidase family U32; Region: Peptidase_U32; cl03113 340100009139 Peptidase family U32; Region: Peptidase_U32; cl03113 340100009140 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 340100009141 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100009142 aminotransferase; Provisional; Region: PRK06105 340100009143 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 340100009144 inhibitor-cofactor binding pocket; inhibition site 340100009145 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009146 catalytic residue [active] 340100009147 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 340100009148 Transcriptional regulator; Region: Transcrip_reg; cl00361 340100009149 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 340100009150 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 340100009151 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100009152 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 340100009153 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 340100009154 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 340100009155 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 340100009156 active site 340100009157 (T/H)XGH motif; other site 340100009158 Oligomerisation domain; Region: Oligomerisation; cl00519 340100009159 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 340100009160 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 340100009161 Maf-like protein; Region: Maf; pfam02545 340100009162 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 340100009163 active site 340100009164 dimer interface [polypeptide binding]; other site 340100009165 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340100009166 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 340100009167 ribonuclease G; Provisional; Region: PRK11712 340100009168 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 340100009169 homodimer interface [polypeptide binding]; other site 340100009170 oligonucleotide binding site [chemical binding]; other site 340100009171 Integral membrane protein TerC family; Region: TerC; cl10468 340100009172 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 340100009173 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100009174 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 340100009175 Walker A/P-loop; other site 340100009176 ATP binding site [chemical binding]; other site 340100009177 Q-loop/lid; other site 340100009178 ABC transporter signature motif; other site 340100009179 Walker B; other site 340100009180 D-loop; other site 340100009181 H-loop/switch region; other site 340100009182 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 340100009183 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 340100009184 putative active site [active] 340100009185 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100009186 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 340100009187 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 340100009188 putative metal binding site; other site 340100009189 Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins; Region: CE4_Ecf1_like_5s; cd10969 340100009190 putative active site [active] 340100009191 putative metal binding site [ion binding]; other site 340100009192 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100009193 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 340100009194 putative ADP-binding pocket [chemical binding]; other site 340100009195 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 340100009196 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 340100009197 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 340100009198 generic binding surface I; other site 340100009199 generic binding surface II; other site 340100009200 Cupin domain; Region: Cupin_2; cl09118 340100009201 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 340100009202 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 340100009203 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 340100009204 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 340100009205 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 340100009206 PhoU domain; Region: PhoU; pfam01895 340100009207 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009208 NMT1-like family; Region: NMT1_2; cl15260 340100009209 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009210 NMT1-like family; Region: NMT1_2; cl15260 340100009211 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 340100009212 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 340100009213 DNA polymerase I; Provisional; Region: PRK05755 340100009214 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 340100009215 active site 340100009216 metal binding site 1 [ion binding]; metal-binding site 340100009217 putative 5' ssDNA interaction site; other site 340100009218 metal binding site 3; metal-binding site 340100009219 metal binding site 2 [ion binding]; metal-binding site 340100009220 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 340100009221 putative DNA binding site [nucleotide binding]; other site 340100009222 putative metal binding site [ion binding]; other site 340100009223 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 340100009224 active site 340100009225 catalytic site [active] 340100009226 substrate binding site [chemical binding]; other site 340100009227 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 340100009228 active site 340100009229 DNA binding site [nucleotide binding] 340100009230 catalytic site [active] 340100009231 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 340100009232 Helix-turn-helix domains; Region: HTH; cl00088 340100009233 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100009234 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100009235 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 340100009236 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 340100009237 G1 box; other site 340100009238 putative GEF interaction site [polypeptide binding]; other site 340100009239 GTP/Mg2+ binding site [chemical binding]; other site 340100009240 Switch I region; other site 340100009241 G2 box; other site 340100009242 G3 box; other site 340100009243 Switch II region; other site 340100009244 G4 box; other site 340100009245 G5 box; other site 340100009246 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 340100009247 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 340100009248 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 340100009249 RNA binding site [nucleotide binding]; other site 340100009250 active site 340100009251 Ribosome-binding factor A; Region: RBFA; cl00542 340100009252 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 340100009253 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 340100009254 translation initiation factor IF-2; Region: IF-2; TIGR00487 340100009255 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 340100009256 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 340100009257 G1 box; other site 340100009258 putative GEF interaction site [polypeptide binding]; other site 340100009259 GTP/Mg2+ binding site [chemical binding]; other site 340100009260 Switch I region; other site 340100009261 G2 box; other site 340100009262 G3 box; other site 340100009263 Switch II region; other site 340100009264 G4 box; other site 340100009265 G5 box; other site 340100009266 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 340100009267 Translation-initiation factor 2; Region: IF-2; pfam11987 340100009268 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 340100009269 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 340100009270 NusA N-terminal domain; Region: NusA_N; pfam08529 340100009271 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 340100009272 RNA binding site [nucleotide binding]; other site 340100009273 homodimer interface [polypeptide binding]; other site 340100009274 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 340100009275 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 340100009276 G-X-X-G motif; other site 340100009277 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 340100009278 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 340100009279 ribosome maturation protein RimP; Reviewed; Region: PRK00092 340100009280 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 340100009281 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 340100009282 Sm1 motif; other site 340100009283 D3 - B interaction site; other site 340100009284 D1 - D2 interaction site; other site 340100009285 Hfq - Hfq interaction site; other site 340100009286 RNA binding pocket [nucleotide binding]; other site 340100009287 Sm2 motif; other site 340100009288 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 340100009289 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 340100009290 RNA binding surface [nucleotide binding]; other site 340100009291 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 340100009292 probable active site [active] 340100009293 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 340100009294 transcriptional regulator; Provisional; Region: PRK10632 340100009295 Helix-turn-helix domains; Region: HTH; cl00088 340100009296 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 340100009297 putative effector binding pocket; other site 340100009298 dimerization interface [polypeptide binding]; other site 340100009299 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 340100009300 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100009301 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 340100009302 Cupin domain; Region: Cupin_2; cl09118 340100009303 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 340100009304 putative substrate translocation pore; other site 340100009305 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 340100009306 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009307 Helix-turn-helix domains; Region: HTH; cl00088 340100009308 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 340100009309 putative substrate binding pocket [chemical binding]; other site 340100009310 putative dimerization interface [polypeptide binding]; other site 340100009311 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009312 Helix-turn-helix domains; Region: HTH; cl00088 340100009313 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100009314 dimerization interface [polypeptide binding]; other site 340100009315 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100009316 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 340100009317 maleylacetoacetate isomerase; Region: maiA; TIGR01262 340100009318 C-terminal domain interface [polypeptide binding]; other site 340100009319 GSH binding site (G-site) [chemical binding]; other site 340100009320 putative dimer interface [polypeptide binding]; other site 340100009321 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 340100009322 dimer interface [polypeptide binding]; other site 340100009323 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 340100009324 N-terminal domain interface [polypeptide binding]; other site 340100009325 LytB protein; Region: LYTB; cl00507 340100009326 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 340100009327 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 340100009328 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100009329 MPN+ (JAMM) motif; other site 340100009330 Zinc-binding site [ion binding]; other site 340100009331 Putative cyclase; Region: Cyclase; cl00814 340100009332 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 340100009333 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 340100009334 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 340100009335 multidrug efflux protein; Reviewed; Region: PRK01766 340100009336 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 340100009337 DNA repair protein RadA; Provisional; Region: PRK11823 340100009338 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 340100009339 Walker A motif/ATP binding site; other site 340100009340 ATP binding site [chemical binding]; other site 340100009341 Walker B motif; other site 340100009342 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340100009343 von Willebrand factor; Region: vWF_A; pfam12450 340100009344 VWA subgroup: 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...; Region: vWA_subgroup; cd01465 340100009345 metal ion-dependent adhesion site (MIDAS); other site 340100009346 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 340100009347 RNA polymerase sigma factor; Provisional; Region: PRK12513 340100009348 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100009349 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 340100009350 DNA binding residues [nucleotide binding] 340100009351 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100009352 classical (c) SDRs; Region: SDR_c; cd05233 340100009353 NAD(P) binding site [chemical binding]; other site 340100009354 active site 340100009355 alanine racemase; Reviewed; Region: dadX; PRK03646 340100009356 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 340100009357 active site 340100009358 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100009359 substrate binding site [chemical binding]; other site 340100009360 catalytic residues [active] 340100009361 dimer interface [polypeptide binding]; other site 340100009362 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 340100009363 active site lid residues [active] 340100009364 substrate binding pocket [chemical binding]; other site 340100009365 catalytic residues [active] 340100009366 substrate-Mg2+ binding site; other site 340100009367 aspartate-rich region 1; other site 340100009368 aspartate-rich region 2; other site 340100009369 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 340100009370 active site lid residues [active] 340100009371 substrate binding pocket [chemical binding]; other site 340100009372 catalytic residues [active] 340100009373 substrate-Mg2+ binding site; other site 340100009374 aspartate-rich region 1; other site 340100009375 aspartate-rich region 2; other site 340100009376 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 340100009377 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100009378 Helix-turn-helix domains; Region: HTH; cl00088 340100009379 putative transposase OrfB; Reviewed; Region: PHA02517 340100009380 HTH-like domain; Region: HTH_21; pfam13276 340100009381 Integrase core domain; Region: rve; cl01316 340100009382 Integrase core domain; Region: rve_3; cl15866 340100009383 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 340100009384 FlgD Ig-like domain; Region: FlgD_ig; cl15790 340100009385 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 340100009386 ApbE family; Region: ApbE; cl00643 340100009387 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100009388 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like1; cd06200 340100009389 FAD binding pocket [chemical binding]; other site 340100009390 FAD binding motif [chemical binding]; other site 340100009391 catalytic residues [active] 340100009392 NAD binding pocket [chemical binding]; other site 340100009393 phosphate binding motif [ion binding]; other site 340100009394 beta-alpha-beta structure motif; other site 340100009395 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 340100009396 Clp amino terminal domain; Region: Clp_N; pfam02861 340100009397 Clp amino terminal domain; Region: Clp_N; pfam02861 340100009398 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 340100009399 Walker A motif; other site 340100009400 ATP binding site [chemical binding]; other site 340100009401 Walker B motif; other site 340100009402 arginine finger; other site 340100009403 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 340100009404 Walker A motif; other site 340100009405 ATP binding site [chemical binding]; other site 340100009406 Walker B motif; other site 340100009407 arginine finger; other site 340100009408 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340100009409 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 340100009410 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 340100009411 ligand binding site [chemical binding]; other site 340100009412 flexible hinge region; other site 340100009413 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 340100009414 putative switch regulator; other site 340100009415 non-specific DNA interactions [nucleotide binding]; other site 340100009416 DNA binding site [nucleotide binding] 340100009417 sequence specific DNA binding site [nucleotide binding]; other site 340100009418 putative cAMP binding site [chemical binding]; other site 340100009419 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 340100009420 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 340100009421 dimer interface [polypeptide binding]; other site 340100009422 ADP-ribose binding site [chemical binding]; other site 340100009423 active site 340100009424 nudix motif; other site 340100009425 metal binding site [ion binding]; metal-binding site 340100009426 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 340100009427 active site 340100009428 Zn binding site [ion binding]; other site 340100009429 NlpE N-terminal domain; Region: NlpE; cl01138 340100009430 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 340100009431 Cupin domain; Region: Cupin_2; cl09118 340100009432 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009433 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100009434 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009435 LysE type translocator; Region: LysE; cl00565 340100009436 Protein of unknown function (DUF342); Region: DUF342; pfam03961 340100009437 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 340100009438 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 340100009439 OsmC-like protein; Region: OsmC; cl00767 340100009440 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100009441 Helix-turn-helix domains; Region: HTH; cl00088 340100009442 Predicted acetyltransferase [General function prediction only]; Region: COG3153 340100009443 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100009444 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 340100009445 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100009446 conserved cys residue [active] 340100009447 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009448 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 340100009449 putative substrate translocation pore; other site 340100009450 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100009451 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 340100009452 N-terminal plug; other site 340100009453 ligand-binding site [chemical binding]; other site 340100009454 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 340100009455 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 340100009456 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 340100009457 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 340100009458 trimer interface [polypeptide binding]; other site 340100009459 eyelet of channel; other site 340100009460 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 340100009461 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 340100009462 N-terminal plug; other site 340100009463 ligand-binding site [chemical binding]; other site 340100009464 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100009465 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 340100009466 active site 340100009467 benzoate transport; Region: 2A0115; TIGR00895 340100009468 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 340100009469 putative substrate translocation pore; other site 340100009470 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100009471 FCD domain; Region: FCD; cl11656 340100009472 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 340100009473 putative substrate translocation pore; other site 340100009474 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100009475 Helix-turn-helix domains; Region: HTH; cl00088 340100009476 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100009477 dimerization interface [polypeptide binding]; other site 340100009478 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 340100009479 Helix-turn-helix domains; Region: HTH; cl00088 340100009480 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100009481 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 340100009482 active site 340100009483 catalytic site [active] 340100009484 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 340100009485 active site 340100009486 catalytic site [active] 340100009487 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009488 NMT1-like family; Region: NMT1_2; cl15260 340100009489 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100009490 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100009491 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; cl15754 340100009492 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 340100009493 active site 340100009494 substrate binding site [chemical binding]; other site 340100009495 Mg2+ binding site [ion binding]; other site 340100009496 Phospholipid methyltransferase; Region: PEMT; cl00763 340100009497 Cytochrome c; Region: Cytochrom_C; cl11414 340100009498 Cytochrome c; Region: Cytochrom_C; cl11414 340100009499 Cytochrome c; Region: Cytochrom_C; cl11414 340100009500 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100009501 Cytochrome c; Region: Cytochrom_C; cl11414 340100009502 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100009503 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 340100009504 D-pathway; other site 340100009505 Low-spin heme binding site [chemical binding]; other site 340100009506 Putative water exit pathway; other site 340100009507 Binuclear center (active site) [active] 340100009508 K-pathway; other site 340100009509 Putative proton exit pathway; other site 340100009510 MASE1; Region: MASE1; pfam05231 340100009511 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_5; cd08511 340100009512 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100009513 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100009514 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100009515 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100009516 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100009517 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009518 DNA-binding site [nucleotide binding]; DNA binding site 340100009519 FCD domain; Region: FCD; cl11656 340100009520 Dehydratase family; Region: ILVD_EDD; cl00340 340100009521 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 340100009522 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009523 NMT1-like family; Region: NMT1_2; cl15260 340100009524 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 340100009525 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 340100009526 conserved cys residue [active] 340100009527 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009528 Protein of unknown function (DUF1428); Region: DUF1428; cl02319 340100009529 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_8; cd07246 340100009530 putative dimer interface [polypeptide binding]; other site 340100009531 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100009532 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100009533 Coenzyme A binding pocket [chemical binding]; other site 340100009534 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100009535 Haemolysin-III related; Region: HlyIII; cl03831 340100009536 TIGR03442 family protein; Region: TIGR03442 340100009537 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 340100009538 putative active site [active] 340100009539 putative dimer interface [polypeptide binding]; other site 340100009540 Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate...; Region: SO_family_Moco_dimer; cd02110 340100009541 Moco binding site; other site 340100009542 metal coordination site [ion binding]; other site 340100009543 dimerization interface [polypeptide binding]; other site 340100009544 Cytochrome c; Region: Cytochrom_C; cl11414 340100009545 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100009546 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 340100009547 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 340100009548 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 340100009549 active site 340100009550 catalytic tetrad [active] 340100009551 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 340100009552 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 340100009553 motif II; other site 340100009554 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100009555 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340100009556 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 340100009557 Walker A/P-loop; other site 340100009558 ATP binding site [chemical binding]; other site 340100009559 Q-loop/lid; other site 340100009560 ABC transporter signature motif; other site 340100009561 Walker B; other site 340100009562 D-loop; other site 340100009563 H-loop/switch region; other site 340100009564 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 340100009565 FixH; Region: FixH; cl01254 340100009566 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 340100009567 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100009568 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 340100009569 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 340100009570 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 340100009571 Cytochrome c; Region: Cytochrom_C; cl11414 340100009572 Cytochrome c; Region: Cytochrom_C; cl11414 340100009573 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cl00282 340100009574 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 340100009575 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 340100009576 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 340100009577 Low-spin heme binding site [chemical binding]; other site 340100009578 Putative water exit pathway; other site 340100009579 Binuclear center (active site) [active] 340100009580 Putative proton exit pathway; other site 340100009581 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 340100009582 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 340100009583 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 340100009584 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 340100009585 dimerization interface [polypeptide binding]; other site 340100009586 putative DNA binding site [nucleotide binding]; other site 340100009587 putative Zn2+ binding site [ion binding]; other site 340100009588 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 340100009589 active site residue [active] 340100009590 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 340100009591 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 340100009592 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 340100009593 tetramer interface [polypeptide binding]; other site 340100009594 active site 340100009595 Mg2+/Mn2+ binding site [ion binding]; other site 340100009596 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 340100009597 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340100009598 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 340100009599 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 340100009600 putative substrate translocation pore; other site 340100009601 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 340100009602 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 340100009603 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 340100009604 active site 340100009605 catalytic site [active] 340100009606 putative DNA binding site [nucleotide binding]; other site 340100009607 GIY-YIG motif/motif A; other site 340100009608 metal binding site [ion binding]; metal-binding site 340100009609 UvrB/uvrC motif; Region: UVR; pfam02151 340100009610 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 340100009611 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 340100009612 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 340100009613 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 340100009614 active site 340100009615 hydrophilic channel; other site 340100009616 dimerization interface [polypeptide binding]; other site 340100009617 catalytic residues [active] 340100009618 active site lid [active] 340100009619 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100009620 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100009621 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100009622 Protein export membrane protein; Region: SecD_SecF; cl14618 340100009623 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 340100009624 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 340100009625 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 340100009626 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 340100009627 DNA binding site [nucleotide binding] 340100009628 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 340100009629 nucleophile elbow; other site 340100009630 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 340100009631 Patatin phospholipase; Region: DUF3734; pfam12536 340100009632 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 340100009633 Helix-turn-helix domains; Region: HTH; cl00088 340100009634 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 340100009635 TOBE domain; Region: TOBE_2; cl01440 340100009636 TOBE domain; Region: TOBE_2; cl01440 340100009637 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 340100009638 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100009639 Walker A/P-loop; other site 340100009640 ATP binding site [chemical binding]; other site 340100009641 Q-loop/lid; other site 340100009642 ABC transporter signature motif; other site 340100009643 Walker B; other site 340100009644 D-loop; other site 340100009645 H-loop/switch region; other site 340100009646 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 340100009647 TM-ABC transporter signature motif; other site 340100009648 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 340100009649 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 340100009650 zinc binding site [ion binding]; other site 340100009651 putative ligand binding site [chemical binding]; other site 340100009652 DctM-like transporters; Region: DctM; pfam06808 340100009653 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100009654 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100009655 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100009656 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100009657 malonyl-CoA synthase; Validated; Region: PRK07514 340100009658 AMP-binding enzyme; Region: AMP-binding; cl15778 340100009659 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100009660 enoyl-CoA hydratase; Provisional; Region: PRK06127 340100009661 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 340100009662 substrate binding site [chemical binding]; other site 340100009663 oxyanion hole (OAH) forming residues; other site 340100009664 trimer interface [polypeptide binding]; other site 340100009665 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 340100009666 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 340100009667 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009668 DNA-binding site [nucleotide binding]; DNA binding site 340100009669 FCD domain; Region: FCD; cl11656 340100009670 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; cl15754 340100009671 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100009672 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 340100009673 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100009674 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100009675 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100009676 active site 340100009677 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009678 NMT1-like family; Region: NMT1_2; cl15260 340100009679 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 340100009680 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100009681 CoA-ligase; Region: Ligase_CoA; cl02894 340100009682 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100009683 enoyl-CoA hydratase; Provisional; Region: PRK08290 340100009684 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 340100009685 substrate binding site [chemical binding]; other site 340100009686 oxyanion hole (OAH) forming residues; other site 340100009687 trimer interface [polypeptide binding]; other site 340100009688 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100009689 Helix-turn-helix domains; Region: HTH; cl00088 340100009690 beta-ketothiolase; Provisional; Region: PRK09051 340100009691 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 340100009692 dimer interface [polypeptide binding]; other site 340100009693 active site 340100009694 enoyl-CoA hydratase; Provisional; Region: PRK09245 340100009695 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 340100009696 substrate binding site [chemical binding]; other site 340100009697 oxyanion hole (OAH) forming residues; other site 340100009698 trimer interface [polypeptide binding]; other site 340100009699 putative transposase OrfB; Reviewed; Region: PHA02517 340100009700 HTH-like domain; Region: HTH_21; pfam13276 340100009701 Integrase core domain; Region: rve; cl01316 340100009702 Integrase core domain; Region: rve_3; cl15866 340100009703 Helix-turn-helix domains; Region: HTH; cl00088 340100009704 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100009705 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100009706 active site 340100009707 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100009708 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100009709 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100009710 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 340100009711 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 340100009712 NADP binding site [chemical binding]; other site 340100009713 dimer interface [polypeptide binding]; other site 340100009714 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100009715 Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues; Region: MR_like; cd03316 340100009716 active site pocket [active] 340100009717 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100009718 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 340100009719 ligand binding site [chemical binding]; other site 340100009720 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 340100009721 TM-ABC transporter signature motif; other site 340100009722 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 340100009723 TM-ABC transporter signature motif; other site 340100009724 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100009725 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100009726 Walker A/P-loop; other site 340100009727 ATP binding site [chemical binding]; other site 340100009728 Q-loop/lid; other site 340100009729 ABC transporter signature motif; other site 340100009730 Walker B; other site 340100009731 D-loop; other site 340100009732 H-loop/switch region; other site 340100009733 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100009734 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100009735 Walker A/P-loop; other site 340100009736 ATP binding site [chemical binding]; other site 340100009737 Q-loop/lid; other site 340100009738 ABC transporter signature motif; other site 340100009739 Walker B; other site 340100009740 D-loop; other site 340100009741 H-loop/switch region; other site 340100009742 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100009743 Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues; Region: MR_like; cd03316 340100009744 active site pocket [active] 340100009745 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100009746 active site 1 [active] 340100009747 dimer interface [polypeptide binding]; other site 340100009748 hexamer interface [polypeptide binding]; other site 340100009749 active site 2 [active] 340100009750 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 340100009751 hexamer interface [polypeptide binding]; other site 340100009752 active site 2 [active] 340100009753 dimer interface [polypeptide binding]; other site 340100009754 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100009755 Helix-turn-helix domains; Region: HTH; cl00088 340100009756 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100009757 dimerization interface [polypeptide binding]; other site 340100009758 substrate binding pocket [chemical binding]; other site 340100009759 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100009760 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100009761 PYR/PP interface [polypeptide binding]; other site 340100009762 dimer interface [polypeptide binding]; other site 340100009763 TPP binding site [chemical binding]; other site 340100009764 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100009765 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 340100009766 TPP-binding site [chemical binding]; other site 340100009767 Helix-turn-helix domains; Region: HTH; cl00088 340100009768 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100009769 dimerization interface [polypeptide binding]; other site 340100009770 substrate binding pocket [chemical binding]; other site 340100009771 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100009772 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100009773 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 340100009774 active site 340100009775 catalytic site [active] 340100009776 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009777 NMT1-like family; Region: NMT1_2; cl15260 340100009778 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 340100009779 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 340100009780 Walker A/P-loop; other site 340100009781 ATP binding site [chemical binding]; other site 340100009782 Q-loop/lid; other site 340100009783 ABC transporter signature motif; other site 340100009784 Walker B; other site 340100009785 D-loop; other site 340100009786 H-loop/switch region; other site 340100009787 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 340100009788 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 340100009789 dimer interface [polypeptide binding]; other site 340100009790 conserved gate region; other site 340100009791 putative PBP binding loops; other site 340100009792 ABC-ATPase subunit interface; other site 340100009793 NMT1-like family; Region: NMT1_2; cl15260 340100009794 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 340100009795 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 340100009796 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100009797 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 340100009798 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 340100009799 putative substrate translocation pore; other site 340100009800 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 340100009801 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 340100009802 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 340100009803 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100009804 putative ligand binding site [chemical binding]; other site 340100009805 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 340100009806 TM-ABC transporter signature motif; other site 340100009807 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 340100009808 TM-ABC transporter signature motif; other site 340100009809 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100009810 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100009811 Walker A/P-loop; other site 340100009812 ATP binding site [chemical binding]; other site 340100009813 Q-loop/lid; other site 340100009814 ABC transporter signature motif; other site 340100009815 Walker B; other site 340100009816 D-loop; other site 340100009817 H-loop/switch region; other site 340100009818 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 340100009819 Sulfate transporter family; Region: Sulfate_transp; cl15842 340100009820 Sulfate transporter family; Region: Sulfate_transp; cl15842 340100009821 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 340100009822 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 340100009823 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 340100009824 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100009825 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 340100009826 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 340100009827 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 340100009828 Cl- selectivity filter; other site 340100009829 Cl- binding residues [ion binding]; other site 340100009830 pore gating glutamate residue; other site 340100009831 dimer interface [polypeptide binding]; other site 340100009832 FOG: CBS domain [General function prediction only]; Region: COG0517 340100009833 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc; cd04612 340100009834 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 340100009835 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 340100009836 putative substrate translocation pore; other site 340100009837 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 340100009838 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 340100009839 HIGH motif; other site 340100009840 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340100009841 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100009842 active site 340100009843 KMSKS motif; other site 340100009844 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 340100009845 tRNA binding surface [nucleotide binding]; other site 340100009846 Lipopolysaccharide-assembly; Region: LptE; cl01125 340100009847 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 340100009848 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 340100009849 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 340100009850 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 340100009851 putative catalytic cysteine [active] 340100009852 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009853 Helix-turn-helix domains; Region: HTH; cl00088 340100009854 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100009855 dimerization interface [polypeptide binding]; other site 340100009856 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100009857 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 340100009858 