-- dump date 20140619_004206 -- class Genbank::misc_feature -- table misc_feature_note -- id note 340100000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 340100000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 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; cd