putative substrate translocation pore; other site 340100009859 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100009860 hypothetical protein; Provisional; Region: PRK01842 340100009861 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100009862 Helix-turn-helix domains; Region: HTH; cl00088 340100009863 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 340100009864 dimerization interface [polypeptide binding]; other site 340100009865 substrate binding pocket [chemical binding]; other site 340100009866 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 340100009867 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 340100009868 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100009869 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100009870 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009871 DNA-binding site [nucleotide binding]; DNA binding site 340100009872 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 340100009873 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009874 homodimer interface [polypeptide binding]; other site 340100009875 catalytic residue [active] 340100009876 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100009877 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100009878 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100009879 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 340100009880 homodimer interface [polypeptide binding]; other site 340100009881 NAD binding site [chemical binding]; other site 340100009882 catalytic residues [active] 340100009883 substrate binding pocket [chemical binding]; other site 340100009884 flexible flap; other site 340100009885 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 340100009886 EamA-like transporter family; Region: EamA; cl01037 340100009887 YCII-related domain; Region: YCII; cl00999 340100009888 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 340100009889 LysE type translocator; Region: LysE; cl00565 340100009890 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100009891 Helix-turn-helix domains; Region: HTH; cl00088 340100009892 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; Region: PBP2_BenM_CatM_CatR; cd08445 340100009893 dimerizarion interface [polypeptide binding]; other site 340100009894 CrgA pocket; other site 340100009895 substrate binding pocket [chemical binding]; other site 340100009896 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100009897 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 340100009898 octamer interface [polypeptide binding]; other site 340100009899 active site 340100009900 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009901 NMT1-like family; Region: NMT1_2; cl15260 340100009902 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 340100009903 GST_N family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of...; Region: GST_N_Sigma_like; cd03039 340100009904 glutathione s-transferase; Provisional; Region: PTZ00057 340100009905 GSH binding site (G-site) [chemical binding]; other site 340100009906 C-terminal domain interface [polypeptide binding]; other site 340100009907 dimer interface [polypeptide binding]; other site 340100009908 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 340100009909 dimer interface [polypeptide binding]; other site 340100009910 N-terminal domain interface [polypeptide binding]; other site 340100009911 substrate binding pocket (H-site) [chemical binding]; other site 340100009912 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 340100009913 active site 340100009914 substrate binding site [chemical binding]; other site 340100009915 catalytic site [active] 340100009916 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 340100009917 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 340100009918 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 340100009919 substrate binding site [chemical binding]; other site 340100009920 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 340100009921 substrate binding site [chemical binding]; other site 340100009922 ligand binding site [chemical binding]; other site 340100009923 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009924 Helix-turn-helix domains; Region: HTH; cl00088 340100009925 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 340100009926 putative dimerization interface [polypeptide binding]; other site 340100009927 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 340100009928 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100009929 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009930 NMT1-like family; Region: NMT1_2; cl15260 340100009931 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100009932 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 340100009933 N-terminal plug; other site 340100009934 ligand-binding site [chemical binding]; other site 340100009935 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100009936 3-hydroxyacyl-CoA dehydrogenase; Validated; Region: PRK06129 340100009937 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100009938 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100009939 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100009940 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100009941 catalytic residue [active] 340100009942 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 340100009943 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100009944 Walker A/P-loop; other site 340100009945 ATP binding site [chemical binding]; other site 340100009946 Q-loop/lid; other site 340100009947 ABC transporter signature motif; other site 340100009948 Walker B; other site 340100009949 D-loop; other site 340100009950 H-loop/switch region; other site 340100009951 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 340100009952 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100009953 Walker A/P-loop; other site 340100009954 ATP binding site [chemical binding]; other site 340100009955 Q-loop/lid; other site 340100009956 ABC transporter signature motif; other site 340100009957 Walker B; other site 340100009958 D-loop; other site 340100009959 H-loop/switch region; other site 340100009960 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 340100009961 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 340100009962 active site 340100009963 catalytic tetrad [active] 340100009964 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009965 Helix-turn-helix domains; Region: HTH; cl00088 340100009966 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 340100009967 putative effector binding pocket; other site 340100009968 putative dimerization interface [polypeptide binding]; other site 340100009969 aconitate hydratase; Provisional; Region: acnA; PRK12881 340100009970 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 340100009971 substrate binding site [chemical binding]; other site 340100009972 ligand binding site [chemical binding]; other site 340100009973 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 340100009974 substrate binding site [chemical binding]; other site 340100009975 Protein of unknown function (DUF2863); Region: DUF2863; pfam11062 340100009976 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 340100009977 elongation factor P; Validated; Region: PRK00529 340100009978 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 340100009979 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 340100009980 RNA binding site [nucleotide binding]; other site 340100009981 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 340100009982 RNA binding site [nucleotide binding]; other site 340100009983 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 340100009984 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 340100009985 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 340100009986 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 340100009987 Walker A motif; other site 340100009988 ATP binding site [chemical binding]; other site 340100009989 Walker B motif; other site 340100009990 arginine finger; other site 340100009991 Helix-turn-helix domains; Region: HTH; cl00088 340100009992 Predicted membrane protein [Function unknown]; Region: COG4655 340100009993 TadE-like protein; Region: TadE; cl10688 340100009994 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 340100009995 TPR repeat; Region: TPR_11; pfam13414 340100009996 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 340100009997 binding surface 340100009998 TPR motif; other site 340100009999 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340100010000 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 340100010001 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340100010002 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 340100010003 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 340100010004 ATP binding site [chemical binding]; other site 340100010005 Walker A motif; other site 340100010006 hexamer interface [polypeptide binding]; other site 340100010007 Walker B motif; other site 340100010008 Response regulator receiver domain; Region: Response_reg; pfam00072 340100010009 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100010010 active site 340100010011 phosphorylation site [posttranslational modification] 340100010012 intermolecular recognition site; other site 340100010013 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 340100010014 dimerization interface [polypeptide binding]; other site 340100010015 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100010016 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 340100010017 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100010018 SAF domain; Region: SAF; cl00555 340100010019 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 340100010020 TadE-like protein; Region: TadE; cl10688 340100010021 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 340100010022 Flp/Fap pilin component; Region: Flp_Fap; cl01585 340100010023 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 340100010024 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 340100010025 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 340100010026 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340100010027 Helix-turn-helix domains; Region: HTH; cl00088 340100010028 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 340100010029 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100010030 Walker A/P-loop; other site 340100010031 ATP binding site [chemical binding]; other site 340100010032 Q-loop/lid; other site 340100010033 ABC transporter signature motif; other site 340100010034 Walker B; other site 340100010035 D-loop; other site 340100010036 H-loop/switch region; other site 340100010037 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100010038 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100010039 Walker A/P-loop; other site 340100010040 ATP binding site [chemical binding]; other site 340100010041 Q-loop/lid; other site 340100010042 ABC transporter signature motif; other site 340100010043 Walker B; other site 340100010044 D-loop; other site 340100010045 H-loop/switch region; other site 340100010046 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100010047 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 340100010048 dimer interface [polypeptide binding]; other site 340100010049 conserved gate region; other site 340100010050 putative PBP binding loops; other site 340100010051 ABC-ATPase subunit interface; other site 340100010052 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100010053 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 340100010054 dimer interface [polypeptide binding]; other site 340100010055 putative PBP binding loops; other site 340100010056 ABC-ATPase subunit interface; other site 340100010057 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_18; cd08505 340100010058 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100010059 Staphylococcal nuclease homologues; Region: SNc; smart00318 340100010060 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 340100010061 Catalytic site; other site 340100010062 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 340100010063 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 340100010064 metabolite-proton symporter; Region: 2A0106; TIGR00883 340100010065 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 340100010066 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100010067 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 340100010068 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100010069 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 340100010070 D-pathway; other site 340100010071 Putative ubiquinol binding site [chemical binding]; other site 340100010072 Low-spin heme (heme b) binding site [chemical binding]; other site 340100010073 Putative water exit pathway; other site 340100010074 Binuclear center (heme o3/CuB) [ion binding]; other site 340100010075 K-pathway; other site 340100010076 Putative proton exit pathway; other site 340100010077 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 340100010078 Subunit I/III interface [polypeptide binding]; other site 340100010079 Subunit III/IV interface [polypeptide binding]; other site 340100010080 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 340100010081 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 340100010082 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 340100010083 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100010084 Family description; Region: UvrD_C_2; cl15862 340100010085 Protein of unknown function DUF72; Region: DUF72; cl00777 340100010086 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100010087 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100010088 DNA-binding site [nucleotide binding]; DNA binding site 340100010089 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 340100010090 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100010091 homodimer interface [polypeptide binding]; other site 340100010092 catalytic residue [active] 340100010093 4-aminobutyrate aminotransferase; Provisional; Region: PRK06777 340100010094 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 340100010095 inhibitor-cofactor binding pocket; inhibition site 340100010096 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100010097 catalytic residue [active] 340100010098 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100010099 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100010100 tetramerization interface [polypeptide binding]; other site 340100010101 NAD(P) binding site [chemical binding]; other site 340100010102 catalytic residues [active] 340100010103 PAP-phosphatase_like domains. PAP-phosphatase is a member of the inositol monophosphatase family, and catalyses the hydrolysis of 3'-phosphoadenosine-5'-phosphate (PAP) to AMP. In Saccharomyces cerevisiae, HAL2 (MET22) is involved in methionine...; Region: PAP_phosphatase; cd01517 340100010104 active site 340100010105 putative lithium-binding site [ion binding]; other site 340100010106 substrate binding site [chemical binding]; other site 340100010107 NAD-dependent deacetylase; Provisional; Region: PRK05333 340100010108 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 340100010109 serine O-acetyltransferase; Region: cysE; TIGR01172 340100010110 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 340100010111 trimer interface [polypeptide binding]; other site 340100010112 active site 340100010113 substrate binding site [chemical binding]; other site 340100010114 CoA binding site [chemical binding]; other site 340100010115 Helix-turn-helix domains; Region: HTH; cl00088 340100010116 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 340100010117 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 340100010118 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100010119 active site 340100010120 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 340100010121 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 340100010122 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 340100010123 dimer interface [polypeptide binding]; other site 340100010124 active site 340100010125 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 340100010126 substrate binding site [chemical binding]; other site 340100010127 oxyanion hole (OAH) forming residues; other site 340100010128 trimer interface [polypeptide binding]; other site 340100010129 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 340100010130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010131 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100010132 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340100010133 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 340100010134 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010135 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100010136 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 340100010137 substrate binding site [chemical binding]; other site 340100010138 oxyanion hole (OAH) forming residues; other site 340100010139 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 340100010140 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 340100010141 dimer interface [polypeptide binding]; other site 340100010142 active site 340100010143 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 340100010144 AMP-binding enzyme; Region: AMP-binding; cl15778 340100010145 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100010146 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 340100010147 Sulfatase; Region: Sulfatase; cl10460 340100010148 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010149 NMT1-like family; Region: NMT1_2; cl15260 340100010150 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100010151 Helix-turn-helix domains; Region: HTH; cl00088 340100010152 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 340100010153 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 340100010154 N-terminal plug; other site 340100010155 ligand-binding site [chemical binding]; other site 340100010156 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010157 NMT1-like family; Region: NMT1_2; cl15260 340100010158 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100010159 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 340100010160 active site 340100010161 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100010162 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100010163 DNA-binding site [nucleotide binding]; DNA binding site 340100010164 FCD domain; Region: FCD; cl11656 340100010165 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 340100010166 putative substrate translocation pore; other site 340100010167 Cupin domain; Region: Cupin_2; cl09118 340100010168 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100010169 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100010170 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 340100010171 dimerization interface [polypeptide binding]; other site 340100010172 putative DNA binding site [nucleotide binding]; other site 340100010173 putative Zn2+ binding site [ion binding]; other site 340100010174 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 340100010175 FMN binding site [chemical binding]; other site 340100010176 active site 340100010177 substrate binding site [chemical binding]; other site 340100010178 catalytic residue [active] 340100010179 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 340100010180 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100010181 FMN binding site [chemical binding]; other site 340100010182 substrate binding site [chemical binding]; other site 340100010183 putative catalytic residue [active] 340100010184 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010185 NMT1-like family; Region: NMT1_2; cl15260 340100010186 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010187 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010188 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 340100010189 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 340100010190 substrate binding site [chemical binding]; other site 340100010191 oxyanion hole (OAH) forming residues; other site 340100010192 trimer interface [polypeptide binding]; other site 340100010193 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100010194 Helix-turn-helix domains; Region: HTH; cl00088 340100010195 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100010196 active site 340100010197 catalytic residues [active] 340100010198 metal binding site [ion binding]; metal-binding site 340100010199 AMP-binding domain protein; Validated; Region: PRK08315 340100010200 AMP-binding enzyme; Region: AMP-binding; cl15778 340100010201 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 340100010202 enoyl-CoA hydratase; Region: PLN02600 340100010203 substrate binding site [chemical binding]; other site 340100010204 oxyanion hole (OAH) forming residues; other site 340100010205 trimer interface [polypeptide binding]; other site 340100010206 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010207 NMT1-like family; Region: NMT1_2; cl15260 340100010208 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010209 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010210 transcriptional regulator; Provisional; Region: PRK10632 340100010211 Helix-turn-helix domains; Region: HTH; cl00088 340100010212 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 340100010213 putative effector binding pocket; other site 340100010214 dimerization interface [polypeptide binding]; other site 340100010215 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 340100010216 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 340100010217 putative NAD(P) binding site [chemical binding]; other site 340100010218 dimer interface [polypeptide binding]; other site 340100010219 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 340100010220 DNA polymerase Ligase (LigD); Region: LigD_N; cl11819 340100010221 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 340100010222 active site 340100010223 DNA binding site [nucleotide binding] 340100010224 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 340100010225 DNA binding site [nucleotide binding] 340100010226 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 340100010227 nucleotide binding site [chemical binding]; other site 340100010228 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 340100010229 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 340100010230 putative DNA binding site [nucleotide binding]; other site 340100010231 putative homodimer interface [polypeptide binding]; other site 340100010232 Cysteine dioxygenase type I; Region: CDO_I; cl15835 340100010233 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 340100010234 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 340100010235 putative active site [active] 340100010236 heme pocket [chemical binding]; other site 340100010237 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 340100010238 dimer interface [polypeptide binding]; other site 340100010239 phosphorylation site [posttranslational modification] 340100010240 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 340100010241 ATP binding site [chemical binding]; other site 340100010242 Mg2+ binding site [ion binding]; other site 340100010243 G-X-G motif; other site 340100010244 Response regulator receiver domain; Region: Response_reg; pfam00072 340100010245 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100010246 active site 340100010247 phosphorylation site [posttranslational modification] 340100010248 intermolecular recognition site; other site 340100010249 dimerization interface [polypeptide binding]; other site 340100010250 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 340100010251 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 340100010252 putative acyl-acceptor binding pocket; other site 340100010253 aspartate kinase; Reviewed; Region: PRK06635 340100010254 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 340100010255 putative nucleotide binding site [chemical binding]; other site 340100010256 putative catalytic residues [active] 340100010257 putative Mg ion binding site [ion binding]; other site 340100010258 putative aspartate binding site [chemical binding]; other site 340100010259 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 340100010260 putative allosteric regulatory site; other site 340100010261 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 340100010262 putative allosteric regulatory residue; other site 340100010263 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 340100010264 Ligand Binding Site [chemical binding]; other site 340100010265 TilS substrate binding domain; Region: TilS; pfam09179 340100010266 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340100010267 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 340100010268 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100010269 endonuclease III; Region: ENDO3c; smart00478 340100010270 minor groove reading motif; other site 340100010271 helix-hairpin-helix signature motif; other site 340100010272 substrate binding pocket [chemical binding]; other site 340100010273 active site 340100010274 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 340100010275 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 340100010276 active site 340100010277 HIGH motif; other site 340100010278 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 340100010279 KMSKS motif; other site 340100010280 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 340100010281 tRNA binding surface [nucleotide binding]; other site 340100010282 anticodon binding site; other site 340100010283 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 340100010284 binding surface 340100010285 Tetratricopeptide repeat; Region: TPR_16; pfam13432 340100010286 TPR motif; other site 340100010287 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 340100010288 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 340100010289 substrate binding site [chemical binding]; other site 340100010290 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 340100010291 putative active site [active] 340100010292 putative metal binding site [ion binding]; other site 340100010293 Bacitracin resistance protein BacA; Region: BacA; cl00858 340100010294 Integral membrane protein TerC family; Region: TerC; cl10468 340100010295 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 340100010296 Transporter associated domain; Region: CorC_HlyC; cl08393 340100010297 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 340100010298 active site 340100010299 dimerization interface [polypeptide binding]; other site 340100010300 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 340100010301 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340100010302 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010303 NMT1-like family; Region: NMT1_2; cl15260 340100010304 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100010305 Helix-turn-helix domains; Region: HTH; cl00088 340100010306 DNA-binding interface [nucleotide binding]; DNA binding site 340100010307 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100010308 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 340100010309 Conserved TM helix; Region: TM_helix; pfam05552 340100010310 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100010311 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 340100010312 Imelysin; Region: Peptidase_M75; cl09159 340100010313 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 340100010314 Imelysin; Region: Peptidase_M75; cl09159 340100010315 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 340100010316 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100010317 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 340100010318 Dodecin; Region: Dodecin; cl01328 340100010319 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 340100010320 MutS domain I; Region: MutS_I; pfam01624 340100010321 MutS domain II; Region: MutS_II; pfam05188 340100010322 MutS family domain IV; Region: MutS_IV; pfam05190 340100010323 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 340100010324 Walker A/P-loop; other site 340100010325 ATP binding site [chemical binding]; other site 340100010326 Q-loop/lid; other site 340100010327 ABC transporter signature motif; other site 340100010328 Walker B; other site 340100010329 D-loop; other site 340100010330 H-loop/switch region; other site 340100010331 Cupin superfamily protein; Region: Cupin_4; pfam08007 340100010332 JmjC domain, hydroxylase; Region: JmjC; cl15814 340100010333 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 340100010334 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 340100010335 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340100010336 dihydrodipicolinate synthase; Region: dapA; TIGR00674 340100010337 dimer interface [polypeptide binding]; other site 340100010338 active site 340100010339 catalytic residue [active] 340100010340 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 340100010341 active site 340100010342 putative substrate binding region [chemical binding]; other site 340100010343 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 340100010344 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 340100010345 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340100010346 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 340100010347 active site 340100010348 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 340100010349 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 340100010350 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100010351 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100010352 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010353 short chain dehydrogenase; Provisional; Region: PRK12939 340100010354 NAD(P) binding site [chemical binding]; other site 340100010355 active site 340100010356 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 340100010357 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 340100010358 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 340100010359 putative active site [active] 340100010360 catalytic site [active] 340100010361 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 340100010362 putative active site [active] 340100010363 catalytic site [active] 340100010364 3-carboxy-cis,cis-muconate cycloisomerase; Provisional; Region: PRK09053 340100010365 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 340100010366 tetramer interface [polypeptide binding]; other site 340100010367 active site 340100010368 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 340100010369 sequence-specific DNA binding site [nucleotide binding]; other site 340100010370 salt bridge; other site 340100010371 Cupin domain; Region: Cupin_2; cl09118 340100010372 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010373 FAD dependent oxidoreductase; Region: DAO; pfam01266 340100010374 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100010375 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 340100010376 dimer interface [polypeptide binding]; other site 340100010377 conserved gate region; other site 340100010378 putative PBP binding loops; other site 340100010379 ABC-ATPase subunit interface; other site 340100010380 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 340100010381 dimer interface [polypeptide binding]; other site 340100010382 conserved gate region; other site 340100010383 putative PBP binding loops; other site 340100010384 ABC-ATPase subunit interface; other site 340100010385 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100010386 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 340100010387 substrate binding pocket [chemical binding]; other site 340100010388 membrane-bound complex binding site; other site 340100010389 hinge residues; other site 340100010390 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100010391 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100010392 Walker A/P-loop; other site 340100010393 ATP binding site [chemical binding]; other site 340100010394 Q-loop/lid; other site 340100010395 ABC transporter signature motif; other site 340100010396 Walker B; other site 340100010397 D-loop; other site 340100010398 H-loop/switch region; other site 340100010399 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 340100010400 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100010401 tetrameric interface [polypeptide binding]; other site 340100010402 NAD binding site [chemical binding]; other site 340100010403 catalytic residues [active] 340100010404 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cl00248 340100010405 substrate binding site [chemical binding]; other site 340100010406 dimerization interface [polypeptide binding]; other site 340100010407 active site 340100010408 calcium binding site [ion binding]; other site 340100010409 NMT1-like family; Region: NMT1_2; cl15260 340100010410 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100010411 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 340100010412 dimerization interface [polypeptide binding]; other site 340100010413 putative DNA binding site [nucleotide binding]; other site 340100010414 putative Zn2+ binding site [ion binding]; other site 340100010415 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_6; cd08899 340100010416 putative hydrophobic ligand binding site [chemical binding]; other site 340100010417 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 340100010418 putative substrate translocation pore; other site 340100010419 Propionate catabolism activator; Region: PrpR_N; pfam06506 340100010420 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 340100010421 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 340100010422 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 340100010423 Walker A motif; other site 340100010424 ATP binding site [chemical binding]; other site 340100010425 Walker B motif; other site 340100010426 arginine finger; other site 340100010427 Helix-turn-helix domains; Region: HTH; cl00088 340100010428 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010429 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010430 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010431 NMT1-like family; Region: NMT1_2; cl15260 340100010432 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 340100010433 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 340100010434 catalytic triad [active] 340100010435 conserved cis-peptide bond; other site 340100010436 dihydrolipoamide dehydrogenase; Validated; Region: PRK05976 340100010437 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100010438 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100010439 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 340100010440 E3 interaction surface; other site 340100010441 lipoyl attachment site [posttranslational modification]; other site 340100010442 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11857 340100010443 e3 binding domain; Region: E3_binding; pfam02817 340100010444 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 340100010445 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 340100010446 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 340100010447 alpha subunit interface [polypeptide binding]; other site 340100010448 TPP binding site [chemical binding]; other site 340100010449 heterodimer interface [polypeptide binding]; other site 340100010450 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100010451 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal; Region: OxoDH_E1alpha_N; pfam12573 340100010452 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 340100010453 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 340100010454 tetramer interface [polypeptide binding]; other site 340100010455 TPP-binding site [chemical binding]; other site 340100010456 heterodimer interface [polypeptide binding]; other site 340100010457 phosphorylation loop region [posttranslational modification] 340100010458 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100010459 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 340100010460 C-terminal domain interface [polypeptide binding]; other site 340100010461 GSH binding site (G-site) [chemical binding]; other site 340100010462 dimer interface [polypeptide binding]; other site 340100010463 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 340100010464 N-terminal domain interface [polypeptide binding]; other site 340100010465 dimer interface [polypeptide binding]; other site 340100010466 substrate binding pocket (H-site) [chemical binding]; other site 340100010467 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 340100010468 RNA binding surface [nucleotide binding]; other site 340100010469 MgtC family; Region: MgtC; pfam02308 340100010470 Fic/DOC family; Region: Fic; cl00960 340100010471 Predicted permease; Region: DUF318; pfam03773 340100010472 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 340100010473 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100010474 putative active site [active] 340100010475 metal binding site [ion binding]; metal-binding site 340100010476 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 340100010477 dimer interface [polypeptide binding]; other site 340100010478 FMN binding site [chemical binding]; other site 340100010479 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100010480 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100010481 outer membrane receptor FepA; Provisional; Region: PRK13528 340100010482 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 340100010483 N-terminal plug; other site 340100010484 ligand-binding site [chemical binding]; other site 340100010485 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100010486 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 340100010487 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 340100010488 Walker A/P-loop; other site 340100010489 ATP binding site [chemical binding]; other site 340100010490 Q-loop/lid; other site 340100010491 ABC transporter signature motif; other site 340100010492 Walker B; other site 340100010493 D-loop; other site 340100010494 H-loop/switch region; other site 340100010495 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 340100010496 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 340100010497 dimer interface [polypeptide binding]; other site 340100010498 conserved gate region; other site 340100010499 putative PBP binding loops; other site 340100010500 ABC-ATPase subunit interface; other site 340100010501 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 340100010502 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 340100010503 dimer interface [polypeptide binding]; other site 340100010504 conserved gate region; other site 340100010505 putative PBP binding loops; other site 340100010506 ABC-ATPase subunit interface; other site 340100010507 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100010508 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 340100010509 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 340100010510 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 340100010511 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 340100010512 putative active site [active] 340100010513 catalytic site [active] 340100010514 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 340100010515 putative domain interface [polypeptide binding]; other site 340100010516 putative active site [active] 340100010517 catalytic site [active] 340100010518 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 340100010519 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100010520 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 340100010521 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 340100010522 active site 340100010523 substrate binding site [chemical binding]; other site 340100010524 metal binding site [ion binding]; metal-binding site 340100010525 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 340100010526 dihydropteroate synthase; Region: DHPS; TIGR01496 340100010527 substrate binding pocket [chemical binding]; other site 340100010528 dimer interface [polypeptide binding]; other site 340100010529 inhibitor binding site; inhibition site 340100010530 FtsH Extracellular; Region: FtsH_ext; pfam06480 340100010531 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 340100010532 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 340100010533 Walker A motif; other site 340100010534 ATP binding site [chemical binding]; other site 340100010535 Walker B motif; other site 340100010536 arginine finger; other site 340100010537 Peptidase family M41; Region: Peptidase_M41; pfam01434 340100010538 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; cl15754 340100010539 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 340100010540 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 340100010541 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 340100010542 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 340100010543 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 340100010544 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 340100010545 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 340100010546 uracil-xanthine permease; Region: ncs2; TIGR00801 340100010547 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100010548 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 340100010549 dimer interface [polypeptide binding]; other site 340100010550 conserved gate region; other site 340100010551 putative PBP binding loops; other site 340100010552 ABC-ATPase subunit interface; other site 340100010553 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 340100010554 dimer interface [polypeptide binding]; other site 340100010555 conserved gate region; other site 340100010556 putative PBP binding loops; other site 340100010557 ABC-ATPase subunit interface; other site 340100010558 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 340100010559 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100010560 Walker A/P-loop; other site 340100010561 ATP binding site [chemical binding]; other site 340100010562 Q-loop/lid; other site 340100010563 ABC transporter signature motif; other site 340100010564 Walker B; other site 340100010565 D-loop; other site 340100010566 H-loop/switch region; other site 340100010567 TOBE domain; Region: TOBE_2; cl01440 340100010568 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010569 Helix-turn-helix domains; Region: HTH; cl00088 340100010570 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 340100010571 dimerization interface [polypeptide binding]; other site 340100010572 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 340100010573 catalytic core [active] 340100010574 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 340100010575 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010576 NAD(P) binding site [chemical binding]; other site 340100010577 active site 340100010578 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 340100010579 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100010580 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100010581 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 340100010582 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100010583 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100010584 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 340100010585 IMP binding site; other site 340100010586 dimer interface [polypeptide binding]; other site 340100010587 interdomain contacts; other site 340100010588 partial ornithine binding site; other site 340100010589 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 340100010590 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 340100010591 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 340100010592 catalytic site [active] 340100010593 subunit interface [polypeptide binding]; other site 340100010594 transaldolase-like protein; Provisional; Region: PTZ00411 340100010595 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 340100010596 active site 340100010597 dimer interface [polypeptide binding]; other site 340100010598 catalytic residue [active] 340100010599 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 340100010600 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100010601 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 340100010602 dimer interface [polypeptide binding]; other site 340100010603 conserved gate region; other site 340100010604 putative PBP binding loops; other site 340100010605 ABC-ATPase subunit interface; other site 340100010606 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 340100010607 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100010608 Walker A/P-loop; other site 340100010609 ATP binding site [chemical binding]; other site 340100010610 Q-loop/lid; other site 340100010611 ABC transporter signature motif; other site 340100010612 Walker B; other site 340100010613 D-loop; other site 340100010614 H-loop/switch region; other site 340100010615 NMT1-like family; Region: NMT1_2; cl15260 340100010616 NMT1/THI5 like; Region: NMT1; pfam09084 340100010617 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010618 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010619 recombination protein RecR; Reviewed; Region: recR; PRK00076 340100010620 RecR protein; Region: RecR; pfam02132 340100010621 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 340100010622 putative active site [active] 340100010623 putative metal-binding site [ion binding]; other site 340100010624 tetramer interface [polypeptide binding]; other site 340100010625 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 340100010626 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 340100010627 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 340100010628 Walker A motif; other site 340100010629 ATP binding site [chemical binding]; other site 340100010630 Walker B motif; other site 340100010631 arginine finger; other site 340100010632 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 340100010633 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK12323 340100010634 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100010635 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 340100010636 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 340100010637 Family description; Region: UvrD_C_2; cl15862 340100010638 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 340100010639 probable DNA repair protein; Region: TIGR03623 340100010640 probable DNA repair protein; Region: TIGR03623 340100010641 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 340100010642 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100010643 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 340100010644 putative substrate translocation pore; other site 340100010645 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 340100010646 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100010647 Ribbon-helix-helix domain; Region: RHH_4; cl01775 340100010648 intracellular protease, PfpI family; Region: PfpI; TIGR01382 340100010649 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 340100010650 conserved cys residue [active] 340100010651 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 340100010652 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 340100010653 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 340100010654 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 340100010655 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 340100010656 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 340100010657 putative deacylase active site [active] 340100010658 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 340100010659 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 340100010660 DNA binding site [nucleotide binding] 340100010661 Int/Topo IB signature motif; other site 340100010662 active site 340100010663 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100010664 Helix-turn-helix domains; Region: HTH; cl00088 340100010665 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100010666 dimerization interface [polypeptide binding]; other site 340100010667 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100010668 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100010669 PYR/PP interface [polypeptide binding]; other site 340100010670 dimer interface [polypeptide binding]; other site 340100010671 TPP binding site [chemical binding]; other site 340100010672 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100010673 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 340100010674 TPP-binding site [chemical binding]; other site 340100010675 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 340100010676 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100010677 FAD binding site [chemical binding]; other site 340100010678 substrate binding pocket [chemical binding]; other site 340100010679 catalytic base [active] 340100010680 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 340100010681 putative active site [active] 340100010682 putative catalytic site [active] 340100010683 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 340100010684 4Fe-4S binding domain; Region: Fer4; cl02805 340100010685 4Fe-4S binding domain; Region: Fer4; cl02805 340100010686 These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer...; Region: CYPOR_like_FNR; cd06208 340100010687 dimerization interface [polypeptide binding]; other site 340100010688 FAD binding pocket [chemical binding]; other site 340100010689 FAD binding motif [chemical binding]; other site 340100010690 catalytic residues [active] 340100010691 NAD binding pocket [chemical binding]; other site 340100010692 phosphate binding motif [ion binding]; other site 340100010693 beta-alpha-beta structure motif; other site 340100010694 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 340100010695 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 340100010696 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 340100010697 substrate binding site [chemical binding]; other site 340100010698 oxyanion hole (OAH) forming residues; other site 340100010699 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 340100010700 oxyanion hole (OAH) forming residues; other site 340100010701 trimer interface [polypeptide binding]; other site 340100010702 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 340100010703 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 340100010704 non-specific DNA binding site [nucleotide binding]; other site 340100010705 salt bridge; other site 340100010706 sequence-specific DNA binding site [nucleotide binding]; other site 340100010707 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 340100010708 ADP binding site [chemical binding]; other site 340100010709 magnesium binding site [ion binding]; other site 340100010710 putative shikimate binding site; other site 340100010711 aldehyde dehydrogenase; Provisional; Region: PRK11903 340100010712 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 340100010713 NAD(P) binding site [chemical binding]; other site 340100010714 catalytic residues [active] 340100010715 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 340100010716 AMP-binding enzyme; Region: AMP-binding; cl15778 340100010717 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100010718 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100010719 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100010720 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 340100010721 putative ligand binding site [chemical binding]; other site 340100010722 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 340100010723 TM-ABC transporter signature motif; other site 340100010724 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 340100010725 TM-ABC transporter signature motif; other site 340100010726 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100010727 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100010728 Walker A/P-loop; other site 340100010729 ATP binding site [chemical binding]; other site 340100010730 Q-loop/lid; other site 340100010731 ABC transporter signature motif; other site 340100010732 Walker B; other site 340100010733 D-loop; other site 340100010734 H-loop/switch region; other site 340100010735 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100010736 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100010737 Walker A/P-loop; other site 340100010738 ATP binding site [chemical binding]; other site 340100010739 Q-loop/lid; other site 340100010740 ABC transporter signature motif; other site 340100010741 Walker B; other site 340100010742 D-loop; other site 340100010743 H-loop/switch region; other site 340100010744 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100010745 Helix-turn-helix domains; Region: HTH; cl00088 340100010746 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 340100010747 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100010748 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 340100010749 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100010750 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 340100010751 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 340100010752 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 340100010753 Helix-turn-helix domains; Region: HTH; cl00088 340100010754 transcriptional regulator; Provisional; Region: PRK10632 340100010755 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 340100010756 putative effector binding pocket; other site 340100010757 dimerization interface [polypeptide binding]; other site 340100010758 hypothetical protein; Validated; Region: PRK07586 340100010759 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100010760 PYR/PP interface [polypeptide binding]; other site 340100010761 dimer interface [polypeptide binding]; other site 340100010762 TPP binding site [chemical binding]; other site 340100010763 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 340100010764 TPP-binding site [chemical binding]; other site 340100010765 dimer interface [polypeptide binding]; other site 340100010766 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 340100010767 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010768 Helix-turn-helix domains; Region: HTH; cl00088 340100010769 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 340100010770 dimerization interface [polypeptide binding]; other site 340100010771 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010772 NMT1-like family; Region: NMT1_2; cl15260 340100010773 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100010774 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100010775 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 340100010776 Helix-turn-helix domains; Region: HTH; cl00088 340100010777 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100010778 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 340100010779 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 340100010780 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 340100010781 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100010782 AIR carboxylase; Region: AIRC; cl00310 340100010783 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 340100010784 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 340100010785 ATP binding site [chemical binding]; other site 340100010786 active site 340100010787 substrate binding site [chemical binding]; other site 340100010788 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 340100010789 hypothetical protein; Provisional; Region: PRK08185 340100010790 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 340100010791 intersubunit interface [polypeptide binding]; other site 340100010792 active site 340100010793 zinc binding site [ion binding]; other site 340100010794 Na+ binding site [ion binding]; other site 340100010795 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 340100010796 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 340100010797 rRNA binding site [nucleotide binding]; other site 340100010798 predicted 30S ribosome binding site; other site 340100010799 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 340100010800 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 340100010801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010802 NMT1-like family; Region: NMT1_2; cl15260 340100010803 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100010804 Helix-turn-helix domains; Region: HTH; cl00088 340100010805 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100010806 dimerization interface [polypeptide binding]; other site 340100010807 substrate binding pocket [chemical binding]; other site 340100010808 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100010809 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 340100010810 MPT binding site; other site 340100010811 trimer interface [polypeptide binding]; other site 340100010812 Phosphate transporter family; Region: PHO4; cl00396 340100010813 Phosphate transporter family; Region: PHO4; cl00396 340100010814 AzlC protein; Region: AzlC; cl00570 340100010815 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100010816 Coenzyme A binding pocket [chemical binding]; other site 340100010817 Mycothiol maleylpyruvate isomerase N-terminal domain; Region: MDMPI_N; cl00986 340100010818 glutathione S-transferase; Provisional; Region: PRK15113 340100010819 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 340100010820 C-terminal domain interface [polypeptide binding]; other site 340100010821 GSH binding site (G-site) [chemical binding]; other site 340100010822 dimer interface [polypeptide binding]; other site 340100010823 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100010824 dimer interface [polypeptide binding]; other site 340100010825 substrate binding pocket (H-site) [chemical binding]; other site 340100010826 N-terminal domain interface [polypeptide binding]; other site 340100010827 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 340100010828 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100010829 PHB de-polymerase C-terminus; Region: PHB_depo_C; cl14907 340100010830 cyanate hydratase; Validated; Region: PRK02866 340100010831 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 340100010832 oligomer interface [polypeptide binding]; other site 340100010833 active site 340100010834 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 340100010835 Phosphoglycerate kinase; Region: PGK; pfam00162 340100010836 substrate binding site [chemical binding]; other site 340100010837 hinge regions; other site 340100010838 ADP binding site [chemical binding]; other site 340100010839 catalytic site [active] 340100010840 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010841 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 340100010842 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 340100010843 transketolase; Reviewed; Region: PRK12753 340100010844 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 340100010845 TPP-binding site [chemical binding]; other site 340100010846 dimer interface [polypeptide binding]; other site 340100010847 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 340100010848 PYR/PP interface [polypeptide binding]; other site 340100010849 dimer interface [polypeptide binding]; other site 340100010850 TPP binding site [chemical binding]; other site 340100010851 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100010852 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 340100010853 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 340100010854 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 340100010855 putative RNAase interaction site [polypeptide binding]; other site 340100010856 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 340100010857 active site 340100010858 nucleophile elbow; other site 340100010859 malic enzyme; Reviewed; Region: PRK12862 340100010860 Malic enzyme, N-terminal domain; Region: malic; pfam00390 340100010861 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 340100010862 putative NAD(P) binding site [chemical binding]; other site 340100010863 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 340100010864 aminotransferase; Validated; Region: PRK07337 340100010865 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 340100010866 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100010867 homodimer interface [polypeptide binding]; other site 340100010868 catalytic residue [active] 340100010869 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100010870 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100010871 catalytic residue [active] 340100010872 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 340100010873 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 340100010874 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 340100010875 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 340100010876 [4Fe-4S] binding site [ion binding]; other site 340100010877 molybdopterin cofactor binding site; other site 340100010878 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 340100010879 molybdopterin cofactor binding site; other site 340100010880 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 340100010881 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 340100010882 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 340100010883 [2Fe-2S] cluster binding site [ion binding]; other site 340100010884 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 340100010885 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100010886 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 340100010887 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 340100010888 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100010889 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 340100010890 ANTAR domain; Region: ANTAR; cl04297 340100010891 siroheme synthase; Provisional; Region: cysG; PRK10637 340100010892 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010893 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 340100010894 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 340100010895 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100010896 active site 340100010897 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100010898 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 340100010899 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 340100010900 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 340100010901 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 340100010902 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 340100010903 Preprotein translocase subunit; Region: YajC; cl00806 340100010904 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 340100010905 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 340100010906 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 340100010907 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 340100010908 Protein export membrane protein; Region: SecD_SecF; cl14618 340100010909 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 340100010910 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 340100010911 Protein export membrane protein; Region: SecD_SecF; cl14618 340100010912 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100010913 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 340100010914 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 340100010915 substrate binding pocket [chemical binding]; other site 340100010916 PAP2_like proteins, Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS), the major...; Region: PAP2_lipid_A_1_phosphatase; cd03389 340100010917 active site 340100010918 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 340100010919 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 340100010920 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 340100010921 FeS/SAM binding site; other site 340100010922 TRAM domain; Region: TRAM; cl01282 340100010923 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 340100010924 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100010925 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 340100010926 FOG: CBS domain [General function prediction only]; Region: COG0517 340100010927 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 340100010928 Transporter associated domain; Region: CorC_HlyC; cl08393 340100010929 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 340100010930 putative active site [active] 340100010931 catalytic triad [active] 340100010932 putative dimer interface [polypeptide binding]; other site 340100010933 Helix-turn-helix domains; Region: HTH; cl00088 340100010934 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100010935 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 340100010936 putative effector binding pocket; other site 340100010937 putative dimerization interface [polypeptide binding]; other site 340100010938 DoxX; Region: DoxX; cl00976 340100010939 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 340100010940 short chain dehydrogenase; Provisional; Region: PRK12937 340100010941 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 340100010942 NADP binding site [chemical binding]; other site 340100010943 homodimer interface [polypeptide binding]; other site 340100010944 active site 340100010945 substrate binding site [chemical binding]; other site 340100010946 biotin synthase; Region: bioB; TIGR00433 340100010947 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 340100010948 FeS/SAM binding site; other site 340100010949 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 340100010950 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 340100010951 putative MFS family transporter protein; Provisional; Region: PRK03633 340100010952 putative substrate translocation pore; other site 340100010953 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 340100010954 catalytic triad [active] 340100010955 dimer interface [polypeptide binding]; other site 340100010956 AsmA family; Region: AsmA; pfam05170 340100010957 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100010958 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100010959 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100010960 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100010961 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 340100010962 trimer interface [polypeptide binding]; other site 340100010963 dimer interface [polypeptide binding]; other site 340100010964 putative active site [active] 340100010965 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 340100010966 MoaE interaction surface [polypeptide binding]; other site 340100010967 MoeB interaction surface [polypeptide binding]; other site 340100010968 thiocarboxylated glycine; other site 340100010969 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 340100010970 MoaE homodimer interface [polypeptide binding]; other site 340100010971 MoaD interaction [polypeptide binding]; other site 340100010972 active site residues [active] 340100010973 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 340100010974 MPT binding site; other site 340100010975 trimer interface [polypeptide binding]; other site 340100010976 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 340100010977 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 340100010978 dimer interface [polypeptide binding]; other site 340100010979 putative functional site; other site 340100010980 putative MPT binding site; other site 340100010981 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100010982 Helix-turn-helix domains; Region: HTH; cl00088 340100010983 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100010984 NMT1-like family; Region: NMT1_2; cl15260 340100010985 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010986 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010987 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 340100010988 substrate binding site [chemical binding]; other site 340100010989 oxyanion hole (OAH) forming residues; other site 340100010990 trimer interface [polypeptide binding]; other site 340100010991 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100010992 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100010993 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 340100010994 AMP-binding enzyme; Region: AMP-binding; cl15778 340100010995 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 340100010996 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 340100010997 FeS/SAM binding site; other site 340100010998 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 340100010999 Helix-turn-helix domains; Region: HTH; cl00088 340100011000 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011001 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100011002 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 340100011003 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a...; Region: TRX_Fd_NuoE_FDH_gamma; cd03081 340100011004 putative dimer interface [polypeptide binding]; other site 340100011005 [2Fe-2S] cluster binding site [ion binding]; other site 340100011006 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 340100011007 putative dimer interface [polypeptide binding]; other site 340100011008 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 340100011009 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 340100011010 SLBB domain; Region: SLBB; pfam10531 340100011011 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 340100011012 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 340100011013 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 340100011014 catalytic loop [active] 340100011015 iron binding site [ion binding]; other site 340100011016 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 340100011017 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 340100011018 [4Fe-4S] binding site [ion binding]; other site 340100011019 molybdopterin cofactor binding site; other site 340100011020 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 340100011021 molybdopterin cofactor binding site; other site 340100011022 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 340100011023 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 340100011024 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 340100011025 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 340100011026 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 340100011027 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 340100011028 S-adenosylmethionine binding site [chemical binding]; other site 340100011029 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 340100011030 Chromate transporter; Region: Chromate_transp; pfam02417 340100011031 Chromate transporter; Region: Chromate_transp; pfam02417 340100011032 threonine and homoserine efflux system; Provisional; Region: PRK10532 340100011033 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100011034 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 340100011035 putative NAD(P) binding site [chemical binding]; other site 340100011036 putative active site [active] 340100011037 N-formylglutamate amidohydrolase; Region: FGase; cl01522 340100011038 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 340100011039 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 340100011040 RNA polymerase sigma factor; Provisional; Region: PRK12547 340100011041 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100011042 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 340100011043 DNA binding residues [nucleotide binding] 340100011044 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 340100011045 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 340100011046 Protein of unknown function (DUF520); Region: DUF520; cl00723 340100011047 Copper resistance protein D; Region: CopD; cl00563 340100011048 integrase; Provisional; Region: PRK09692 340100011049 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 340100011050 active site 340100011051 Int/Topo IB signature motif; other site 340100011052 TrbM; Region: TrbM; cl06455 340100011053 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100011054 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100011055 catalytic residue [active] 340100011056 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 340100011057 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 340100011058 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 340100011059 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 340100011060 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 340100011061 Type IV secretion system proteins; Region: T4SS; pfam07996 340100011062 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340100011063 VirB8 protein; Region: VirB8; cl01500 340100011064 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100011065 VirB7 interaction site; other site 340100011066 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 340100011067 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 340100011068 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 340100011069 Walker A motif; other site 340100011070 hexamer interface [polypeptide binding]; other site 340100011071 ATP binding site [chemical binding]; other site 340100011072 Walker B motif; other site 340100011073 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100011074 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 340100011075 Walker A motif; other site 340100011076 ATP binding site [chemical binding]; other site 340100011077 Walker B motif; other site 340100011078 Helix-turn-helix domains; Region: HTH; cl00088 340100011079 putative transposase OrfB; Reviewed; Region: PHA02517 340100011080 HTH-like domain; Region: HTH_21; pfam13276 340100011081 Integrase core domain; Region: rve; cl01316 340100011082 Integrase core domain; Region: rve_3; cl15866 340100011083 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 340100011084 FCD domain; Region: FCD; cl11656 340100011085 glutathione reductase; Validated; Region: PRK06116 340100011086 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100011087 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100011088 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 340100011089 glutathionine S-transferase; Provisional; Region: PRK10542 340100011090 C-terminal domain interface [polypeptide binding]; other site 340100011091 GSH binding site (G-site) [chemical binding]; other site 340100011092 dimer interface [polypeptide binding]; other site 340100011093 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100011094 dimer interface [polypeptide binding]; other site 340100011095 N-terminal domain interface [polypeptide binding]; other site 340100011096 substrate binding pocket (H-site) [chemical binding]; other site 340100011097 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100011098 GST_N family, unknown subfamily 2; 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_2; cd03047 340100011099 putative C-terminal domain interface [polypeptide binding]; other site 340100011100 putative GSH binding site (G-site) [chemical binding]; other site 340100011101 putative dimer interface [polypeptide binding]; other site 340100011102 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100011103 putative N-terminal domain interface [polypeptide binding]; other site 340100011104 putative dimer interface [polypeptide binding]; other site 340100011105 putative substrate binding pocket (H-site) [chemical binding]; other site 340100011106 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100011107 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 340100011108 C-terminal domain interface [polypeptide binding]; other site 340100011109 GSH binding site (G-site) [chemical binding]; other site 340100011110 dimer interface [polypeptide binding]; other site 340100011111 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100011112 N-terminal domain interface [polypeptide binding]; other site 340100011113 dimer interface [polypeptide binding]; other site 340100011114 substrate binding pocket (H-site) [chemical binding]; other site 340100011115 Helix-turn-helix domains; Region: HTH; cl00088 340100011116 YCII-related domain; Region: YCII; cl00999 340100011117 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100011118 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 340100011119 active site 340100011120 dimer interface [polypeptide binding]; other site 340100011121 metal binding site [ion binding]; metal-binding site 340100011122 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340100011123 Helix-turn-helix domains; Region: HTH; cl00088 340100011124 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100011125 Integrase core domain; Region: rve; cl01316 340100011126 Integrase core domain; Region: rve_3; cl15866 340100011127 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340100011128 metal binding site [ion binding]; metal-binding site 340100011129 substrate binding pocket [chemical binding]; other site 340100011130 Dienelactone hydrolase family; Region: DLH; pfam01738 340100011131 Helix-turn-helix domains; Region: HTH; cl00088 340100011132 Winged helix-turn helix; Region: HTH_29; pfam13551 340100011133 Helix-turn-helix domains; Region: HTH; cl00088 340100011134 Integrase core domain; Region: rve; cl01316 340100011135 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 340100011136 Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO); Region: Rieske_RO_Alpha_BPDO_like; cd03472 340100011137 beta subunit interaction site [polypeptide binding]; other site 340100011138 alpha subunit interaction site [polypeptide binding]; other site 340100011139 iron-sulfur cluster [ion binding]; other site 340100011140 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 340100011141 beta subunit interface [polypeptide binding]; other site 340100011142 alpha subunit interface [polypeptide binding]; other site 340100011143 active site 340100011144 substrate binding site [chemical binding]; other site 340100011145 Fe binding site [ion binding]; other site 340100011146 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 340100011147 inter-subunit interface; other site 340100011148 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 340100011149 [2Fe-2S] cluster binding site [ion binding]; other site 340100011150 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 340100011151 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100011152 cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase; Region: BphB_TodD; TIGR03325 340100011153 cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)-like, classical (c) SDRs; Region: BphB-like_SDR_c; cd05348 340100011154 NAD binding site [chemical binding]; other site 340100011155 active site 340100011156 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 340100011157 iron-sulfur cluster [ion binding]; other site 340100011158 [2Fe-2S] cluster binding site [ion binding]; other site 340100011159 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 340100011160 hydrophobic ligand binding site; other site 340100011161 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 340100011162 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 340100011163 putative substrate translocation pore; other site 340100011164 metabolite-proton symporter; Region: 2A0106; TIGR00883 340100011165 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100011166 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100011167 Helix-turn-helix domains; Region: HTH; cl00088 340100011168 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100011169 The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_CbnR; cd08486 340100011170 dimerization interface [polypeptide binding]; other site 340100011171 putative substrate binding pocket [chemical binding]; other site 340100011172 chlorocatechol 1,2-dioxygenases (1,2-CCDs) (type II enzymes) are homodimeric intradiol dioxygenases that degrade chlorocatechols via the addition of molecular oxygen and the subsequent cleavage between two adjacent hydroxyl groups. This reaction is part...; Region: 1,2-CCD; cd03462 340100011173 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 340100011174 dimer interface [polypeptide binding]; other site 340100011175 active site 340100011176 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 340100011177 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100011178 octamer interface [polypeptide binding]; other site 340100011179 active site 340100011180 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011181 NMT1-like family; Region: NMT1_2; cl15260 340100011182 Dienelactone hydrolase family; Region: DLH; pfam01738 340100011183 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100011184 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 340100011185 active site 340100011186 dimer interface [polypeptide binding]; other site 340100011187 metal binding site [ion binding]; metal-binding site 340100011188 Helix-turn-helix domain; Region: HTH_18; pfam12833 340100011189 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100011190 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100011191 Walker A/P-loop; other site 340100011192 ATP binding site [chemical binding]; other site 340100011193 Q-loop/lid; other site 340100011194 ABC transporter signature motif; other site 340100011195 Walker B; other site 340100011196 D-loop; other site 340100011197 H-loop/switch region; other site 340100011198 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100011199 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100011200 Walker A/P-loop; other site 340100011201 ATP binding site [chemical binding]; other site 340100011202 Q-loop/lid; other site 340100011203 ABC transporter signature motif; other site 340100011204 Walker B; other site 340100011205 D-loop; other site 340100011206 H-loop/switch region; other site 340100011207 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 340100011208 TM-ABC transporter signature motif; other site 340100011209 Winged helix-turn helix; Region: HTH_29; pfam13551 340100011210 Integrase core domain; Region: rve; cl01316 340100011211 Integrase core domain; Region: rve_3; cl15866 340100011212 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 340100011213 Walker A motif; other site 340100011214 ATP binding site [chemical binding]; other site 340100011215 Walker B motif; other site 340100011216 Helix-turn-helix domains; Region: HTH; cl00088 340100011217 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 340100011218 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 340100011219 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 340100011220 Integrase core domain; Region: rve; cl01316 340100011221 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 340100011222 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 340100011223 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 340100011224 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 340100011225 Helix-turn-helix domains; Region: HTH; cl00088 340100011226 putative transposase OrfB; Reviewed; Region: PHA02517 340100011227 HTH-like domain; Region: HTH_21; pfam13276 340100011228 Integrase core domain; Region: rve; cl01316 340100011229 Integrase core domain; Region: rve_3; cl15866 340100011230 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 340100011231 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 340100011232 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100011233 Family description; Region: UvrD_C_2; cl15862 340100011234 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 340100011235 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 340100011236 dimer interface [polypeptide binding]; other site 340100011237 ssDNA binding site [nucleotide binding]; other site 340100011238 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100011239 Domain of unknown function (DUF3560); Region: DUF3560; pfam12083 340100011240 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100011241 MPN+ (JAMM) motif; other site 340100011242 Zinc-binding site [ion binding]; other site 340100011243 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340100011244 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 340100011245 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 340100011246 catalytic residues [active] 340100011247 central insert; other site 340100011248 Cytochrome C biogenesis protein; Region: CcmH; cl01179 340100011249 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 340100011250 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 340100011251 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 340100011252 binding surface 340100011253 TPR motif; other site 340100011254 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100011255 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 340100011256 putative transposase OrfB; Reviewed; Region: PHA02517 340100011257 HTH-like domain; Region: HTH_21; pfam13276 340100011258 Integrase core domain; Region: rve; cl01316 340100011259 Integrase core domain; Region: rve_3; cl15866 340100011260 Helix-turn-helix domains; Region: HTH; cl00088 340100011261 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 340100011262 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011263 active site 340100011264 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 340100011265 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100011266 Helix-turn-helix domains; Region: HTH; cl00088 340100011267 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100011268 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 340100011269 active site 340100011270 oxalacetate binding site [chemical binding]; other site 340100011271 citrylCoA binding site [chemical binding]; other site 340100011272 coenzyme A binding site [chemical binding]; other site 340100011273 catalytic triad [active] 340100011274 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100011275 active site 2 [active] 340100011276 active site 1 [active] 340100011277 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100011278 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011279 active site 340100011280 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100011281 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340100011282 NAD(P) binding site [chemical binding]; other site 340100011283 homotetramer interface [polypeptide binding]; other site 340100011284 homodimer interface [polypeptide binding]; other site 340100011285 active site 340100011286 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100011287 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011288 CoA-ligase; Region: Ligase_CoA; cl02894 340100011289 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100011290 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011291 NMT1-like family; Region: NMT1_2; cl15260 340100011292 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100011293 Flavin Reductases; Region: FlaRed; cl00801 340100011294 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 340100011295 Ligand binding site [chemical binding]; other site 340100011296 Electron transfer flavoprotein domain; Region: ETF; pfam01012 340100011297 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 340100011298 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 340100011299 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 340100011300 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011301 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 340100011302 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 340100011303 active site 340100011304 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 340100011305 non-specific DNA binding site [nucleotide binding]; other site 340100011306 salt bridge; other site 340100011307 sequence-specific DNA binding site [nucleotide binding]; other site 340100011308 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100011309 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 340100011310 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 340100011311 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011312 NMT1-like family; Region: NMT1_2; cl15260 340100011313 aspartate aminotransferase; Provisional; Region: PRK05764 340100011314 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 340100011315 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100011316 homodimer interface [polypeptide binding]; other site 340100011317 catalytic residue [active] 340100011318 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 340100011319 homotrimer interaction site [polypeptide binding]; other site 340100011320 putative active site [active] 340100011321 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011322 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011323 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100011324 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011325 DNA-binding site [nucleotide binding]; DNA binding site 340100011326 FCD domain; Region: FCD; cl11656 340100011327 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100011328 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100011329 PYR/PP interface [polypeptide binding]; other site 340100011330 dimer interface [polypeptide binding]; other site 340100011331 TPP binding site [chemical binding]; other site 340100011332 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 340100011333 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 340100011334 TPP-binding site [chemical binding]; other site 340100011335 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100011336 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011337 DNA-binding site [nucleotide binding]; DNA binding site 340100011338 FCD domain; Region: FCD; cl11656 340100011339 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011340 Helix-turn-helix domains; Region: HTH; cl00088 340100011341 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011342 Helix-turn-helix domains; Region: HTH; cl00088 340100011343 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100011344 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011345 DNA-binding site [nucleotide binding]; DNA binding site 340100011346 UTRA domain; Region: UTRA; cl01230 340100011347 NMT1-like family; Region: NMT1_2; cl15260 340100011348 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 340100011349 Fumarase C-terminus; Region: Fumerase_C; cl00795 340100011350 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011351 Helix-turn-helix domains; Region: HTH; cl00088 340100011352 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340100011353 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100011354 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 340100011355 active site 340100011356 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011357 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011358 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100011359 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100011360 DNA binding site [nucleotide binding] 340100011361 domain linker motif; other site 340100011362 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_10; cd06292 340100011363 putative dimerization interface [polypeptide binding]; other site 340100011364 putative ligand binding site [chemical binding]; other site 340100011365 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100011366 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100011367 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100011368 DctM-like transporters; Region: DctM; pfam06808 340100011369 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100011370 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 340100011371 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 340100011372 putative substrate translocation pore; other site 340100011373 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100011374 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 340100011375 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 340100011376 nitrate reductase, beta subunit; Region: narH; TIGR01660 340100011377 4Fe-4S binding domain; Region: Fer4; cl02805 340100011378 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 340100011379 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 340100011380 [4Fe-4S] binding site [ion binding]; other site 340100011381 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 340100011382 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 340100011383 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 340100011384 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 340100011385 molybdopterin cofactor binding site; other site 340100011386 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_5; cd07238 340100011387 dimer interface [polypeptide binding]; other site 340100011388 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100011389 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100011390 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 340100011391 FMN binding site [chemical binding]; other site 340100011392 substrate binding site [chemical binding]; other site 340100011393 putative catalytic residue [active] 340100011394 Cupin domain; Region: Cupin_2; cl09118 340100011395 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100011396 EamA-like transporter family; Region: EamA; cl01037 340100011397 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 340100011398 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 340100011399 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 340100011400 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 340100011401 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 340100011402 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 340100011403 Cytochrome c; Region: Cytochrom_C; cl11414 340100011404 Cytochrome c; Region: Cytochrom_C; cl11414 340100011405 putative acetyltransferase; Provisional; Region: PRK03624 340100011406 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100011407 Coenzyme A binding pocket [chemical binding]; other site 340100011408 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 340100011409 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 340100011410 N-terminal plug; other site 340100011411 ligand-binding site [chemical binding]; other site 340100011412 Protein of unknown function, DUF488; Region: DUF488; cl01246 340100011413 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; cl15754 340100011414 YceI-like domain; Region: YceI; cl01001 340100011415 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 340100011416 active site 340100011417 intersubunit interface [polypeptide binding]; other site 340100011418 Zn2+ binding site [ion binding]; other site 340100011419 amidase; Provisional; Region: PRK07486 340100011420 Amidase; Region: Amidase; cl11426 340100011421 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 340100011422 putative acetyltransferase; Provisional; Region: PRK03624 340100011423 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100011424 Coenzyme A binding pocket [chemical binding]; other site 340100011425 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 340100011426 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 340100011427 putative metal binding site [ion binding]; other site 340100011428 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 340100011429 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 340100011430 E-class dimer interface [polypeptide binding]; other site 340100011431 P-class dimer interface [polypeptide binding]; other site 340100011432 active site 340100011433 Cu2+ binding site [ion binding]; other site 340100011434 Zn2+ binding site [ion binding]; other site 340100011435 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 340100011436 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 340100011437 Walker A motif; other site 340100011438 ATP binding site [chemical binding]; other site 340100011439 Walker B motif; other site 340100011440 arginine finger; other site 340100011441 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340100011442 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 340100011443 putative dimer interface [polypeptide binding]; other site 340100011444 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 340100011445 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 340100011446 active site 340100011447 catalytic tetrad [active] 340100011448 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 340100011449 intersubunit interface [polypeptide binding]; other site 340100011450 active site 340100011451 Zn2+ binding site [ion binding]; other site 340100011452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011453 NMT1-like family; Region: NMT1_2; cl15260 340100011454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011455 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100011456 Cupin domain; Region: Cupin_2; cl09118 340100011457 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100011458 Helix-turn-helix domains; Region: HTH; cl00088 340100011459 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 340100011460 Domain of unknown function (DUF802); Region: DUF802; pfam05650 340100011461 hypothetical protein; Provisional; Region: PRK09040 340100011462 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100011463 ligand binding site [chemical binding]; other site 340100011464 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 340100011465 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100011466 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 340100011467 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 340100011468 active site 340100011469 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100011470 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011471 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011472 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100011473 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100011474 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100011475 Walker A/P-loop; other site 340100011476 ATP binding site [chemical binding]; other site 340100011477 Q-loop/lid; other site 340100011478 ABC transporter signature motif; other site 340100011479 Walker B; other site 340100011480 D-loop; other site 340100011481 H-loop/switch region; other site 340100011482 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100011483 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100011484 Walker A/P-loop; other site 340100011485 ATP binding site [chemical binding]; other site 340100011486 Q-loop/lid; other site 340100011487 ABC transporter signature motif; other site 340100011488 Walker B; other site 340100011489 D-loop; other site 340100011490 H-loop/switch region; other site 340100011491 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100011492 D-ala-D-ala transporter subunit; Provisional; Region: PRK09881 340100011493 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 340100011494 dimer interface [polypeptide binding]; other site 340100011495 conserved gate region; other site 340100011496 putative PBP binding loops; other site 340100011497 ABC-ATPase subunit interface; other site 340100011498 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 340100011499 dimer interface [polypeptide binding]; other site 340100011500 conserved gate region; other site 340100011501 putative PBP binding loops; other site 340100011502 ABC-ATPase subunit interface; other site 340100011503 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100011504 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_12; cd08491 340100011505 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100011506 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 340100011507 putative active site [active] 340100011508 catalytic residue [active] 340100011509 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100011510 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011511 DNA-binding site [nucleotide binding]; DNA binding site 340100011512 FCD domain; Region: FCD; cl11656 340100011513 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 340100011514 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011515 Helix-turn-helix domains; Region: HTH; cl00088 340100011516 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 340100011517 putative effector binding pocket; other site 340100011518 dimerization interface [polypeptide binding]; other site 340100011519 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 340100011520 Argininosuccinate lyase [Amino acid transport and metabolism]; Region: ArgH; COG0165 340100011521 active sites [active] 340100011522 tetramer interface [polypeptide binding]; other site 340100011523 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 340100011524 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100011525 NMT1-like family; Region: NMT1_2; cl15260 340100011526 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100011527 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100011528 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100011529 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100011530 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 340100011531 substrate binding pocket [chemical binding]; other site 340100011532 membrane-bound complex binding site; other site 340100011533 hinge residues; other site 340100011534 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 340100011535 selenophosphate synthetase; Provisional; Region: PRK00943 340100011536 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 340100011537 dimerization interface [polypeptide binding]; other site 340100011538 putative ATP binding site [chemical binding]; other site 340100011539 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 340100011540 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 340100011541 active site residue [active] 340100011542 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 340100011543 putative hydrophobic ligand binding site [chemical binding]; other site 340100011544 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100011545 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100011546 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100011547 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100011548 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 340100011549 Clp protease; Region: CLP_protease; pfam00574 340100011550 oligomer interface [polypeptide binding]; other site 340100011551 active site residues [active] 340100011552 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100011553 GST_N family, unknown subfamily 2; 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_2; cd03047 340100011554 putative C-terminal domain interface [polypeptide binding]; other site 340100011555 putative GSH binding site (G-site) [chemical binding]; other site 340100011556 putative dimer interface [polypeptide binding]; other site 340100011557 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100011558 putative N-terminal domain interface [polypeptide binding]; other site 340100011559 putative dimer interface [polypeptide binding]; other site 340100011560 putative substrate binding pocket (H-site) [chemical binding]; other site 340100011561 Protein of unknown function (DUF1470); Region: DUF1470; pfam07336 340100011562 CGNR zinc finger; Region: zf-CGNR; pfam11706 340100011563 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100011564 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100011565 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100011566 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100011567 enoyl-CoA hydratase; Provisional; Region: PRK06495 340100011568 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 340100011569 substrate binding site [chemical binding]; other site 340100011570 oxyanion hole (OAH) forming residues; other site 340100011571 trimer interface [polypeptide binding]; other site 340100011572 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100011573 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100011574 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100011575 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 340100011576 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011577 active site 340100011578 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100011579 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011580 active site 340100011581 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011582 NMT1-like family; Region: NMT1_2; cl15260 340100011583 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011584 Helix-turn-helix domains; Region: HTH; cl00088 340100011585 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100011586 putative dimerization interface [polypeptide binding]; other site 340100011587 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100011588 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 340100011589 active site 340100011590 putative glutathione S-transferase; Provisional; Region: PRK10357 340100011591 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 340100011592 putative C-terminal domain interface [polypeptide binding]; other site 340100011593 putative GSH binding site (G-site) [chemical binding]; other site 340100011594 putative dimer interface [polypeptide binding]; other site 340100011595 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 340100011596 dimer interface [polypeptide binding]; other site 340100011597 N-terminal domain interface [polypeptide binding]; other site 340100011598 putative substrate binding pocket (H-site) [chemical binding]; other site 340100011599 Flavin Reductases; Region: FlaRed; cl00801 340100011600 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011601 NMT1-like family; Region: NMT1_2; cl15260 340100011602 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011603 NMT1-like family; Region: NMT1_2; cl15260 340100011604 GAF domain; Region: GAF_2; pfam13185 340100011605 GAF domain; Region: GAF; cl15785 340100011606 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 340100011607 Helix-turn-helix domains; Region: HTH; cl00088 340100011608 short chain dehydrogenase; Provisional; Region: PRK12829 340100011609 classical (c) SDRs; Region: SDR_c; cd05233 340100011610 NAD(P) binding site [chemical binding]; other site 340100011611 active site 340100011612 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100011613 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 340100011614 putative ligand binding site [chemical binding]; other site 340100011615 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 340100011616 TM-ABC transporter signature motif; other site 340100011617 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 340100011618 TM-ABC transporter signature motif; other site 340100011619 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100011620 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100011621 Walker A/P-loop; other site 340100011622 ATP binding site [chemical binding]; other site 340100011623 Q-loop/lid; other site 340100011624 ABC transporter signature motif; other site 340100011625 Walker B; other site 340100011626 D-loop; other site 340100011627 H-loop/switch region; other site 340100011628 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100011629 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100011630 Walker A/P-loop; other site 340100011631 ATP binding site [chemical binding]; other site 340100011632 Q-loop/lid; other site 340100011633 ABC transporter signature motif; other site 340100011634 Walker B; other site 340100011635 D-loop; other site 340100011636 H-loop/switch region; other site 340100011637 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl15827 340100011638 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011639 NAD(P) binding site [chemical binding]; other site 340100011640 active site 340100011641 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 340100011642 active site 340100011643 Zn binding site [ion binding]; other site 340100011644 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011645 NMT1-like family; Region: NMT1_2; cl15260 340100011646 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011647 Helix-turn-helix domains; Region: HTH; cl00088 340100011648 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 340100011649 dimerization interface [polypeptide binding]; other site 340100011650 amino acid transporter; Region: 2A0306; TIGR00909 340100011651 Cupin domain; Region: Cupin_2; cl09118 340100011652 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100011653 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100011654 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100011655 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 340100011656 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100011657 putative active site [active] 340100011658 putative metal binding site [ion binding]; other site 340100011659 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 340100011660 intersubunit interface [polypeptide binding]; other site 340100011661 active site 340100011662 Zn2+ binding site [ion binding]; other site 340100011663 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011664 NMT1-like family; Region: NMT1_2; cl15260 340100011665 Flavin Reductases; Region: FlaRed; cl00801 340100011666 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011667 Helix-turn-helix domains; Region: HTH; cl00088 340100011668 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 340100011669 putative effector binding pocket; other site 340100011670 dimerization interface [polypeptide binding]; other site 340100011671 Response regulator receiver domain; Region: Response_reg; pfam00072 340100011672 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100011673 active site 340100011674 phosphorylation site [posttranslational modification] 340100011675 intermolecular recognition site; other site 340100011676 dimerization interface [polypeptide binding]; other site 340100011677 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100011678 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100011679 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100011680 active site 340100011681 phosphorylation site [posttranslational modification] 340100011682 intermolecular recognition site; other site 340100011683 dimerization interface [polypeptide binding]; other site 340100011684 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 340100011685 DNA binding residues [nucleotide binding] 340100011686 dimerization interface [polypeptide binding]; other site 340100011687 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 340100011688 Catalytic domain of Protein Kinases; Region: PKc; cd00180 340100011689 active site 340100011690 ATP binding site [chemical binding]; other site 340100011691 substrate binding site [chemical binding]; other site 340100011692 activation loop (A-loop); other site 340100011693 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100011694 Predicted ATPase [General function prediction only]; Region: COG3899 340100011695 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 340100011696 GAF domain; Region: GAF; cl15785 340100011697 PAS domain S-box; Region: sensory_box; TIGR00229 340100011698 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 340100011699 putative active site [active] 340100011700 heme pocket [chemical binding]; other site 340100011701 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 340100011702 dimer interface [polypeptide binding]; other site 340100011703 phosphorylation site [posttranslational modification] 340100011704 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 340100011705 ATP binding site [chemical binding]; other site 340100011706 Mg2+ binding site [ion binding]; other site 340100011707 G-X-G motif; other site 340100011708 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 340100011709 oligomerisation interface [polypeptide binding]; other site 340100011710 mobile loop; other site 340100011711 roof hairpin; other site 340100011712 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 340100011713 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 340100011714 ring oligomerisation interface [polypeptide binding]; other site 340100011715 ATP/Mg binding site [chemical binding]; other site 340100011716 stacking interactions; other site 340100011717 hinge regions; other site 340100011718 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 340100011719 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100011720 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 340100011721 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100011722 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 340100011723 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 340100011724 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100011725 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100011726 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100011727 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100011728 putative transposase OrfB; Reviewed; Region: PHA02517 340100011729 HTH-like domain; Region: HTH_21; pfam13276 340100011730 Integrase core domain; Region: rve; cl01316 340100011731 Integrase core domain; Region: rve_3; cl15866 340100011732 Helix-turn-helix domains; Region: HTH; cl00088 340100011733 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 340100011734 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 340100011735 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 340100011736 The starvation sensing protein RpsA from E.coli and its homologs are lactonizing enzymes whose putative targets are homoserine lactone (HSL)-derivative. They are part of the mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of...; Region: rpsA; cd03322 340100011737 putative active site pocket [active] 340100011738 putative metal binding site [ion binding]; other site 340100011739 SAF domain; Region: SAF; cl00555 340100011740 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 340100011741 Altronate dehydratase [Carbohydrate transport and metabolism]; Region: UxaA; COG2721 340100011742 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 340100011743 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100011744 short chain dehydrogenase; Provisional; Region: PRK06138 340100011745 human DHRS6-like, classical (c) SDRs; Region: DHRS6_like_SDR_c; cd05368 340100011746 NAD binding site [chemical binding]; other site 340100011747 homotetramer interface [polypeptide binding]; other site 340100011748 homodimer interface [polypeptide binding]; other site 340100011749 active site 340100011750 DctM-like transporters; Region: DctM; pfam06808 340100011751 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100011752 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100011753 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100011754 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100011755 L-idonate 5-dehydrogenase; Provisional; Region: PRK09880 340100011756 L-idonate 5-dehydrogenase; Region: idonate-5-DH; cd08232 340100011757 putative NAD(P) binding site [chemical binding]; other site 340100011758 catalytic Zn binding site [ion binding]; other site 340100011759 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100011760 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011761 DNA-binding site [nucleotide binding]; DNA binding site 340100011762 FCD domain; Region: FCD; cl11656 340100011763 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 340100011764 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 340100011765 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100011766 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 340100011767 active site 340100011768 dimer interface [polypeptide binding]; other site 340100011769 Competence-damaged protein; Region: CinA; cl00666 340100011770 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 340100011771 tetramer interfaces [polypeptide binding]; other site 340100011772 binuclear metal-binding site [ion binding]; other site 340100011773 thiamine monophosphate kinase; Provisional; Region: PRK05731 340100011774 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 340100011775 ATP binding site [chemical binding]; other site 340100011776 dimerization interface [polypeptide binding]; other site 340100011777 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 340100011778 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 340100011779 homopentamer interface [polypeptide binding]; other site 340100011780 active site 340100011781 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 340100011782 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 340100011783 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 340100011784 dimerization interface [polypeptide binding]; other site 340100011785 active site 340100011786 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100011787 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100011788 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 340100011789 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100011790 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100011791 4-hydroxybenzoyl-CoA reductase, alpha subunit; Region: 4hydrxCoA_A; TIGR03194 340100011792 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100011793 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100011794 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100011795 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100011796 NMT1-like family; Region: NMT1_2; cl15260 340100011797 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 340100011798 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100011799 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100011800 Helix-turn-helix domains; Region: HTH; cl00088 340100011801 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100011802 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 340100011803 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 340100011804 substrate binding pocket [chemical binding]; other site 340100011805 membrane-bound complex binding site; other site 340100011806 hinge residues; other site 340100011807 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 340100011808 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 340100011809 Walker A/P-loop; other site 340100011810 ATP binding site [chemical binding]; other site 340100011811 Q-loop/lid; other site 340100011812 ABC transporter signature motif; other site 340100011813 Walker B; other site 340100011814 D-loop; other site 340100011815 H-loop/switch region; other site 340100011816 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 340100011817 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 340100011818 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 340100011819 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 340100011820 putative active site; other site 340100011821 putative metal binding residues [ion binding]; other site 340100011822 signature motif; other site 340100011823 putative triphosphate binding site [ion binding]; other site 340100011824 CHAD domain; Region: CHAD; cl10506 340100011825 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 340100011826 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 340100011827 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100011828 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 340100011829 S-adenosylmethionine binding site [chemical binding]; other site 340100011830 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 340100011831 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 340100011832 active site 340100011833 (T/H)XGH motif; other site 340100011834 hypothetical protein; Provisional; Region: PRK13795 340100011835 Benzoate membrane transport protein; Region: BenE; pfam03594 340100011836 benzoate transporter; Region: benE; TIGR00843 340100011837 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 340100011838 AsmA family; Region: AsmA; pfam05170 340100011839 AsmA-like C-terminal region; Region: AsmA_2; cl15864 340100011840 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 340100011841 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 340100011842 active site 340100011843 purine riboside binding site [chemical binding]; other site 340100011844 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100011845 Helix-turn-helix domains; Region: HTH; cl00088 340100011846 Helix-turn-helix domains; Region: HTH; cl00088 340100011847 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 340100011848 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340100011849 Helix-turn-helix domains; Region: HTH; cl00088 340100011850 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 340100011851 FAD binding pocket [chemical binding]; other site 340100011852 FAD binding motif [chemical binding]; other site 340100011853 phosphate binding motif [ion binding]; other site 340100011854 NAD binding pocket [chemical binding]; other site 340100011855 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 340100011856 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 340100011857 NADP binding site [chemical binding]; other site 340100011858 dimer interface [polypeptide binding]; other site 340100011859 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011860 Helix-turn-helix domains; Region: HTH; cl00088 340100011861 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100011862 dimerization interface [polypeptide binding]; other site 340100011863 Helix-turn-helix domains; Region: HTH; cl00088 340100011864 HTH-like domain; Region: HTH_21; pfam13276 340100011865 Integrase core domain; Region: rve; cl01316 340100011866 Integrase core domain; Region: rve_3; cl15866 340100011867 HTH-like domain; Region: HTH_21; pfam13276 340100011868 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100011869 Integrase core domain; Region: rve; cl01316 340100011870 Integrase core domain; Region: rve_3; cl15866 340100011871 Helix-turn-helix domains; Region: HTH; cl00088 340100011872 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 340100011873 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 340100011874 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 340100011875 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 340100011876 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 340100011877 HsdM N-terminal domain; Region: HsdM_N; pfam12161 340100011878 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 340100011879 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011880 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 340100011881 Helix-turn-helix domains; Region: HTH; cl00088 340100011882 putative transposase OrfB; Reviewed; Region: PHA02517 340100011883 HTH-like domain; Region: HTH_21; pfam13276 340100011884 Integrase core domain; Region: rve; cl01316 340100011885 Integrase core domain; Region: rve_3; cl15866 340100011886 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 340100011887 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100011888 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 340100011889 ATP binding site [chemical binding]; other site 340100011890 putative Mg++ binding site [ion binding]; other site 340100011891 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100011892 nucleotide binding region [chemical binding]; other site 340100011893 ATP-binding site [chemical binding]; other site 340100011894 Predicted transcriptional regulator [Transcription]; Region: COG4190 340100011895 Helix-turn-helix domains; Region: HTH; cl00088 340100011896 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 340100011897 GTP-binding protein YchF; Reviewed; Region: PRK09601 340100011898 YchF GTPase; Region: YchF; cd01900 340100011899 G1 box; other site 340100011900 GTP/Mg2+ binding site [chemical binding]; other site 340100011901 Switch I region; other site 340100011902 G2 box; other site 340100011903 Switch II region; other site 340100011904 G3 box; other site 340100011905 G4 box; other site 340100011906 G5 box; other site 340100011907 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 340100011908 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 340100011909 putative substrate translocation pore; other site 340100011910 Predicted transcriptional regulator [Transcription]; Region: COG2345 340100011911 CAAX protease self-immunity; Region: Abi; cl00558 340100011912 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 340100011913 putative active site [active] 340100011914 catalytic residue [active] 340100011915 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 340100011916 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 340100011917 5S rRNA interface [nucleotide binding]; other site 340100011918 CTC domain interface [polypeptide binding]; other site 340100011919 L16 interface [polypeptide binding]; other site 340100011920 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 340100011921 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 340100011922 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100011923 active site 340100011924 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 340100011925 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 340100011926 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 340100011927 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 340100011928 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 340100011929 TPR motif; other site 340100011930 binding surface 340100011931 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 340100011932 binding surface 340100011933 TPR motif; other site 340100011934 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 340100011935 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 340100011936 DNA binding site [nucleotide binding] 340100011937 catalytic residue [active] 340100011938 H2TH interface [polypeptide binding]; other site 340100011939 putative catalytic residues [active] 340100011940 turnover-facilitating residue; other site 340100011941 intercalation triad [nucleotide binding]; other site 340100011942 8OG recognition residue [nucleotide binding]; other site 340100011943 putative reading head residues; other site 340100011944 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 340100011945 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 340100011946 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340100011947 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 340100011948 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011949 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011950 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 340100011951 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011952 Helix-turn-helix domains; Region: HTH; cl00088 340100011953 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 340100011954 putative effector binding pocket; other site 340100011955 putative dimerization interface [polypeptide binding]; other site 340100011956 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 340100011957 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 340100011958 motif II; other site 340100011959 NMT1-like family; Region: NMT1_2; cl15260 340100011960 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 340100011961 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1; Region: PLPDE_III_DSD_D-TA_like_1; cd06812 340100011962 dimer interface [polypeptide binding]; other site 340100011963 active site 340100011964 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100011965 substrate binding site [chemical binding]; other site 340100011966 catalytic residue [active] 340100011967 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 340100011968 homotrimer interaction site [polypeptide binding]; other site 340100011969 putative active site [active] 340100011970 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 340100011971 Helix-turn-helix domains; Region: HTH; cl00088 340100011972 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 340100011973 substrate binding pocket [chemical binding]; other site 340100011974 dimerization interface [polypeptide binding]; other site 340100011975 Cupin domain; Region: Cupin_2; cl09118 340100011976 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 340100011977 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 340100011978 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100011979 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100011980 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 340100011981 dimer interface [polypeptide binding]; other site 340100011982 phosphorylation site [posttranslational modification] 340100011983 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 340100011984 ATP binding site [chemical binding]; other site 340100011985 Mg2+ binding site [ion binding]; other site 340100011986 G-X-G motif; other site 340100011987 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100011988 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100011989 active site 340100011990 phosphorylation site [posttranslational modification] 340100011991 intermolecular recognition site; other site 340100011992 dimerization interface [polypeptide binding]; other site 340100011993 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 340100011994 DNA binding site [nucleotide binding] 340100011995 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100011996 FAD binding domain; Region: FAD_binding_4; pfam01565 340100011997 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 340100011998 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 340100011999 active site 340100012000 substrate binding site [chemical binding]; other site 340100012001 metal binding site [ion binding]; metal-binding site 340100012002 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 340100012003 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 340100012004 active site 340100012005 dimer interface [polypeptide binding]; other site 340100012006 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 340100012007 dimer interface [polypeptide binding]; other site 340100012008 active site 340100012009 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 340100012010 putative ADP-binding pocket [chemical binding]; other site 340100012011 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 340100012012 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 340100012013 putative ADP-binding pocket [chemical binding]; other site 340100012014 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 340100012015 putative ADP-binding pocket [chemical binding]; other site 340100012016 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 340100012017 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 340100012018 active site 340100012019 dimer interface [polypeptide binding]; other site 340100012020 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 340100012021 Ligand Binding Site [chemical binding]; other site 340100012022 Molecular Tunnel; other site 340100012023 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100012024 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 340100012025 putative ADP-binding pocket [chemical binding]; other site 340100012026 MviN-like protein; Region: MVIN; pfam03023 340100012027 Vi polysaccharide biosynthesis protein TviC; Provisional; Region: PRK15181 340100012028 UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs; Region: UDP_AE_SDR_e; cd05256 340100012029 NAD binding site [chemical binding]; other site 340100012030 substrate binding site [chemical binding]; other site 340100012031 homodimer interface [polypeptide binding]; other site 340100012032 active site 340100012033 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 340100012034 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012035 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340100012036 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012037 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 340100012038 Mg++ binding site [ion binding]; other site 340100012039 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 340100012040 putative catalytic motif [active] 340100012041 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 340100012042 diiron binding motif [ion binding]; other site 340100012043 OsmC-like protein; Region: OsmC; cl00767 340100012044 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 340100012045 dimerization interface [polypeptide binding]; other site 340100012046 active site 340100012047 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 340100012048 folate binding site [chemical binding]; other site 340100012049 NADP+ binding site [chemical binding]; other site 340100012050 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 340100012051 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100012052 DNA-binding site [nucleotide binding]; DNA binding site 340100012053 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 340100012054 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012055 homodimer interface [polypeptide binding]; other site 340100012056 catalytic residue [active] 340100012057 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 340100012058 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 340100012059 inhibitor-cofactor binding pocket; inhibition site 340100012060 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012061 catalytic residue [active] 340100012062 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 340100012063 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100012064 tetrameric interface [polypeptide binding]; other site 340100012065 NAD binding site [chemical binding]; other site 340100012066 catalytic residues [active] 340100012067 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100012068 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100012069 MlrC C-terminus; Region: MlrC_C; pfam07171 340100012070 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_16; cd08502 340100012071 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100012072 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100012073 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 340100012074 dimer interface [polypeptide binding]; other site 340100012075 conserved gate region; other site 340100012076 putative PBP binding loops; other site 340100012077 ABC-ATPase subunit interface; other site 340100012078 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100012079 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 340100012080 dimer interface [polypeptide binding]; other site 340100012081 conserved gate region; other site 340100012082 putative PBP binding loops; other site 340100012083 ABC-ATPase subunit interface; other site 340100012084 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100012085 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100012086 Walker A/P-loop; other site 340100012087 ATP binding site [chemical binding]; other site 340100012088 Q-loop/lid; other site 340100012089 ABC transporter signature motif; other site 340100012090 Walker B; other site 340100012091 D-loop; other site 340100012092 H-loop/switch region; other site 340100012093 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100012094 Walker A/P-loop; other site 340100012095 ATP binding site [chemical binding]; other site 340100012096 Q-loop/lid; other site 340100012097 ABC transporter signature motif; other site 340100012098 Walker B; other site 340100012099 D-loop; other site 340100012100 H-loop/switch region; other site 340100012101 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100012102 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100012103 MlrC C-terminus; Region: MlrC_C; pfam07171 340100012104 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 340100012105 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339; cl15420 340100012106 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 340100012107 siroheme synthase, N-terminal domain; Region: cysG_Nterm; TIGR01470 340100012108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012109 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 340100012110 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 340100012111 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 340100012112 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 340100012113 ligand binding site [chemical binding]; other site 340100012114 flexible hinge region; other site 340100012115 Helix-turn-helix domains; Region: HTH; cl00088 340100012116 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 340100012117 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 340100012118 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 340100012119 Low-spin heme binding site [chemical binding]; other site 340100012120 D-pathway; other site 340100012121 Binuclear center (active site) [active] 340100012122 K-pathway; other site 340100012123 Putative proton exit pathway; other site 340100012124 Putative water exit pathway; other site 340100012125 Cytochrome c; Region: Cytochrom_C; cl11414 340100012126 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 340100012127 Subunit I/III interface [polypeptide binding]; other site 340100012128 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012129 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 340100012130 Cytochrome c; Region: Cytochrom_C; cl11414 340100012131 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 340100012132 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 340100012133 Domon-like ligand-binding domains; Region: DOMON_like; cl14783 340100012134 putative ligand binding site [chemical binding]; other site 340100012135 Domon-like ligand-binding domains; Region: DOMON_like; cl14783 340100012136 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 340100012137 Helix-turn-helix domains; Region: HTH; cl00088 340100012138 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100012139 Helix-turn-helix domains; Region: HTH; cl00088 340100012140 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100012141 Helix-turn-helix domains; Region: HTH; cl00088 340100012142 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 340100012143 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 340100012144 FeS/SAM binding site; other site 340100012145 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 340100012146 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 340100012147 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 340100012148 Cytochrome c; Region: Cytochrom_C; cl11414 340100012149 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 340100012150 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 340100012151 structural tetrad; other site 340100012152 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 340100012153 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012154 Walker A/P-loop; other site 340100012155 ATP binding site [chemical binding]; other site 340100012156 Q-loop/lid; other site 340100012157 ABC transporter signature motif; other site 340100012158 Walker B; other site 340100012159 D-loop; other site 340100012160 H-loop/switch region; other site 340100012161 CcmB protein; Region: CcmB; cl01016 340100012162 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340100012163 CcmE; Region: CcmE; cl00994 340100012164 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340100012165 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 340100012166 catalytic residues [active] 340100012167 central insert; other site 340100012168 Cytochrome C biogenesis protein; Region: CcmH; cl01179 340100012169 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 340100012170 binding surface 340100012171 TPR motif; other site 340100012172 glycine dehydrogenase; Provisional; Region: PRK05367 340100012173 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 340100012174 tetramer interface [polypeptide binding]; other site 340100012175 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012176 catalytic residue [active] 340100012177 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 340100012178 tetramer interface [polypeptide binding]; other site 340100012179 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012180 catalytic residue [active] 340100012181 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 340100012182 lipoyl attachment site [posttranslational modification]; other site 340100012183 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 340100012184 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 340100012185 ferredoxin-type protein; Provisional; Region: PRK10194 340100012186 4Fe-4S binding domain; Region: Fer4; cl02805 340100012187 NapD protein; Region: NapD; cl01163 340100012188 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 340100012189 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 340100012190 [4Fe-4S] binding site [ion binding]; other site 340100012191 molybdopterin cofactor binding site; other site 340100012192 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 340100012193 molybdopterin cofactor binding site; other site 340100012194 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 340100012195 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 340100012196 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100012197 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100012198 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 340100012199 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 340100012200 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 340100012201 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 340100012202 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 340100012203 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 340100012204 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 340100012205 HI0933-like protein; Region: HI0933_like; pfam03486 340100012206 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012207 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 340100012208 arginine decarboxylase; Provisional; Region: PRK15029 340100012209 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 340100012210 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100012211 catalytic residue [active] 340100012212 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 340100012213 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 340100012214 active site 340100012215 metal binding site [ion binding]; metal-binding site 340100012216 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340100012217 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 340100012218 trimer interface [polypeptide binding]; other site 340100012219 active site 340100012220 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 340100012221 Family of unknown function (DUF490); Region: DUF490; pfam04357 340100012222 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 340100012223 Surface antigen; Region: Bac_surface_Ag; cl03097 340100012224 Domain of unknown function DUF59; Region: DUF59; cl00941 340100012225 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 340100012226 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 340100012227 Walker A motif; other site 340100012228 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 340100012229 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 340100012230 active site 340100012231 HIGH motif; other site 340100012232 KMSKS motif; other site 340100012233 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 340100012234 tRNA binding surface [nucleotide binding]; other site 340100012235 anticodon binding site; other site 340100012236 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 340100012237 dimer interface [polypeptide binding]; other site 340100012238 putative tRNA-binding site [nucleotide binding]; other site 340100012239 rhodanese superfamily protein; Provisional; Region: PRK05320 340100012240 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 340100012241 active site residue [active] 340100012242 META domain; Region: META; cl01245 340100012243 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 340100012244 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100012245 active site 340100012246 phosphorylation site [posttranslational modification] 340100012247 intermolecular recognition site; other site 340100012248 dimerization interface [polypeptide binding]; other site 340100012249 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 340100012250 DNA binding site [nucleotide binding] 340100012251 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100012252 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 340100012253 Uncharacterized protein conserved in bacteria (DUF2094); Region: DUF2094; cl01611 340100012254 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 340100012255 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 340100012256 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 340100012257 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 340100012258 hypothetical protein; Provisional; Region: PRK07033 340100012259 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 340100012260 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100012261 ligand binding site [chemical binding]; other site 340100012262 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 340100012263 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 340100012264 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 340100012265 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 340100012266 phosphopeptide binding site; other site 340100012267 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 340100012268 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 340100012269 Walker A motif; other site 340100012270 ATP binding site [chemical binding]; other site 340100012271 Walker B motif; other site 340100012272 arginine finger; other site 340100012273 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 340100012274 Walker A motif; other site 340100012275 ATP binding site [chemical binding]; other site 340100012276 Walker B motif; other site 340100012277 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340100012278 Uncharacterized protein conserved in bacteria (DUF2195); Region: DUF2195; cl02042 340100012279 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 340100012280 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 340100012281 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 340100012282 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 340100012283 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 340100012284 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 340100012285 ImpE protein; Region: ImpE; pfam07024 340100012286 Protein of unknown function (DUF796); Region: DUF796; cl01226 340100012287 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 340100012288 Protein of unknown function (DUF877); Region: DUF877; pfam05943 340100012289 Protein of unknown function (DUF770); Region: DUF770; cl01402 340100012290 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 340100012291 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 340100012292 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 340100012293 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 340100012294 dimerization interface [polypeptide binding]; other site 340100012295 BON domain; Region: BON; cl02771 340100012296 Protein of unknwon function (DUF3008); Region: DUF3008; pfam11450 340100012297 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 340100012298 homotrimer interaction site [polypeptide binding]; other site 340100012299 putative active site [active] 340100012300 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100012301 minor groove reading motif; other site 340100012302 helix-hairpin-helix signature motif; other site 340100012303 substrate binding pocket [chemical binding]; other site 340100012304 active site 340100012305 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100012306 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012307 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 340100012308 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012309 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100012310 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340100012311 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100012312 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 340100012313 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 340100012314 dimer interface [polypeptide binding]; other site 340100012315 active site 340100012316 Fimbrial protein; Region: Fimbrial; cl01416 340100012317 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 340100012318 PapC N-terminal domain; Region: PapC_N; pfam13954 340100012319 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100012320 PapC C-terminal domain; Region: PapC_C; pfam13953 340100012321 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 340100012322 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 340100012323 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 340100012324 Fimbrial protein; Region: Fimbrial; cl01416 340100012325 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 340100012326 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100012327 conserved cys residue [active] 340100012328 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012329 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 340100012330 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 340100012331 tetramer interface [polypeptide binding]; other site 340100012332 heme binding pocket [chemical binding]; other site 340100012333 NADPH binding site [chemical binding]; other site 340100012334 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340100012335 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 340100012336 Isochorismatase family; Region: Isochorismatase; pfam00857 340100012337 catalytic triad [active] 340100012338 dimer interface [polypeptide binding]; other site 340100012339 conserved cis-peptide bond; other site 340100012340 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100012341 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100012342 Walker A/P-loop; other site 340100012343 ATP binding site [chemical binding]; other site 340100012344 Q-loop/lid; other site 340100012345 ABC transporter signature motif; other site 340100012346 Walker B; other site 340100012347 D-loop; other site 340100012348 H-loop/switch region; other site 340100012349 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 340100012350 dimer interface [polypeptide binding]; other site 340100012351 conserved gate region; other site 340100012352 putative PBP binding loops; other site 340100012353 ABC-ATPase subunit interface; other site 340100012354 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100012355 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 340100012356 dimer interface [polypeptide binding]; other site 340100012357 conserved gate region; other site 340100012358 putative PBP binding loops; other site 340100012359 ABC-ATPase subunit interface; other site 340100012360 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100012361 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 340100012362 substrate binding pocket [chemical binding]; other site 340100012363 membrane-bound complex binding site; other site 340100012364 hinge residues; other site 340100012365 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 340100012366 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 340100012367 active site residue [active] 340100012368 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic...; Region: 4RHOD_Repeat_2; cd01533 340100012369 active site residue [active] 340100012370 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 340100012371 active site residue [active] 340100012372 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 340100012373 active site residue [active] 340100012374 cystathionine beta-lyase, bacterial; Region: cysta_beta_ly_B; TIGR01324 340100012375 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 340100012376 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100012377 catalytic residue [active] 340100012378 Cysteine dioxygenase type I; Region: CDO_I; cl15835 340100012379 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012380 Helix-turn-helix domains; Region: HTH; cl00088 340100012381 The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; Region: PBP2_LrhA_like; cd08439 340100012382 putative dimerization interface [polypeptide binding]; other site 340100012383 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012384 Helix-turn-helix domains; Region: HTH; cl00088 340100012385 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 340100012386 dimerization interface [polypeptide binding]; other site 340100012387 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 340100012388 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012389 progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs; Region: 5beta-POR_like_SDR_a; cd08948 340100012390 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 340100012391 NAD(P) binding site [chemical binding]; other site 340100012392 active site 340100012393 NMT1-like family; Region: NMT1_2; cl15260 340100012394 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100012395 Strictosidine synthase; Region: Str_synth; pfam03088 340100012396 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100012397 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012398 Helix-turn-helix domains; Region: HTH; cl00088 340100012399 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 340100012400 putative dimerization interface [polypeptide binding]; other site 340100012401 Repair protein; Region: Repair_PSII; cl01535 340100012402 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 340100012403 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 340100012404 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; cl15373 340100012405 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340100012406 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100012407 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 340100012408 DNA binding residues [nucleotide binding] 340100012409 dimerization interface [polypeptide binding]; other site 340100012410 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100012411 DctM-like transporters; Region: DctM; pfam06808 340100012412 NMT1-like family; Region: NMT1_2; cl15260 340100012413 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100012414 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 340100012415 substrate binding site [chemical binding]; other site 340100012416 oxyanion hole (OAH) forming residues; other site 340100012417 trimer interface [polypeptide binding]; other site 340100012418 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100012419 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100012420 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012421 NMT1-like family; Region: NMT1_2; cl15260 340100012422 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012423 Helix-turn-helix domains; Region: HTH; cl00088 340100012424 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 340100012425 putative dimerization interface [polypeptide binding]; other site 340100012426 LysE type translocator; Region: LysE; cl00565 340100012427 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 340100012428 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 340100012429 molybdopterin cofactor binding site [chemical binding]; other site 340100012430 substrate binding site [chemical binding]; other site 340100012431 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 340100012432 molybdopterin cofactor binding site; other site 340100012433 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012434 NMT1-like family; Region: NMT1_2; cl15260 340100012435 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 340100012436 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100012437 putative NAD(P) binding site [chemical binding]; other site 340100012438 putative active site [active] 340100012439 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100012440 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340100012441 dimer interface [polypeptide binding]; other site 340100012442 active site 340100012443 catalytic residue [active] 340100012444 cystathionine beta-lyase; Provisional; Region: PRK09028 340100012445 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 340100012446 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100012447 catalytic residue [active] 340100012448 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 340100012449 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 340100012450 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012451 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 340100012452 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 340100012453 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 340100012454 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012455 Helix-turn-helix domains; Region: HTH; cl00088 340100012456 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 340100012457 dimerization interface [polypeptide binding]; other site 340100012458 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100012459 Helix-turn-helix domains; Region: HTH; cl00088 340100012460 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100012461 Helix-turn-helix domains; Region: HTH; cl00088 340100012462 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100012463 dimerization interface [polypeptide binding]; other site 340100012464 substrate binding pocket [chemical binding]; other site 340100012465 Predicted transcriptional regulator [Transcription]; Region: COG2378 340100012466 WYL domain; Region: WYL; cl14852 340100012467 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_c; cd10311 340100012468 putative active site [active] 340100012469 catalytic site [active] 340100012470 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 340100012471 ATP binding site [chemical binding]; other site 340100012472 putative Mg++ binding site [ion binding]; other site 340100012473 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 340100012474 nucleotide binding region [chemical binding]; other site 340100012475 ATP-binding site [chemical binding]; other site 340100012476 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 340100012477 metal ion-dependent adhesion site (MIDAS); other site 340100012478 Proteins of 100 residues with WXG; Region: WXG100; cl02005 340100012479 Transposase domain (DUF772); Region: DUF772; cl15789 340100012480 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 340100012481 Transposase domain (DUF772); Region: DUF772; cl15789 340100012482 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100012483 putative acyltransferase; Provisional; Region: PRK05790 340100012484 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 340100012485 dimer interface [polypeptide binding]; other site 340100012486 active site 340100012487 Transposase domain (DUF772); Region: DUF772; cl15789 340100012488 Transposase domain (DUF772); Region: DUF772; cl15789 340100012489 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 340100012490 Helix-turn-helix domains; Region: HTH; cl00088 340100012491 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100012492 Helix-turn-helix domains; Region: HTH; cl00088 340100012493 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 340100012494 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 340100012495 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100012496 Protein export membrane protein; Region: SecD_SecF; cl14618 340100012497 Protein export membrane protein; Region: SecD_SecF; cl14618 340100012498 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 340100012499 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 340100012500 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 340100012501 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 340100012502 Helix-turn-helix domains; Region: HTH; cl00088 340100012503 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100012504 Helix-turn-helix domains; Region: HTH; cl00088 340100012505 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 340100012506 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012507 NMT1-like family; Region: NMT1_2; cl15260 340100012508 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 340100012509 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 340100012510 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 340100012511 active site 340100012512 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 340100012513 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100012514 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100012515 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100012516 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 340100012517 DNA-binding site [nucleotide binding]; DNA binding site 340100012518 FCD domain; Region: FCD; cl11656 340100012519 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 340100012520 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 340100012521 active site 340100012522 catalytic tetrad [active] 340100012523 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 340100012524 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100012525 active site 340100012526 catalytic tetrad [active] 340100012527 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 340100012528 Transposase domain (DUF772); Region: DUF772; cl15789 340100012529 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100012530 Domain of unknown function DUF87; Region: DUF87; pfam01935 340100012531 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100012532 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100012533 Protein of unknown function (DUF2859); Region: DUF2859; cl12633 340100012534 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100012535 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 340100012536 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012537 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012538 H-loop/switch region; other site 340100012539 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012540 Walker A/P-loop; other site 340100012541 ATP binding site [chemical binding]; other site 340100012542 ABC transporter; Region: ABC_tran; pfam00005 340100012543 Q-loop/lid; other site 340100012544 ABC transporter signature motif; other site 340100012545 Walker B; other site 340100012546 D-loop; other site 340100012547 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 340100012548 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100012549 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a...; Region: ABCC_MRP_Like; cd03228 340100012550 Walker A/P-loop; other site 340100012551 ATP binding site [chemical binding]; other site 340100012552 Q-loop/lid; other site 340100012553 ABC transporter signature motif; other site 340100012554 Walker B; other site 340100012555 D-loop; other site 340100012556 H-loop/switch region; other site 340100012557 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 340100012558 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 340100012559 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 340100012560 ABC-ATPase subunit interface; other site 340100012561 dimer interface [polypeptide binding]; other site 340100012562 putative PBP binding regions; other site 340100012563 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 340100012564 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 340100012565 intersubunit interface [polypeptide binding]; other site 340100012566 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100012567 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 340100012568 N-terminal plug; other site 340100012569 ligand-binding site [chemical binding]; other site 340100012570 Cupin domain; Region: Cupin_2; cl09118 340100012571 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012572 Helix-turn-helix domain; Region: HTH_18; pfam12833 340100012573 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012575 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 340100012576 dimer interface [polypeptide binding]; other site 340100012577 ssDNA binding site [nucleotide binding]; other site 340100012578 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100012579 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100012580 ParB-like nuclease domain; Region: ParBc; cl02129 340100012581 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 340100012582 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100012583 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012584 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100012585 Helix-turn-helix domains; Region: HTH; cl00088 340100012586 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100012587 Helix-turn-helix domains; Region: HTH; cl00088 340100012588 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 340100012589 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340100012590 substrate binding pocket [chemical binding]; other site 340100012591 chain length determination region; other site 340100012592 substrate-Mg2+ binding site; other site 340100012593 catalytic residues [active] 340100012594 aspartate-rich region 1; other site 340100012595 active site lid residues [active] 340100012596 aspartate-rich region 2; other site 340100012597 Helix-turn-helix domains; Region: HTH; cl00088 340100012598 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100012599 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 340100012600 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 340100012601 Cupin domain; Region: Cupin_2; cl09118 340100012602 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 340100012603 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100012604 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012605 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100012606 dimerization interface [polypeptide binding]; other site 340100012607 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 340100012608 salt bridge; other site 340100012609 non-specific DNA binding site [nucleotide binding]; other site 340100012610 sequence-specific DNA binding site [nucleotide binding]; other site 340100012611 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012612 Helix-turn-helix domains; Region: HTH; cl00088 340100012613 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100012614 dimerization interface [polypeptide binding]; other site 340100012615 substrate binding pocket [chemical binding]; other site 340100012616 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 340100012617 Ligand Binding Site [chemical binding]; other site 340100012618 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 340100012619 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100012620 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100012621 dimerization interface [polypeptide binding]; other site 340100012622 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 340100012623 sequence-specific DNA binding site [nucleotide binding]; other site 340100012624 salt bridge; other site 340100012625 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100012626 Helix-turn-helix domains; Region: HTH; cl00088 340100012627 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100012628 dimerization interface [polypeptide binding]; other site 340100012629 substrate binding pocket [chemical binding]; other site 340100012630 Predicted transcriptional regulator [Transcription]; Region: COG2378 340100012631 WYL domain; Region: WYL; cl14852 340100012632 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_c; cd10311 340100012633 putative active site [active] 340100012634 catalytic site [active] 340100012635 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 340100012636 ATP binding site [chemical binding]; other site 340100012637 putative Mg++ binding site [ion binding]; other site 340100012638 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 340100012639 nucleotide binding region [chemical binding]; other site 340100012640 ATP-binding site [chemical binding]; other site 340100012641 Domain of unknown function (DUF4391); Region: DUF4391; pfam14335 340100012642 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012643 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012644 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012645 Restriction endonuclease [Defense mechanisms]; Region: COG3587 340100012646 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 340100012647 ATP binding site [chemical binding]; other site 340100012648 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 340100012649 metal ion-dependent adhesion site (MIDAS); other site 340100012650 Proteins of 100 residues with WXG; Region: WXG100; cl02005 340100012651 Integrase core domain; Region: rve_3; cl15866 340100012652 Helix-turn-helix domains; Region: HTH; cl00088 340100012653 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012654 CRISPR/Cas system-associated protein Csx1; Region: Csx1_III-U; cl11817 340100012655 Domain of unknown function (DUF1887); Region: DUF1887; pfam09002 340100012656 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 340100012657 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 340100012658 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100012659 active site 340100012660 ATP binding site [chemical binding]; other site 340100012661 substrate binding site [chemical binding]; other site 340100012662 activation loop (A-loop); other site 340100012663 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 340100012664 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012665 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012666 Family description; Region: UvrD_C_2; cl15862 340100012667 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 340100012668 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 340100012669 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 340100012670 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100012671 Putative helicase; Region: TraI_2; pfam07514 340100012672 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100012673 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340100012674 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 340100012675 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 340100012676 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100012677 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100012678 TraU protein; Region: TraU; cl06067 340100012679 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 340100012680 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100012681 MPN+ (JAMM) motif; other site 340100012682 Zinc-binding site [ion binding]; other site 340100012683 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100012684 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100012685 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100012686 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100012687 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 340100012688 Protein of unknown function (DUF2895); Region: DUF2895; cl12968 340100012689 Protein of unknown function (DUF3487); Region: DUF3487; cl13432 340100012690 Protein of unknown function (DUF2976); Region: DUF2976; cl12739 340100012691 Protein of unknown function (DUF3262); Region: DUF3262; cl13160 340100012692 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100012693 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100012694 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 340100012695 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100012696 Domain of unknown function DUF87; Region: DUF87; pfam01935 340100012697 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100012698 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100012699 Protein of unknown function (DUF2859); Region: DUF2859; cl12633 340100012700 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340100012701 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100012702 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100012703 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 340100012704 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012705 Family description; Region: UvrD_C_2; cl15862 340100012706 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 340100012707 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 340100012708 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012709 ABC transporter signature motif; other site 340100012710 Walker B; other site 340100012711 D-loop; other site 340100012712 H-loop/switch region; other site 340100012713 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 340100012714 putative active site [active] 340100012715 putative metal-binding site [ion binding]; other site 340100012716 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 340100012717 nucleotide binding region [chemical binding]; other site 340100012718 ATP-binding site [chemical binding]; other site 340100012719 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100012720 putative active site [active] 340100012721 putative NTP binding site [chemical binding]; other site 340100012722 putative nucleic acid binding site [nucleotide binding]; other site 340100012723 Type II intron maturase; Region: Intron_maturas2; pfam01348 340100012724 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012725 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100012726 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100012727 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100012728 putative active site [active] 340100012729 putative NTP binding site [chemical binding]; other site 340100012730 putative nucleic acid binding site [nucleotide binding]; other site 340100012731 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100012732 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 340100012733 active site 340100012734 Helix-turn-helix domains; Region: HTH; cl00088 340100012735 putative transposase OrfB; Reviewed; Region: PHA02517 340100012736 HTH-like domain; Region: HTH_21; pfam13276 340100012737 Integrase core domain; Region: rve; cl01316 340100012738 Integrase core domain; Region: rve_3; cl15866 340100012739 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100012740 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340100012741 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100012742 putative active site [active] 340100012743 putative NTP binding site [chemical binding]; other site 340100012744 putative nucleic acid binding site [nucleotide binding]; other site 340100012745 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100012746 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 340100012747 active site 340100012748 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100012749 Domain of unknown function (DUF932); Region: DUF932; cl12129 340100012750 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100012751 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100012752 DNA topoisomerase III; Provisional; Region: PRK07726 340100012753 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 340100012754 active site 340100012755 putative interdomain interaction site [polypeptide binding]; other site 340100012756 putative metal-binding site [ion binding]; other site 340100012757 putative nucleotide binding site [chemical binding]; other site 340100012758 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 340100012759 domain I; other site 340100012760 DNA binding groove [nucleotide binding] 340100012761 phosphate binding site [ion binding]; other site 340100012762 domain II; other site 340100012763 domain III; other site 340100012764 nucleotide binding site [chemical binding]; other site 340100012765 catalytic site [active] 340100012766 domain IV; other site 340100012767 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100012768 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 340100012769 ssDNA binding site [nucleotide binding]; other site 340100012770 dimer interface [polypeptide binding]; other site 340100012771 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100012772 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100012773 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 340100012774 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100012775 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100012776 ParB-like nuclease domain; Region: ParBc; cl02129 340100012777 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100012778 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 340100012779 Magnesium ion binding site [ion binding]; other site 340100012780 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100012781 integrase; Provisional; Region: PRK09692 340100012782 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 340100012783 active site 340100012784 Int/Topo IB signature motif; other site 340100012785 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012786 NMT1-like family; Region: NMT1_2; cl15260 340100012787 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100012788 active site 340100012789 catalytic residues [active] 340100012790 metal binding site [ion binding]; metal-binding site 340100012791 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100012792 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100012793 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012794 Helix-turn-helix domains; Region: HTH; cl00088 340100012795 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 340100012796 putative dimerization interface [polypeptide binding]; other site 340100012797 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; cl15754 340100012798 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 340100012799 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 340100012800 thiS-thiF/thiG interaction site; other site 340100012801 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012802 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 340100012803 BON domain; Region: BON; cl02771 340100012804 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340100012805 putative peptidoglycan binding site; other site 340100012806 signal recognition particle protein; Provisional; Region: PRK10867 340100012807 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 340100012808 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 340100012809 GTP binding site [chemical binding]; other site 340100012810 Signal peptide binding domain; Region: SRP_SPB; pfam02978 340100012811 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340100012812 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 340100012813 amidase catalytic site [active] 340100012814 Zn binding residues [ion binding]; other site 340100012815 substrate binding site [chemical binding]; other site 340100012816 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100012817 GST_N family, unknown subfamily 2; 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_2; cd03047 340100012818 putative C-terminal domain interface [polypeptide binding]; other site 340100012819 putative GSH binding site (G-site) [chemical binding]; other site 340100012820 putative dimer interface [polypeptide binding]; other site 340100012821 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100012822 putative N-terminal domain interface [polypeptide binding]; other site 340100012823 putative dimer interface [polypeptide binding]; other site 340100012824 putative substrate binding pocket (H-site) [chemical binding]; other site 340100012825 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100012826 Helix-turn-helix domains; Region: HTH; cl00088 340100012827 hypothetical protein; Provisional; Region: PRK07538 340100012828 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012829 Protein of unknown function (DUF3237); Region: DUF3237; cl07905 340100012830 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012831 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340100012832 DNA-binding interface [nucleotide binding]; DNA binding site 340100012833 HTH-like domain; Region: HTH_21; pfam13276 340100012834 Integrase core domain; Region: rve; cl01316 340100012835 Integrase core domain; Region: rve_3; cl15866 340100012836 NMT1-like family; Region: NMT1_2; cl15260 340100012837 heat shock protein 90; Provisional; Region: PRK05218 340100012838 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 340100012839 ATP binding site [chemical binding]; other site 340100012840 Mg2+ binding site [ion binding]; other site 340100012841 G-X-G motif; other site 340100012842 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100012843 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 340100012844 FMN-binding domain; Region: FMN_bind; cl01081 340100012845 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 340100012846 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100012847 nitrous-oxide reductase; Validated; Region: PRK02888 340100012848 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100012849 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 340100012850 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 340100012851 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340100012852 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 340100012853 Walker A/P-loop; other site 340100012854 ATP binding site [chemical binding]; other site 340100012855 Q-loop/lid; other site 340100012856 ABC transporter signature motif; other site 340100012857 Walker B; other site 340100012858 D-loop; other site 340100012859 H-loop/switch region; other site 340100012860 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340100012861 NosL; Region: NosL; cl01769 340100012862 ApbE family; Region: ApbE; cl00643 340100012863 HTH-like domain; Region: HTH_21; pfam13276 340100012864 Integrase core domain; Region: rve; cl01316 340100012865 Integrase core domain; Region: rve_3; cl15866 340100012866 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340100012867 DNA-binding interface [nucleotide binding]; DNA binding site 340100012868 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100012869 FAD binding domain; Region: FAD_binding_4; pfam01565 340100012870 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 340100012871 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 340100012872 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100012873 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100012874 DNA-binding site [nucleotide binding]; DNA binding site 340100012875 FCD domain; Region: FCD; cl11656 340100012876 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 340100012877 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 340100012878 homodimer interface [polypeptide binding]; other site 340100012879 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012880 catalytic residue [active] 340100012881 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012882 NMT1-like family; Region: NMT1_2; cl15260 340100012883 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100012884 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 340100012885 enoyl-CoA hydratase; Provisional; Region: PRK06127 340100012886 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 340100012887 substrate binding site [chemical binding]; other site 340100012888 oxyanion hole (OAH) forming residues; other site 340100012889 trimer interface [polypeptide binding]; other site 340100012890 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100012891 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100012892 nitrate transmembrane transporter; Provisional; Region: PLN00028 340100012893 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 340100012894 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100012895 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012896 Walker A/P-loop; other site 340100012897 ATP binding site [chemical binding]; other site 340100012898 Q-loop/lid; other site 340100012899 ABC transporter signature motif; other site 340100012900 Walker B; other site 340100012901 D-loop; other site 340100012902 H-loop/switch region; other site 340100012903 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100012904 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 340100012905 TM-ABC transporter signature motif; other site 340100012906 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 340100012907 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 340100012908 N- and C-terminal domain interface [polypeptide binding]; other site 340100012909 active site 340100012910 MgATP binding site [chemical binding]; other site 340100012911 catalytic site [active] 340100012912 metal binding site [ion binding]; metal-binding site 340100012913 carbohydrate binding site [chemical binding]; other site 340100012914 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 340100012915 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100012916 classical (c) SDRs; Region: SDR_c; cd05233 340100012917 NAD(P) binding site [chemical binding]; other site 340100012918 active site 340100012919 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100012920 DctM-like transporters; Region: DctM; pfam06808 340100012921 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100012922 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100012923 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100012924 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100012925 Helix-turn-helix domains; Region: HTH; cl00088 340100012926 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100012927 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 340100012928 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 340100012929 active site 340100012930 acyl-CoA synthetase; Validated; Region: PRK07470 340100012931 AMP-binding enzyme; Region: AMP-binding; cl15778 340100012932 Domain of unknown function (DUF296); Region: DUF296; cl00720 340100012933 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 340100012934 classical (c) SDRs; Region: SDR_c; cd05233 340100012935 NAD(P) binding site [chemical binding]; other site 340100012936 active site 340100012937 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 340100012938 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 340100012939 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340100012940 putative acyl-acceptor binding pocket; other site 340100012941 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340100012942 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340100012943 Predicted membrane protein [Function unknown]; Region: COG4648 340100012944 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 340100012945 AMP-binding enzyme; Region: AMP-binding; cl15778 340100012946 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 340100012947 active site 2 [active] 340100012948 active site 1 [active] 340100012949 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 340100012950 Ligand binding site; other site 340100012951 Putative Catalytic site; other site 340100012952 DXD motif; other site 340100012953 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340100012954 putative acyl-acceptor binding pocket; other site 340100012955 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 340100012956 active site 340100012957 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 340100012958 Predicted transcriptional regulator [Transcription]; Region: COG2932 340100012959 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100012960 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100012961 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 340100012962 Mu DNA binding, I gamma subdomain; Region: HTH_Tnp_Mu_2; pfam09039 340100012963 Integrase core domain; Region: rve; cl01316 340100012964 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 340100012965 Uncharacterized ATPase, putative transposase [General function prediction only]; Region: COG2842 340100012966 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100012967 Mu B transposition protein, C terminal; Region: Phage-MuB_C; pfam09077 340100012968 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 340100012969 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 340100012970 Mor transcription activator family; Region: Mor; cl02360 340100012971 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 340100012972 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100012973 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100012974 catalytic residue [active] 340100012975 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 340100012976 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 340100012977 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 340100012978 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 340100012979 Protein of unknown function (DUF935); Region: DUF935; pfam06074 340100012980 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 340100012981 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 340100012982 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 340100012983 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 340100012984 Domain of unknown function (DUF1834); Region: DUF1834; cl02087 340100012985 Protein of unknown function (DUF2635); Region: DUF2635; pfam10948 340100012986 Mu-like prophage tail sheath protein gpL [General function prediction only]; Region: COG4386 340100012987 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 340100012988 Phage tail tube protein; Region: Tail_tube; pfam10618 340100012989 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 340100012990 DNA circulation protein N-terminus; Region: DNA_circ_N; pfam07157 340100012991 Mu-like prophage DNA circulation protein [General function prediction only]; Region: COG4228 340100012992 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 340100012993 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 340100012994 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 340100012995 Phage protein GP46; Region: GP46; cl01814 340100012996 Baseplate J-like protein; Region: Baseplate_J; cl01294 340100012997 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 340100012998 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012999 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013000 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 340100013001 DNA binding site [nucleotide binding] 340100013002 Int/Topo IB signature motif; other site 340100013003 active site 340100013004 Predicted exporter [General function prediction only]; Region: COG4258 340100013005 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 340100013006 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013007 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 340100013008 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 340100013009 active site 340100013010 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 340100013011 putative active site 1 [active] 340100013012 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100013013 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013014 NAD(P) binding site [chemical binding]; other site 340100013015 active site 340100013016 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 340100013017 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 340100013018 dimer interface [polypeptide binding]; other site 340100013019 active site 340100013020 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013021 NMT1-like family; Region: NMT1_2; cl15260 340100013022 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013023 Helix-turn-helix domains; Region: HTH; cl00088 340100013024 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 340100013025 dimerization interface [polypeptide binding]; other site 340100013026 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100013027 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340100013028 Walker A/P-loop; other site 340100013029 ATP binding site [chemical binding]; other site 340100013030 Q-loop/lid; other site 340100013031 ABC transporter signature motif; other site 340100013032 Walker B; other site 340100013033 D-loop; other site 340100013034 H-loop/switch region; other site 340100013035 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100013036 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 340100013037 dimer interface [polypeptide binding]; other site 340100013038 conserved gate region; other site 340100013039 putative PBP binding loops; other site 340100013040 ABC-ATPase subunit interface; other site 340100013041 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 340100013042 dimer interface [polypeptide binding]; other site 340100013043 conserved gate region; other site 340100013044 putative PBP binding loops; other site 340100013045 ABC-ATPase subunit interface; other site 340100013046 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100013047 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 340100013048 substrate binding pocket [chemical binding]; other site 340100013049 membrane-bound complex binding site; other site 340100013050 hinge residues; other site 340100013051 aspartate aminotransferase; Provisional; Region: PRK05764 340100013052 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 340100013053 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100013054 homodimer interface [polypeptide binding]; other site 340100013055 catalytic residue [active] 340100013056 hypothetical protein; Validated; Region: PRK06201 340100013057 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 340100013058 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013059 Helix-turn-helix domains; Region: HTH; cl00088 340100013060 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 340100013061 putative dimerization interface [polypeptide binding]; other site 340100013062 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; cl09155 340100013063 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100013064 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100013065 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013066 NMT1-like family; Region: NMT1_2; cl15260 340100013067 Putative cyclase; Region: Cyclase; cl00814 340100013068 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 340100013069 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 340100013070 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100013071 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100013072 fec operon regulator FecR; Reviewed; Region: PRK09774 340100013073 FecR protein; Region: FecR; pfam04773 340100013074 Secretin and TonB N terminus short domain; Region: STN; cl06624 340100013075 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 340100013076 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 340100013077 N-terminal plug; other site 340100013078 ligand-binding site [chemical binding]; other site 340100013079 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100013080 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100013081 classical (c) SDRs; Region: SDR_c; cd05233 340100013082 NAD(P) binding site [chemical binding]; other site 340100013083 active site 340100013084 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013085 NMT1-like family; Region: NMT1_2; cl15260 340100013086 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 340100013087 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 340100013088 substrate binding pocket [chemical binding]; other site 340100013089 active site 340100013090 iron coordination sites [ion binding]; other site 340100013091 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100013092 Helix-turn-helix domains; Region: HTH; cl00088 340100013093 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100013094 dimerization interface [polypeptide binding]; other site 340100013095 substrate binding pocket [chemical binding]; other site 340100013096 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 340100013097 kynureninase; Region: kynureninase; TIGR01814 340100013098 Fimbrial protein; Region: Fimbrial; cl01416 340100013099 Fimbrial protein; Region: Fimbrial; cl01416 340100013100 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 340100013101 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 340100013102 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 340100013103 PapC N-terminal domain; Region: PapC_N; pfam13954 340100013104 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100013105 PapC C-terminal domain; Region: PapC_C; pfam13953 340100013106 Fimbrial protein; Region: Fimbrial; cl01416 340100013107 sensory histidine kinase AtoS; Provisional; Region: PRK11360 340100013108 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 340100013109 dimer interface [polypeptide binding]; other site 340100013110 phosphorylation site [posttranslational modification] 340100013111 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 340100013112 ATP binding site [chemical binding]; other site 340100013113 Mg2+ binding site [ion binding]; other site 340100013114 G-X-G motif; other site 340100013115 Response regulator receiver domain; Region: Response_reg; pfam00072 340100013116 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013117 active site 340100013118 phosphorylation site [posttranslational modification] 340100013119 intermolecular recognition site; other site 340100013120 dimerization interface [polypeptide binding]; other site 340100013121 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 340100013122 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100013123 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013124 active site 340100013125 phosphorylation site [posttranslational modification] 340100013126 intermolecular recognition site; other site 340100013127 dimerization interface [polypeptide binding]; other site 340100013128 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 340100013129 DNA binding residues [nucleotide binding] 340100013130 dimerization interface [polypeptide binding]; other site 340100013131 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 340100013132 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 340100013133 dimer interface [polypeptide binding]; other site 340100013134 phosphorylation site [posttranslational modification] 340100013135 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 340100013136 ATP binding site [chemical binding]; other site 340100013137 Mg2+ binding site [ion binding]; other site 340100013138 G-X-G motif; other site 340100013139 Response regulator receiver domain; Region: Response_reg; pfam00072 340100013140 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013141 active site 340100013142 phosphorylation site [posttranslational modification] 340100013143 intermolecular recognition site; other site 340100013144 dimerization interface [polypeptide binding]; other site 340100013145 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100013146 Helix-turn-helix domains; Region: HTH; cl00088 340100013147 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 340100013148 putative effector binding pocket; other site 340100013149 dimerization interface [polypeptide binding]; other site 340100013150 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 340100013151 dimer interface [polypeptide binding]; other site 340100013152 FMN binding site [chemical binding]; other site 340100013153 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100013154 EamA-like transporter family; Region: EamA; cl01037 340100013155 tartrate dehydrogenase; Provisional; Region: PRK08194 340100013156 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 340100013157 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013158 NMT1-like family; Region: NMT1_2; cl15260 340100013159 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100013160 Helix-turn-helix domains; Region: HTH; cl00088 340100013161 Helix-turn-helix domains; Region: HTH; cl00088 340100013162 putative transposase OrfB; Reviewed; Region: PHA02517 340100013163 HTH-like domain; Region: HTH_21; pfam13276 340100013164 Integrase core domain; Region: rve; cl01316 340100013165 Integrase core domain; Region: rve_3; cl15866 340100013166 Helix-turn-helix domains; Region: HTH; cl00088 340100013167 transcriptional activator TtdR; Provisional; Region: PRK09801 340100013168 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 340100013169 putative effector binding pocket; other site 340100013170 putative dimerization interface [polypeptide binding]; other site 340100013171 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 340100013172 ABC-ATPase subunit interface; other site 340100013173 dimer interface [polypeptide binding]; other site 340100013174 putative PBP binding regions; other site 340100013175 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 340100013176 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 340100013177 Walker A/P-loop; other site 340100013178 ATP binding site [chemical binding]; other site 340100013179 Q-loop/lid; other site 340100013180 ABC transporter signature motif; other site 340100013181 Walker B; other site 340100013182 D-loop; other site 340100013183 H-loop/switch region; other site 340100013184 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100013185 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_1; cd03326 340100013186 putative active site pocket [active] 340100013187 metal binding site [ion binding]; metal-binding site 340100013188 Helix-turn-helix domains; Region: HTH; cl00088 340100013189 cell density-dependent motility repressor; Provisional; Region: PRK10082 340100013190 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 340100013191 dimerization interface [polypeptide binding]; other site 340100013192 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 340100013193 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100013194 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 340100013195 lysine transporter; Provisional; Region: PRK10836 340100013196 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 340100013197 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100013198 active site 340100013199 catalytic tetrad [active] 340100013200 Helix-turn-helix domains; Region: HTH; cl00088 340100013201 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 340100013202 putative effector binding pocket; other site 340100013203 putative dimerization interface [polypeptide binding]; other site 340100013204 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100013205 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 340100013206 putative ligand binding site [chemical binding]; other site 340100013207 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 340100013208 TM-ABC transporter signature motif; other site 340100013209 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 340100013210 TM-ABC transporter signature motif; other site 340100013211 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100013212 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100013213 Walker A/P-loop; other site 340100013214 ATP binding site [chemical binding]; other site 340100013215 Q-loop/lid; other site 340100013216 ABC transporter signature motif; other site 340100013217 Walker B; other site 340100013218 D-loop; other site 340100013219 H-loop/switch region; other site 340100013220 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100013221 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100013222 Walker A/P-loop; other site 340100013223 ATP binding site [chemical binding]; other site 340100013224 Q-loop/lid; other site 340100013225 ABC transporter signature motif; other site 340100013226 Walker B; other site 340100013227 D-loop; other site 340100013228 H-loop/switch region; other site 340100013229 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100013230 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 340100013231 DNA binding site [nucleotide binding] 340100013232 Int/Topo IB signature motif; other site 340100013233 active site 340100013234 LysE type translocator; Region: LysE; cl00565 340100013235 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100013236 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100013237 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100013238 N-terminal domain interface [polypeptide binding]; other site 340100013239 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 340100013240 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 340100013241 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013242 Helix-turn-helix domains; Region: HTH; cl00088 340100013243 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 340100013244 putative effector binding pocket; other site 340100013245 putative dimerization interface [polypeptide binding]; other site 340100013246 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 340100013247 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 340100013248 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 340100013249 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 340100013250 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100013251 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 340100013252 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100013253 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]; Region: COG4091 340100013254 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013255 SAF domain; Region: SAF; cl00555 340100013256 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013257 Helix-turn-helix domains; Region: HTH; cl00088 340100013258 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100013259 dimerization interface [polypeptide binding]; other site 340100013260 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 340100013261 putative substrate translocation pore; other site 340100013262 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 340100013263 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100013264 active site 340100013265 catalytic tetrad [active] 340100013266 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013267 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100013268 NAD(P) binding site [chemical binding]; other site 340100013269 active site 340100013270 Dehydratase family; Region: ILVD_EDD; cl00340 340100013271 Helix-turn-helix domains; Region: HTH; cl00088 340100013272 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 340100013273 dimerization interface [polypeptide binding]; other site 340100013274 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 340100013275 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100013276 Coenzyme A binding pocket [chemical binding]; other site 340100013277 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100013278 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 340100013279 putative substrate translocation pore; other site 340100013280 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 340100013281 Ligand Binding Site [chemical binding]; other site 340100013282 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 340100013283 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 340100013284 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 340100013285 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013286 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100013287 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100013288 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100013289 classical (c) SDRs; Region: SDR_c; cd05233 340100013290 NAD(P) binding site [chemical binding]; other site 340100013291 active site 340100013292 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 340100013293 Helix-turn-helix domains; Region: HTH; cl00088 340100013294 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100013295 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100013296 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 340100013297 Muconolactone delta-isomerase; Region: MIase; cl01992 340100013298 YCII-related domain; Region: YCII; cl00999 340100013299 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100013300 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 340100013301 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100013302 Putative cyclase; Region: Cyclase; cl00814 340100013303 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 340100013304 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 340100013305 active site clefts [active] 340100013306 zinc binding site [ion binding]; other site 340100013307 dimer interface [polypeptide binding]; other site 340100013308 putative glutathione S-transferase; Provisional; Region: PRK10357 340100013309 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 340100013310 putative C-terminal domain interface [polypeptide binding]; other site 340100013311 putative GSH binding site (G-site) [chemical binding]; other site 340100013312 putative dimer interface [polypeptide binding]; other site 340100013313 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 340100013314 N-terminal domain interface [polypeptide binding]; other site 340100013315 dimer interface [polypeptide binding]; other site 340100013316 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 340100013317 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100013318 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100013319 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 340100013320 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 340100013321 Flavoprotein; Region: Flavoprotein; cl08021 340100013322 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 340100013323 putative GSH binding site [chemical binding]; other site 340100013324 catalytic residues [active] 340100013325 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 340100013326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013327 peptide chain release factor 1; Validated; Region: prfA; PRK00591 340100013328 RF-1 domain; Region: RF-1; cl02875 340100013329 RF-1 domain; Region: RF-1; cl02875 340100013330 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 340100013331 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 340100013332 tRNA; other site 340100013333 putative tRNA binding site [nucleotide binding]; other site 340100013334 putative NADP binding site [chemical binding]; other site 340100013335 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 340100013336 integrase; Provisional; Region: PRK09692 340100013337 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 340100013338 active site 340100013339 Int/Topo IB signature motif; other site 340100013340 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100013341 Protein of unknown function (DUF497); Region: DUF497; cl01108 340100013342 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 340100013343 Antirestriction protein; Region: Antirestrict; pfam03230 340100013344 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340100013345 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 340100013346 ArsC family; Region: ArsC; pfam03960 340100013347 catalytic residues [active] 340100013348 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 340100013349 Membrane transport protein; Region: Mem_trans; cl09117 340100013350 Low molecular weight phosphatase family; Region: LMWPc; cd00115 340100013351 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 340100013352 active site 340100013353 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 340100013354 dimerization interface [polypeptide binding]; other site 340100013355 putative DNA binding site [nucleotide binding]; other site 340100013356 putative Zn2+ binding site [ion binding]; other site 340100013357 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100013358 MPN+ (JAMM) motif; other site 340100013359 Zinc-binding site [ion binding]; other site 340100013360 ParB-like nuclease domain; Region: ParBc; cl02129 340100013361 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100013362 Protein of unknown function (DUF736); Region: DUF736; cl02303 340100013363 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 340100013364 non-specific DNA binding site [nucleotide binding]; other site 340100013365 salt bridge; other site 340100013366 sequence-specific DNA binding site [nucleotide binding]; other site 340100013367 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 340100013368 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 340100013369 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340100013370 Replication initiator protein A; Region: RPA; cl02339 340100013371 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100013372 AAA domain; Region: AAA_31; pfam13614 340100013373 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 340100013374 Walker A motif; other site 340100013375 ATP binding site [chemical binding]; other site 340100013376 P-loop; other site 340100013377 Magnesium ion binding site [ion binding]; other site 340100013378 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 340100013379 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 340100013380 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 340100013381 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 340100013382 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 340100013383 FtsI repressor; Provisional; Region: PRK10883 340100013384 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100013385 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100013386 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 340100013387 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340100013388 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 340100013389 motif II; other site 340100013390 Outer membrane efflux protein; Region: OEP; pfam02321 340100013391 Outer membrane efflux protein; Region: OEP; pfam02321 340100013392 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 340100013393 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 340100013394 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 340100013395 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 340100013396 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 340100013397 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100013398 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 340100013399 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100013400 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 340100013401 Protein of unknown function, DUF; Region: DUF411; cl01142 340100013402 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 340100013403 Cytochrome c; Region: Cytochrom_C; cl11414 340100013404 Copper resistance protein D; Region: CopD; cl00563 340100013405 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340100013406 DNA-binding interface [nucleotide binding]; DNA binding site 340100013407 HTH-like domain; Region: HTH_21; pfam13276 340100013408 Integrase core domain; Region: rve; cl01316 340100013409 Integrase core domain; Region: rve_3; cl15866 340100013410 Bacterial Ig-like domain; Region: Big_5; cl01012 340100013411 Domain of unknown function (DUF305); Region: DUF305; cl15795 340100013412 Protein of unknown function, DUF; Region: DUF411; cl01142 340100013413 multicopper oxidase; Provisional; Region: PRK10965 340100013414 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 340100013415 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 340100013416 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100013417 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100013418 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100013419 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340100013420 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 340100013421 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 340100013422 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 340100013423 dimer interface [polypeptide binding]; other site 340100013424 phosphorylation site [posttranslational modification] 340100013425 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 340100013426 ATP binding site [chemical binding]; other site 340100013427 Mg2+ binding site [ion binding]; other site 340100013428 G-X-G motif; other site 340100013429 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 340100013430 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013431 active site 340100013432 phosphorylation site [posttranslational modification] 340100013433 intermolecular recognition site; other site 340100013434 dimerization interface [polypeptide binding]; other site 340100013435 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 340100013436 DNA binding site [nucleotide binding] 340100013437 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100013438 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100013439 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100013440 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 340100013441 Cation efflux family; Region: Cation_efflux; cl00316 340100013442 YdjC-like protein; Region: YdjC; cl01344 340100013443 Helix-turn-helix domains; Region: HTH; cl00088 340100013444 Integrase core domain; Region: rve; cl01316 340100013445 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100013446 Integrase core domain; Region: rve_3; cl15866 340100013447 GtrA-like protein; Region: GtrA; cl00971 340100013448 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 340100013449 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 340100013450 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 340100013451 Ligand binding site; other site 340100013452 Putative Catalytic site; other site 340100013453 DXD motif; other site 340100013454 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 340100013455 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 340100013456 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 340100013457 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 340100013458 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 340100013459 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 340100013460 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013461 active site 340100013462 phosphorylation site [posttranslational modification] 340100013463 intermolecular recognition site; other site 340100013464 dimerization interface [polypeptide binding]; other site 340100013465 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 340100013466 DNA binding site [nucleotide binding] 340100013467 sensor kinase CusS; Provisional; Region: PRK09835 340100013468 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 340100013469 dimer interface [polypeptide binding]; other site 340100013470 phosphorylation site [posttranslational modification] 340100013471 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 340100013472 ATP binding site [chemical binding]; other site 340100013473 Mg2+ binding site [ion binding]; other site 340100013474 G-X-G motif; other site 340100013475 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013476 active site 340100013477 phosphorylation site [posttranslational modification] 340100013478 intermolecular recognition site; other site 340100013479 dimerization interface [polypeptide binding]; other site 340100013480 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 340100013481 DNA binding site [nucleotide binding] 340100013482 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 340100013483 trimer interface [polypeptide binding]; other site 340100013484 eyelet of channel; other site 340100013485 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100013486 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013487 Helix-turn-helix domains; Region: HTH; cl00088 340100013488 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 340100013489 dimerization interface [polypeptide binding]; other site 340100013490 substrate binding pocket [chemical binding]; other site 340100013491 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 340100013492 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100013493 Walker A motif; other site 340100013494 ATP binding site [chemical binding]; other site 340100013495 Walker B motif; other site 340100013496 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 340100013497 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 340100013498 ATP binding site [chemical binding]; other site 340100013499 Walker A motif; other site 340100013500 hexamer interface [polypeptide binding]; other site 340100013501 Walker B motif; other site 340100013502 TrbC/VIRB2 family; Region: TrbC; cl01583 340100013503 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 340100013504 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 340100013505 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 340100013506 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100013507 Walker A motif; other site 340100013508 ATP binding site [chemical binding]; other site 340100013509 Walker B motif; other site 340100013510 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 340100013511 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 340100013512 conjugal transfer protein TrbL; Provisional; Region: PRK13875 340100013513 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340100013514 VirB8 protein; Region: VirB8; cl01500 340100013515 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100013516 VirB7 interaction site; other site 340100013517 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 340100013518 Protein of unknown function (DUF2274); Region: DUF2274; cl02406 340100013519 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 340100013520 AAA domain; Region: AAA_23; pfam13476 340100013521 AAA domain; Region: AAA_13; pfam13166 340100013522 ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 340100013523 Q-loop/lid; other site 340100013524 ABC transporter signature motif; other site 340100013525 Walker B; other site 340100013526 D-loop; other site 340100013527 H-loop/switch region; other site 340100013528 putative transposase OrfB; Reviewed; Region: PHA02517 340100013529 HTH-like domain; Region: HTH_21; pfam13276 340100013530 Integrase core domain; Region: rve; cl01316 340100013531 Integrase core domain; Region: rve_3; cl15866 340100013532 Helix-turn-helix domains; Region: HTH; cl00088 340100013533 Helix-turn-helix domains; Region: HTH; cl00088 340100013534 putative transposase OrfB; Reviewed; Region: PHA02517 340100013535 HTH-like domain; Region: HTH_21; pfam13276 340100013536 Integrase core domain; Region: rve; cl01316 340100013537 Integrase core domain; Region: rve_3; cl15866 340100013538 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 340100013539 Domain of unknown function (DUF955); Region: DUF955; cl01076 340100013540 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 340100013541 non-specific DNA binding site [nucleotide binding]; other site 340100013542 salt bridge; other site 340100013543 sequence-specific DNA binding site [nucleotide binding]; other site 340100013544 two component system sensor kinase SsrA; Provisional; Region: PRK15347 340100013545 Amidase; Region: Amidase; cl11426 340100013546 Cupin domain; Region: Cupin_2; cl09118 340100013547 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100013548 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100013549 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100013550 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100013551 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 340100013552 dimer interface [polypeptide binding]; other site 340100013553 FMN binding site [chemical binding]; other site 340100013554 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 340100013555 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 340100013556 Trp docking motif [polypeptide binding]; other site 340100013557 putative active site [active] 340100013558 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100013559 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 340100013560 N-terminal plug; other site 340100013561 ligand-binding site [chemical binding]; other site 340100013562 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 340100013563 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 340100013564 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 340100013565 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 340100013566 tetramer interface [polypeptide binding]; other site 340100013567 active site 340100013568 Mg2+/Mn2+ binding site [ion binding]; other site 340100013569 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340100013570 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 340100013571 DNA binding site [nucleotide binding] 340100013572 active site 340100013573 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 340100013574 META domain; Region: META; cl01245 340100013575 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 340100013576 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 340100013577 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 340100013578 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100013579 dimerization interface [polypeptide binding]; other site 340100013580 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100013581 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 340100013582 Walker A/P-loop; other site 340100013583 ATP binding site [chemical binding]; other site 340100013584 Q-loop/lid; other site 340100013585 ABC transporter signature motif; other site 340100013586 Walker B; other site 340100013587 D-loop; other site 340100013588 H-loop/switch region; other site 340100013589 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 340100013590 Helix-turn-helix domains; Region: HTH; cl00088 340100013591 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100013592 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 340100013593 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 340100013594 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 340100013595 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 340100013596 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 340100013597 [4Fe-4S] binding site [ion binding]; other site 340100013598 molybdopterin cofactor binding site; other site 340100013599 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 340100013600 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 340100013601 molybdopterin cofactor binding site; other site 340100013602 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 340100013603 4Fe-4S binding domain; Region: Fer4; cl02805 340100013604 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100013605 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100013606 4Fe-4S binding domain; Region: Fer4; cl02805 340100013607 formate hydrogenlyase complex iron-sulfur subunit; Provisional; Region: PRK12387 340100013608 4Fe-4S binding domain; Region: Fer4; cl02805 340100013609 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 340100013610 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 340100013611 antiporter inner membrane protein; Provisional; Region: PRK11670 340100013612 Domain of unknown function DUF59; Region: DUF59; cl00941 340100013613 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 340100013614 Walker A motif; other site 340100013615 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 340100013616 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 340100013617 GTP binding site; other site 340100013618 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 340100013619 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 340100013620 dimer interface [polypeptide binding]; other site 340100013621 putative functional site; other site 340100013622 putative MPT binding site; other site 340100013623 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 340100013624 Walker A motif; other site 340100013625 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 340100013626 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 340100013627 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 340100013628 putative NADH binding site [chemical binding]; other site 340100013629 putative active site [active] 340100013630 nudix motif; other site 340100013631 putative metal binding site [ion binding]; other site 340100013632 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 340100013633 Sulfatase; Region: Sulfatase; cl10460 340100013634 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340100013635 substrate binding pocket [chemical binding]; other site 340100013636 chain length determination region; other site 340100013637 substrate-Mg2+ binding site; other site 340100013638 catalytic residues [active] 340100013639 aspartate-rich region 1; other site 340100013640 active site lid residues [active] 340100013641 aspartate-rich region 2; other site 340100013642 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 340100013643 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100013644 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100013645 Helix-turn-helix domains; Region: HTH; cl00088 340100013646 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 340100013647 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 340100013648 GTPase CgtA; Reviewed; Region: obgE; PRK12299 340100013649 GTP1/OBG; Region: GTP1_OBG; pfam01018 340100013650 Obg GTPase; Region: Obg; cd01898 340100013651 G1 box; other site 340100013652 GTP/Mg2+ binding site [chemical binding]; other site 340100013653 Switch I region; other site 340100013654 G2 box; other site 340100013655 G3 box; other site 340100013656 Switch II region; other site 340100013657 G4 box; other site 340100013658 G5 box; other site 340100013659 gamma-glutamyl kinase; Provisional; Region: PRK05429 340100013660 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 340100013661 nucleotide binding site [chemical binding]; other site 340100013662 homotetrameric interface [polypeptide binding]; other site 340100013663 putative phosphate binding site [ion binding]; other site 340100013664 putative allosteric binding site; other site 340100013665 PUA domain; Region: PUA; cl00607 340100013666 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100013667 Helix-turn-helix domains; Region: HTH; cl00088 340100013668 DNA binding site [nucleotide binding] 340100013669 bifunctional HTH-domain containing protein/aminotransferase; Provisional; Region: PRK13355 340100013670 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 340100013671 non-specific DNA binding site [nucleotide binding]; other site 340100013672 salt bridge; other site 340100013673 sequence-specific DNA binding site [nucleotide binding]; other site 340100013674 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 340100013675 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 340100013676 ThiC-associated domain; Region: ThiC-associated; pfam13667 340100013677 ThiC family; Region: ThiC; cl08031 340100013678 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 340100013679 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100013680 NAD(P) binding site [chemical binding]; other site 340100013681 catalytic residues [active] 340100013682 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100013683 FAD binding domain; Region: FAD_binding_4; pfam01565 340100013684 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100013685 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100013686 DNA-binding site [nucleotide binding]; DNA binding site 340100013687 FCD domain; Region: FCD; cl11656 340100013688 Isochorismatase family; Region: Isochorismatase; pfam00857 340100013689 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 340100013690 catalytic triad [active] 340100013691 conserved cis-peptide bond; other site 340100013692 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 340100013693 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100013694 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013695 Helix-turn-helix domains; Region: HTH; cl00088 340100013696 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013697 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 340100013698 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 340100013699 ATP binding site [chemical binding]; other site 340100013700 substrate interface [chemical binding]; other site 340100013701 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 340100013702 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 340100013703 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 340100013704 protein binding site [polypeptide binding]; other site 340100013705 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 340100013706 Catalytic dyad [active] 340100013707 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 340100013708 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100013709 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 340100013710 catalytic core [active] 340100013711 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 340100013712 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 340100013713 active site residue [active] 340100013714 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 340100013715 GSH binding site [chemical binding]; other site 340100013716 catalytic residues [active] 340100013717 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 340100013718 SecA binding site; other site 340100013719 Preprotein binding site; other site 340100013720 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 340100013721 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013722 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 340100013723 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013724 NMT1-like family; Region: NMT1_2; cl15260 340100013725 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100013726 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100013727 MlrC C-terminus; Region: MlrC_C; pfam07171 340100013728 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340100013729 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100013730 Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like; Region: ALDH_DhaS; cd07114 340100013731 NAD(P) binding site [chemical binding]; other site 340100013732 catalytic residues [active] 340100013733 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 340100013734 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100013735 active site 340100013736 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 340100013737 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 340100013738 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 340100013739 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 340100013740 Cation transport protein; Region: TrkH; cl10514 340100013741 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 340100013742 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 340100013743 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013744 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; cl15357 340100013745 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013746 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; cl15357 340100013747 Response regulator receiver domain; Region: Response_reg; pfam00072 340100013748 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013749 active site 340100013750 phosphorylation site [posttranslational modification] 340100013751 intermolecular recognition site; other site 340100013752 dimerization interface [polypeptide binding]; other site 340100013753 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 340100013754 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 340100013755 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 340100013756 dimerization interface [polypeptide binding]; other site 340100013757 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 340100013758 dimer interface [polypeptide binding]; other site 340100013759 phosphorylation site [posttranslational modification] 340100013760 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 340100013761 ATP binding site [chemical binding]; other site 340100013762 Mg2+ binding site [ion binding]; other site 340100013763 G-X-G motif; other site 340100013764 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 340100013765 16S rRNA methyltransferase B; Provisional; Region: PRK10901 340100013766 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; cl15754 340100013767 LysE type translocator; Region: LysE; cl00565 340100013768 transcriptional regulator; Provisional; Region: PRK10632 340100013769 Helix-turn-helix domains; Region: HTH; cl00088 340100013770 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 340100013771 putative effector binding pocket; other site 340100013772 putative dimerization interface [polypeptide binding]; other site 340100013773 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100013774 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 340100013775 putative C-terminal domain interface [polypeptide binding]; other site 340100013776 putative GSH binding site (G-site) [chemical binding]; other site 340100013777 putative dimer interface [polypeptide binding]; other site 340100013778 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 340100013779 putative N-terminal domain interface [polypeptide binding]; other site 340100013780 putative dimer interface [polypeptide binding]; other site 340100013781 putative substrate binding pocket (H-site) [chemical binding]; other site 340100013782 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340100013783 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340100013784 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 340100013785 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 340100013786 FAD binding pocket [chemical binding]; other site 340100013787 FAD binding motif [chemical binding]; other site 340100013788 phosphate binding motif [ion binding]; other site 340100013789 beta-alpha-beta structure motif; other site 340100013790 NAD binding pocket [chemical binding]; other site 340100013791 Heme binding pocket [chemical binding]; other site 340100013792 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 340100013793 catalytic loop [active] 340100013794 iron binding site [ion binding]; other site 340100013795 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100013796 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013797 NMT1-like family; Region: NMT1_2; cl15260 340100013798 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 340100013799 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013800 CoA-ligase; Region: Ligase_CoA; cl02894 340100013801 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340100013802 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 340100013803 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100013804 substrate binding site [chemical binding]; other site 340100013805 oxyanion hole (OAH) forming residues; other site 340100013806 trimer interface [polypeptide binding]; other site 340100013807 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100013808 Helix-turn-helix domains; Region: HTH; cl00088 340100013809 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 340100013810 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 340100013811 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 340100013812 FeS/SAM binding site; other site 340100013813 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100013814 Ferritin-like domain; Region: Ferritin; pfam00210 340100013815 dinuclear metal binding motif [ion binding]; other site 340100013816 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 340100013817 phosphoglycolate phosphatase; Provisional; Region: PRK13225 340100013818 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 340100013819 motif II; other site 340100013820 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 340100013821 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 340100013822 putative active site [active] 340100013823 substrate binding site [chemical binding]; other site 340100013824 putative cosubstrate binding site; other site 340100013825 catalytic site [active] 340100013826 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 340100013827 substrate binding site [chemical binding]; other site 340100013828 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 340100013829 active site 340100013830 catalytic residues [active] 340100013831 metal binding site [ion binding]; metal-binding site 340100013832 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 340100013833 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 340100013834 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100013835 active site 340100013836 catalytic residues [active] 340100013837 metal binding site [ion binding]; metal-binding site 340100013838 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 340100013839 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 340100013840 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100013841 homodimer interface [polypeptide binding]; other site 340100013842 catalytic residue [active] 340100013843 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 340100013844 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100013845 catalytic residue [active] 340100013846 Protein of unknown function (DUF461); Region: DUF461; cl01071 340100013847 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 340100013848 Helix-turn-helix domains; Region: HTH; cl00088 340100013849 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100013850 dimerization interface [polypeptide binding]; other site 340100013851 LysE type translocator; Region: LysE; cl00565 340100013852 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100013853 S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic...; Region: S15_NS1_EPRS_RNA-bind; cl00349 340100013854 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100013855 AMP-binding enzyme; Region: AMP-binding; cl15778 340100013856 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100013857 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100013858 Walker A/P-loop; other site 340100013859 ATP binding site [chemical binding]; other site 340100013860 Q-loop/lid; other site 340100013861 ABC transporter signature motif; other site 340100013862 Walker B; other site 340100013863 D-loop; other site 340100013864 H-loop/switch region; other site 340100013865 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 340100013866 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100013867 putative ligand binding site [chemical binding]; other site 340100013868 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 340100013869 TM-ABC transporter signature motif; other site 340100013870 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 340100013871 TM-ABC transporter signature motif; other site 340100013872 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100013873 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100013874 Walker A/P-loop; other site 340100013875 ATP binding site [chemical binding]; other site 340100013876 Q-loop/lid; other site 340100013877 ABC transporter signature motif; other site 340100013878 Walker B; other site 340100013879 D-loop; other site 340100013880 H-loop/switch region; other site 340100013881 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 340100013882 AMP-binding enzyme; Region: AMP-binding; cl15778 340100013883 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 340100013884 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 340100013885 ligand binding site [chemical binding]; other site 340100013886 flexible hinge region; other site 340100013887 Helix-turn-helix domains; Region: HTH; cl00088 340100013888 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 340100013889 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 340100013890 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100013891 active site 340100013892 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 340100013893 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100013894 Coenzyme A binding pocket [chemical binding]; other site 340100013895 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 340100013896 nucleotide binding site/active site [active] 340100013897 HIT family signature motif; other site 340100013898 catalytic residue [active] 340100013899 NnrS protein; Region: NnrS; cl01258 340100013900 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 340100013901 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 340100013902 substrate binding pocket [chemical binding]; other site 340100013903 membrane-bound complex binding site; other site 340100013904 hinge residues; other site 340100013905 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 340100013906 ligand binding site [chemical binding]; other site 340100013907 active site 340100013908 UGI interface [polypeptide binding]; other site 340100013909 catalytic site [active] 340100013910 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 340100013911 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 340100013912 ATP binding site [chemical binding]; other site 340100013913 Mg++ binding site [ion binding]; other site 340100013914 motif III; other site 340100013915 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 340100013916 nucleotide binding region [chemical binding]; other site 340100013917 ATP-binding site [chemical binding]; other site 340100013918 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 340100013919 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13297 340100013920 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 340100013921 active site 340100013922 NTP binding site [chemical binding]; other site 340100013923 metal binding triad [ion binding]; metal-binding site 340100013924 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 340100013925 lytic murein transglycosylase; Provisional; Region: PRK11619 340100013926 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340100013927 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100013928 catalytic residue [active] 340100013929 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 340100013930 Uncharacterized conserved protein [Function unknown]; Region: COG2308 340100013931 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 340100013932 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; cl00980 340100013933 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 340100013934 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 340100013935 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 340100013936 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 340100013937 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 340100013938 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 340100013939 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 340100013940 FAD binding site [chemical binding]; other site 340100013941 Membrane protein of unknown function; Region: DUF360; cl00850 340100013942 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 340100013943 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and...; Region: AdoHcyase; cd00401 340100013944 oligomerization interface [polypeptide binding]; other site 340100013945 active site 340100013946 NAD+ binding site [chemical binding]; other site 340100013947 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100013948 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100013949 active site 340100013950 phosphorylation site [posttranslational modification] 340100013951 intermolecular recognition site; other site 340100013952 dimerization interface [polypeptide binding]; other site 340100013953 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 340100013954 DNA binding residues [nucleotide binding] 340100013955 dimerization interface [polypeptide binding]; other site 340100013956 PAS domain; Region: PAS_9; pfam13426 340100013957 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 340100013958 putative active site [active] 340100013959 heme pocket [chemical binding]; other site 340100013960 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 340100013961 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 340100013962 ATP binding site [chemical binding]; other site 340100013963 Mg2+ binding site [ion binding]; other site 340100013964 G-X-G motif; other site 340100013965 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100013966 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100013967 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100013968 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100013969 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100013970 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100013971 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 340100013972 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 340100013973 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100013974 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 340100013975 substrate binding site [chemical binding]; other site 340100013976 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 340100013977 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 340100013978 substrate binding site [chemical binding]; other site 340100013979 ligand binding site [chemical binding]; other site 340100013980 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013981 NMT1-like family; Region: NMT1_2; cl15260 340100013982 Helix-turn-helix domains; Region: HTH; cl00088 340100013983 transcriptional activator TtdR; Provisional; Region: PRK09801 340100013984 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 340100013985 putative effector binding pocket; other site 340100013986 putative dimerization interface [polypeptide binding]; other site 340100013987 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100013988 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100013989 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013990 Helix-turn-helix domains; Region: HTH; cl00088 340100013991 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 340100013992 putative dimerization interface [polypeptide binding]; other site 340100013993 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013994 NMT1-like family; Region: NMT1_2; cl15260 340100013995 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 340100013996 active site 340100013997 catalytic site [active] 340100013998 S-adenosylmethionine synthetase; Validated; Region: PRK05250 340100013999 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 340100014000 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 340100014001 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 340100014002 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340100014003 putative acyl-acceptor binding pocket; other site 340100014004 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 340100014005 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340100014006 putative acyl-acceptor binding pocket; other site 340100014007 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 340100014008 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 340100014009 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 340100014010 GAF domain; Region: GAF; cl15785 340100014011 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 340100014012 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 340100014013 DNA binding site [nucleotide binding] 340100014014 Int/Topo IB signature motif; other site 340100014015 active site 340100014016 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 340100014017 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 340100014018 N-terminal plug; other site 340100014019 ligand-binding site [chemical binding]; other site 340100014020 High-affinity nickel-transport protein; Region: NicO; cl00964 340100014021 Protein of unknown function (DUF1007); Region: DUF1007; cl01487 340100014022 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 340100014023 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 340100014024 metal binding site [ion binding]; metal-binding site 340100014025 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 340100014026 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 340100014027 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 340100014028 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 340100014029 metal binding site 2 [ion binding]; metal-binding site 340100014030 putative DNA binding helix; other site 340100014031 metal binding site 1 [ion binding]; metal-binding site 340100014032 dimer interface [polypeptide binding]; other site 340100014033 structural Zn2+ binding site [ion binding]; other site 340100014034 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 340100014035 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 340100014036 P-loop, Walker A motif; other site 340100014037 Base recognition motif; other site 340100014038 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 340100014039 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 340100014040 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 340100014041 active site 340100014042 HslU subunit interaction site [polypeptide binding]; other site 340100014043 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 340100014044 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 340100014045 Walker A motif; other site 340100014046 ATP binding site [chemical binding]; other site 340100014047 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100014048 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340100014049 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 340100014050 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 340100014051 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 340100014052 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 340100014053 NAD binding site [chemical binding]; other site 340100014054 substrate binding site [chemical binding]; other site 340100014055 homodimer interface [polypeptide binding]; other site 340100014056 active site 340100014057 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 340100014058 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 340100014059 NADP binding site [chemical binding]; other site 340100014060 active site 340100014061 putative substrate binding site [chemical binding]; other site 340100014062 Cupin domain; Region: Cupin_2; cl09118 340100014063 lipoyl synthase; Provisional; Region: PRK05481 340100014064 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 340100014065 FeS/SAM binding site; other site 340100014066 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 340100014067 Protein of unknown function (DUF493); Region: DUF493; cl01102 340100014068 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 340100014069 homodimer interface [polypeptide binding]; other site 340100014070 substrate-cofactor binding pocket; other site 340100014071 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014072 catalytic residue [active] 340100014073 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 340100014074 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100014075 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 340100014076 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 340100014077 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340100014078 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 340100014079 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 340100014080 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 340100014081 Type III pantothenate kinase; Region: Pan_kinase; cl09130 340100014082 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 340100014083 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 340100014084 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 340100014085 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 340100014086 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 340100014087 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014088 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 340100014089 putative transposase OrfB; Reviewed; Region: PHA02517 340100014090 HTH-like domain; Region: HTH_21; pfam13276 340100014091 Integrase core domain; Region: rve; cl01316 340100014092 Integrase core domain; Region: rve_3; cl15866 340100014093 Helix-turn-helix domains; Region: HTH; cl00088 340100014094 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 340100014095 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 340100014096 putative trimer interface [polypeptide binding]; other site 340100014097 putative active site [active] 340100014098 putative substrate binding site [chemical binding]; other site 340100014099 putative CoA binding site [chemical binding]; other site 340100014100 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 340100014101 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 340100014102 inhibitor-cofactor binding pocket; inhibition site 340100014103 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014104 catalytic residue [active] 340100014105 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 340100014106 active site 340100014107 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 340100014108 homodimer interface [polypeptide binding]; other site 340100014109 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 340100014110 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 340100014111 Mg++ binding site [ion binding]; other site 340100014112 putative catalytic motif [active] 340100014113 putative substrate binding site [chemical binding]; other site 340100014114 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 340100014115 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 340100014116 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 340100014117 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 340100014118 Protein of unknown function (DUF2837); Region: DUF2837; pfam10997 340100014119 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 340100014120 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014121 NAD(P) binding site [chemical binding]; other site 340100014122 active site 340100014123 Helix-turn-helix domains; Region: HTH; cl00088 340100014124 putative transposase OrfB; Reviewed; Region: PHA02517 340100014125 HTH-like domain; Region: HTH_21; pfam13276 340100014126 Integrase core domain; Region: rve; cl01316 340100014127 Integrase core domain; Region: rve_3; cl15866 340100014128 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014129 active site 340100014130 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 340100014131 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 340100014132 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 340100014133 active site 340100014134 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 340100014135 homodimer interface [polypeptide binding]; other site 340100014136 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 340100014137 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 340100014138 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014139 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340100014140 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 340100014141 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340100014142 Walker A/P-loop; other site 340100014143 ATP binding site [chemical binding]; other site 340100014144 Q-loop/lid; other site 340100014145 ABC transporter signature motif; other site 340100014146 Walker B; other site 340100014147 D-loop; other site 340100014148 H-loop/switch region; other site 340100014149 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 340100014150 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014151 NAD(P) binding site [chemical binding]; other site 340100014152 active site 340100014153 O-Antigen ligase; Region: Wzy_C; cl04850 340100014154 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 340100014155 putative hydrophobic ligand binding site [chemical binding]; other site 340100014156 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 340100014157 putative substrate translocation pore; other site 340100014158 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 340100014159 EamA-like transporter family; Region: EamA; cl01037 340100014160 EamA-like transporter family; Region: EamA; cl01037 340100014161 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 340100014162 putative active site [active] 340100014163 catalytic site [active] 340100014164 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 340100014165 putative active site [active] 340100014166 catalytic site [active] 340100014167 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 340100014168 putative catalytic site [active] 340100014169 putative metal binding site [ion binding]; other site 340100014170 putative phosphate binding site [ion binding]; other site 340100014171 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 340100014172 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 340100014173 dimer interface [polypeptide binding]; other site 340100014174 anticodon binding site; other site 340100014175 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 340100014176 homodimer interface [polypeptide binding]; other site 340100014177 motif 1; other site 340100014178 active site 340100014179 motif 2; other site 340100014180 GAD domain; Region: GAD; pfam02938 340100014181 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 340100014182 motif 3; other site 340100014183 Protein of unknown function (DUF502); Region: DUF502; cl01107 340100014184 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 340100014185 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 340100014186 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 340100014187 choline dehydrogenase; Validated; Region: PRK02106 340100014188 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014189 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 340100014190 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 340100014191 S-adenosylmethionine binding site [chemical binding]; other site 340100014192 L-type amino acid transporter; Region: 2A0308; TIGR00911 340100014193 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 340100014194 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 340100014195 dimer interface [polypeptide binding]; other site 340100014196 active site 340100014197 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 340100014198 putative di-iron ligands [ion binding]; other site 340100014199 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 340100014200 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100014201 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340100014202 dimer interface [polypeptide binding]; other site 340100014203 active site 340100014204 catalytic residue [active] 340100014205 GAF domain; Region: GAF; cl15785 340100014206 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 340100014207 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 340100014208 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014209 homodimer interface [polypeptide binding]; other site 340100014210 catalytic residue [active] 340100014211 UbiA prenyltransferase family; Region: UbiA; cl00337 340100014212 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 340100014213 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100014214 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 340100014215 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014216 DNA-binding transcriptional regulator GlcC; Provisional; Region: PRK09990 340100014217 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100014218 DNA-binding site [nucleotide binding]; DNA binding site 340100014219 FCD domain; Region: FCD; cl11656 340100014220 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 340100014221 active site 340100014222 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100014223 Helix-turn-helix domains; Region: HTH; cl00088 340100014224 FCD domain; Region: FCD; cl11656 340100014225 Dehydratase family; Region: ILVD_EDD; cl00340 340100014226 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100014227 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014228 Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs; Region: Gne_like_SDR_e; cd05238 340100014229 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340100014230 putative NAD(P) binding site [chemical binding]; other site 340100014231 active site 340100014232 putative substrate binding site [chemical binding]; other site 340100014233 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100014234 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100014235 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100014236 DctM-like transporters; Region: DctM; pfam06808 340100014237 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 340100014238 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 340100014239 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 340100014240 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014241 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 340100014242 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100014243 substrate binding pocket [chemical binding]; other site 340100014244 membrane-bound complex binding site; other site 340100014245 hinge residues; other site 340100014246 Quinolinate synthetase A protein; Region: NadA; cl00420 340100014247 L-aspartate oxidase; Provisional; Region: PRK09077 340100014248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014249 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340100014250 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 340100014251 oligomerization interface [polypeptide binding]; other site 340100014252 active site 340100014253 metal binding site [ion binding]; metal-binding site 340100014254 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 340100014255 CoenzymeA binding site [chemical binding]; other site 340100014256 subunit interaction site [polypeptide binding]; other site 340100014257 PHB binding site; other site 340100014258 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 340100014259 putative FMN binding site [chemical binding]; other site 340100014260 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100014261 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100014262 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 340100014263 homotrimer interaction site [polypeptide binding]; other site 340100014264 putative active site [active] 340100014265 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 340100014266 acetylornithine deacetylase (ArgE); Region: AcOrn-deacetyl; TIGR01892 340100014267 metal binding site [ion binding]; metal-binding site 340100014268 putative dimer interface [polypeptide binding]; other site 340100014269 metabolite-proton symporter; Region: 2A0106; TIGR00883 340100014270 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 340100014271 putative substrate translocation pore; other site 340100014272 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 340100014273 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 340100014274 tetramer interface [polypeptide binding]; other site 340100014275 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014276 catalytic residue [active] 340100014277 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 340100014278 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 340100014279 AzlC protein; Region: AzlC; cl00570 340100014280 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100014281 NMT1-like family; Region: NMT1_2; cl15260 340100014282 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100014283 Amidase; Region: Amidase; cl11426 340100014284 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100014285 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100014286 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100014287 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 340100014288 Walker A/P-loop; other site 340100014289 ATP binding site [chemical binding]; other site 340100014290 Q-loop/lid; other site 340100014291 ABC transporter signature motif; other site 340100014292 Walker B; other site 340100014293 D-loop; other site 340100014294 H-loop/switch region; other site 340100014295 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100014296 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 340100014297 Walker A/P-loop; other site 340100014298 ATP binding site [chemical binding]; other site 340100014299 Q-loop/lid; other site 340100014300 ABC transporter signature motif; other site 340100014301 Walker B; other site 340100014302 D-loop; other site 340100014303 H-loop/switch region; other site 340100014304 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 340100014305 TM-ABC transporter signature motif; other site 340100014306 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 340100014307 TM-ABC transporter signature motif; other site 340100014308 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100014309 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100014310 DNA binding site [nucleotide binding] 340100014311 domain linker motif; other site 340100014312 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_7; cd06285 340100014313 putative dimerization interface [polypeptide binding]; other site 340100014314 putative ligand binding site [chemical binding]; other site 340100014315 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 340100014316 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 340100014317 putative heme binding pocket [chemical binding]; other site 340100014318 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100014319 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340100014320 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 340100014321 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100014322 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 340100014323 classical (c) SDRs; Region: SDR_c; cd05233 340100014324 NAD(P) binding site [chemical binding]; other site 340100014325 active site 340100014326 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 340100014327 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340100014328 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 340100014329 motif II; other site 340100014330 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 340100014331 dimer interface [polypeptide binding]; other site 340100014332 ssDNA binding site [nucleotide binding]; other site 340100014333 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100014334 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 340100014335 putative substrate translocation pore; other site 340100014336 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 340100014337 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 340100014338 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 340100014339 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 340100014340 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 340100014341 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100014342 putative C-terminal domain interface [polypeptide binding]; other site 340100014343 putative GSH binding site (G-site) [chemical binding]; other site 340100014344 putative dimer interface [polypeptide binding]; other site 340100014345 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 340100014346 putative substrate binding pocket (H-site) [chemical binding]; other site 340100014347 putative N-terminal domain interface [polypeptide binding]; other site 340100014348 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 340100014349 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 340100014350 Zn2+ binding site [ion binding]; other site 340100014351 Mg2+ binding site [ion binding]; other site 340100014352 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 340100014353 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 340100014354 active site 340100014355 dimer interface [polypeptide binding]; other site 340100014356 metal binding site [ion binding]; metal-binding site 340100014357 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 340100014358 shikimate kinase; Reviewed; Region: aroK; PRK00131 340100014359 ADP binding site [chemical binding]; other site 340100014360 magnesium binding site [ion binding]; other site 340100014361 putative shikimate binding site; other site 340100014362 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 340100014363 Transglycosylase; Region: Transgly; cl07896 340100014364 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340100014365 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 340100014366 putative iron binding site [ion binding]; other site 340100014367 diaminopimelate decarboxylase; Region: lysA; TIGR01048 340100014368 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 340100014369 active site 340100014370 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100014371 substrate binding site [chemical binding]; other site 340100014372 catalytic residues [active] 340100014373 dimer interface [polypeptide binding]; other site 340100014374 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340100014375 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 340100014376 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 340100014377 Cytochrome c; Region: Cytochrom_C; cl11414 340100014378 Cytochrome c; Region: Cytochrom_C; cl11414 340100014379 Predicted GTPase [General function prediction only]; Region: COG0218 340100014380 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 340100014381 G1 box; other site 340100014382 GTP/Mg2+ binding site [chemical binding]; other site 340100014383 Switch I region; other site 340100014384 G2 box; other site 340100014385 G3 box; other site 340100014386 Switch II region; other site 340100014387 G4 box; other site 340100014388 G5 box; other site 340100014389 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 340100014390 dimer interface [polypeptide binding]; other site 340100014391 active site 340100014392 aspartate-rich active site metal binding site; other site 340100014393 allosteric magnesium binding site [ion binding]; other site 340100014394 Schiff base residues; other site 340100014395 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 340100014396 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 340100014397 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 340100014398 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 340100014399 DsbD alpha interface [polypeptide binding]; other site 340100014400 catalytic residues [active] 340100014401 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 340100014402 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 340100014403 nucleotide binding site/active site [active] 340100014404 HIT family signature motif; other site 340100014405 catalytic residue [active] 340100014406 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 340100014407 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 340100014408 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 340100014409 alphaNTD homodimer interface [polypeptide binding]; other site 340100014410 alphaNTD - beta interaction site [polypeptide binding]; other site 340100014411 alphaNTD - beta' interaction site [polypeptide binding]; other site 340100014412 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 340100014413 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 340100014414 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 340100014415 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 340100014416 RNA binding surface [nucleotide binding]; other site 340100014417 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 340100014418 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 340100014419 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 340100014420 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 340100014421 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 340100014422 rRNA binding site [nucleotide binding]; other site 340100014423 predicted 30S ribosome binding site; other site 340100014424 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 340100014425 SecY translocase; Region: SecY; pfam00344 340100014426 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 340100014427 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 340100014428 23S rRNA binding site [nucleotide binding]; other site 340100014429 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 340100014430 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 340100014431 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 340100014432 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 340100014433 5S rRNA interface [nucleotide binding]; other site 340100014434 L27 interface [polypeptide binding]; other site 340100014435 23S rRNA interface [nucleotide binding]; other site 340100014436 L5 interface [polypeptide binding]; other site 340100014437 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 340100014438 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 340100014439 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 340100014440 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 340100014441 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 340100014442 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 340100014443 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 340100014444 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 340100014445 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 340100014446 KOW motif; Region: KOW; cl00354 340100014447 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 340100014448 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100014449 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100014450 tetramerization interface [polypeptide binding]; other site 340100014451 NAD(P) binding site [chemical binding]; other site 340100014452 catalytic residues [active] 340100014453 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 340100014454 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 340100014455 23S rRNA interface [nucleotide binding]; other site 340100014456 putative translocon interaction site; other site 340100014457 signal recognition particle (SRP54) interaction site; other site 340100014458 L23 interface [polypeptide binding]; other site 340100014459 trigger factor interaction site; other site 340100014460 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 340100014461 23S rRNA interface [nucleotide binding]; other site 340100014462 5S rRNA interface [nucleotide binding]; other site 340100014463 putative antibiotic binding site [chemical binding]; other site 340100014464 L25 interface [polypeptide binding]; other site 340100014465 L27 interface [polypeptide binding]; other site 340100014466 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 340100014467 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 340100014468 G-X-X-G motif; other site 340100014469 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 340100014470 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 340100014471 putative translocon binding site; other site 340100014472 protein-rRNA interface [nucleotide binding]; other site 340100014473 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 340100014474 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 340100014475 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 340100014476 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 340100014477 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 340100014478 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 340100014479 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 340100014480 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 340100014481 elongation factor Tu; Reviewed; Region: PRK00049 340100014482 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 340100014483 G1 box; other site 340100014484 GEF interaction site [polypeptide binding]; other site 340100014485 GTP/Mg2+ binding site [chemical binding]; other site 340100014486 Switch I region; other site 340100014487 G2 box; other site 340100014488 G3 box; other site 340100014489 Switch II region; other site 340100014490 G4 box; other site 340100014491 G5 box; other site 340100014492 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 340100014493 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 340100014494 Antibiotic Binding Site [chemical binding]; other site 340100014495 elongation factor G; Reviewed; Region: PRK00007 340100014496 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 340100014497 G1 box; other site 340100014498 putative GEF interaction site [polypeptide binding]; other site 340100014499 GTP/Mg2+ binding site [chemical binding]; other site 340100014500 Switch I region; other site 340100014501 G2 box; other site 340100014502 G3 box; other site 340100014503 Switch II region; other site 340100014504 G4 box; other site 340100014505 G5 box; other site 340100014506 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 340100014507 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 340100014508 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 340100014509 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 340100014510 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 340100014511 S17 interaction site [polypeptide binding]; other site 340100014512 S8 interaction site; other site 340100014513 16S rRNA interaction site [nucleotide binding]; other site 340100014514 streptomycin interaction site [chemical binding]; other site 340100014515 23S rRNA interaction site [nucleotide binding]; other site 340100014516 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 340100014517 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100014518 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 340100014519 active site 340100014520 phosphorylation site [posttranslational modification] 340100014521 intermolecular recognition site; other site 340100014522 dimerization interface [polypeptide binding]; other site 340100014523 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 340100014524 DNA binding site [nucleotide binding] 340100014525 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100014526 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100014527 active site 340100014528 phosphorylation site [posttranslational modification] 340100014529 intermolecular recognition site; other site 340100014530 dimerization interface [polypeptide binding]; other site 340100014531 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 340100014532 DNA binding site [nucleotide binding] 340100014533 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340100014534 putative peptidoglycan binding site; other site 340100014535 FecR protein; Region: FecR; pfam04773 340100014536 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 340100014537 CHASE2 domain; Region: CHASE2; cl01732 340100014538 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 340100014539 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 340100014540 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 340100014541 ATP binding site [chemical binding]; other site 340100014542 Mg2+ binding site [ion binding]; other site 340100014543 G-X-G motif; other site 340100014544 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100014545 substrate binding site [chemical binding]; other site 340100014546 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 340100014547 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 340100014548 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 340100014549 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 340100014550 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 340100014551 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 340100014552 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 340100014553 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 340100014554 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 340100014555 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 340100014556 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 340100014557 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 340100014558 DNA binding site [nucleotide binding] 340100014559 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 340100014560 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 340100014561 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 340100014562 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; pfam04563 340100014563 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 340100014564 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 340100014565 RPB11 interaction site [polypeptide binding]; other site 340100014566 RPB12 interaction site [polypeptide binding]; other site 340100014567 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 340100014568 RPB3 interaction site [polypeptide binding]; other site 340100014569 RPB1 interaction site [polypeptide binding]; other site 340100014570 RPB11 interaction site [polypeptide binding]; other site 340100014571 RPB10 interaction site [polypeptide binding]; other site 340100014572 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 340100014573 core dimer interface [polypeptide binding]; other site 340100014574 peripheral dimer interface [polypeptide binding]; other site 340100014575 L10 interface [polypeptide binding]; other site 340100014576 L11 interface [polypeptide binding]; other site 340100014577 putative EF-Tu interaction site [polypeptide binding]; other site 340100014578 putative EF-G interaction site [polypeptide binding]; other site 340100014579 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 340100014580 23S rRNA interface [nucleotide binding]; other site 340100014581 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 340100014582 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 340100014583 mRNA/rRNA interface [nucleotide binding]; other site 340100014584 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 340100014585 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 340100014586 23S rRNA interface [nucleotide binding]; other site 340100014587 L7/L12 interface [polypeptide binding]; other site 340100014588 putative thiostrepton binding site; other site 340100014589 L25 interface [polypeptide binding]; other site 340100014590 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 340100014591 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 340100014592 putative homodimer interface [polypeptide binding]; other site 340100014593 KOW motif; Region: KOW; cl00354 340100014594 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 340100014595 elongation factor Tu; Reviewed; Region: PRK00049 340100014596 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 340100014597 G1 box; other site 340100014598 GEF interaction site [polypeptide binding]; other site 340100014599 GTP/Mg2+ binding site [chemical binding]; other site 340100014600 Switch I region; other site 340100014601 G2 box; other site 340100014602 G3 box; other site 340100014603 Switch II region; other site 340100014604 G4 box; other site 340100014605 G5 box; other site 340100014606 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 340100014607 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 340100014608 Antibiotic Binding Site [chemical binding]; other site 340100014609 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 340100014610 active site 340100014611 homotetramer interface [polypeptide binding]; other site 340100014612 homodimer interface [polypeptide binding]; other site 340100014613 ParB-like nuclease domain; Region: ParBc; cl02129 340100014614 ParB-like partition proteins; Region: parB_part; TIGR00180 340100014615 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100014616 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 340100014617 P-loop; other site 340100014618 Magnesium ion binding site [ion binding]; other site 340100014619 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 340100014620 Magnesium ion binding site [ion binding]; other site 340100014621 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; cl15754 340100014622 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 340100014623 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014624 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 340100014625 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 340100014626 DNA-binding site [nucleotide binding]; DNA binding site 340100014627 RNA-binding motif; other site 340100014628 methionine aminotransferase; Validated; Region: PRK09082 340100014629 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 340100014630 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014631 homodimer interface [polypeptide binding]; other site 340100014632 catalytic residue [active] 340100014633 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 340100014634 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100014635 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100014636 NMT1-like family; Region: NMT1_2; cl15260 340100014637 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 340100014638 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 340100014639 dimer interface [polypeptide binding]; other site 340100014640 phosphorylation site [posttranslational modification] 340100014641 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 340100014642 ATP binding site [chemical binding]; other site 340100014643 Mg2+ binding site [ion binding]; other site 340100014644 G-X-G motif; other site 340100014645 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 340100014646 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100014647 active site 340100014648 phosphorylation site [posttranslational modification] 340100014649 intermolecular recognition site; other site 340100014650 dimerization interface [polypeptide binding]; other site 340100014651 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 340100014652 DNA binding site [nucleotide binding] 340100014653 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 340100014654 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 340100014655 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100014656 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340100014657 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 340100014658 DNA binding site [nucleotide binding] 340100014659 active site 340100014660 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 340100014661 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 340100014662 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 340100014663 putative substrate translocation pore; other site 340100014664 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 340100014665 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 340100014666 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 340100014667 [4Fe-4S] binding site [ion binding]; other site 340100014668 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 340100014669 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 340100014670 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 340100014671 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 340100014672 molybdopterin cofactor binding site; other site 340100014673 nitrate reductase, beta subunit; Region: narH; TIGR01660 340100014674 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 340100014675 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 340100014676 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 340100014677 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340100014678 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 340100014679 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 340100014680 FeS/SAM binding site; other site 340100014681 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 340100014682 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 340100014683 active site clefts [active] 340100014684 zinc binding site [ion binding]; other site 340100014685 dimer interface [polypeptide binding]; other site 340100014686 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 340100014687 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 340100014688 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 340100014689 dimerization interface [polypeptide binding]; other site 340100014690 GAF domain; Region: GAF; cl15785 340100014691 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 340100014692 ATP binding site [chemical binding]; other site 340100014693 Mg2+ binding site [ion binding]; other site 340100014694 G-X-G motif; other site 340100014695 transcriptional regulator NarL; Provisional; Region: PRK10651 340100014696 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340100014697 active site 340100014698 phosphorylation site [posttranslational modification] 340100014699 intermolecular recognition site; other site 340100014700 dimerization interface [polypeptide binding]; other site 340100014701 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 340100014702 dimerization interface [polypeptide binding]; other site 340100014703 DNA binding residues [nucleotide binding] 340100014704 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 340100014705 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 340100014706 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014707 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 340100014708 active site 340100014709 Catalytic domain of Protein Kinases; Region: PKc; cd00180 340100014710 active site 340100014711 ATP binding site [chemical binding]; other site 340100014712 substrate binding site [chemical binding]; other site 340100014713 activation loop (A-loop); other site 340100014714 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 340100014715 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 340100014716 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 340100014717 trmE is a tRNA modification GTPase; Region: trmE; cd04164 340100014718 G1 box; other site 340100014719 GTP/Mg2+ binding site [chemical binding]; other site 340100014720 Switch I region; other site 340100014721 G2 box; other site 340100014722 Switch II region; other site 340100014723 G3 box; other site 340100014724 G4 box; other site 340100014725 G5 box; other site 340100014726 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 340100014727 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 340100014728 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100014729 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100014730 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 340100014731 dimer interface [polypeptide binding]; other site 340100014732 conserved gate region; other site 340100014733 putative PBP binding loops; other site 340100014734 ABC-ATPase subunit interface; other site 340100014735 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100014736 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 340100014737 dimer interface [polypeptide binding]; other site 340100014738 conserved gate region; other site 340100014739 putative PBP binding loops; other site 340100014740 ABC-ATPase subunit interface; other site 340100014741 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100014742 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100014743 Walker A/P-loop; other site 340100014744 ATP binding site [chemical binding]; other site 340100014745 Q-loop/lid; other site 340100014746 ABC transporter signature motif; other site 340100014747 Walker B; other site 340100014748 D-loop; other site 340100014749 H-loop/switch region; other site 340100014750 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100014751 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 340100014752 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100014753 Walker A/P-loop; other site 340100014754 ATP binding site [chemical binding]; other site 340100014755 Q-loop/lid; other site 340100014756 ABC transporter signature motif; other site 340100014757 Walker B; other site 340100014758 D-loop; other site 340100014759 H-loop/switch region; other site 340100014760 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100014761 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100014762 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100014763 metal binding site [ion binding]; metal-binding site 340100014764 putative dimer interface [polypeptide binding]; other site 340100014765 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 340100014766 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 340100014767 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100014768 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 340100014769 Walker A/P-loop; other site 340100014770 ATP binding site [chemical binding]; other site 340100014771 Q-loop/lid; other site 340100014772 ABC transporter signature motif; other site 340100014773 Walker B; other site 340100014774 D-loop; other site 340100014775 H-loop/switch region; other site 340100014776 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 340100014777 putative PBP binding loops; other site 340100014778 dimer interface [polypeptide binding]; other site 340100014779 ABC-ATPase subunit interface; other site 340100014780 membrane protein insertase; Provisional; Region: PRK01318 340100014781 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 340100014782 Haemolytic domain; Region: Haemolytic; cl00506 340100014783 Ribonuclease P; Region: Ribonuclease_P; cl00457 340100014784 Ribosomal protein L34; Region: Ribosomal_L34; cl00370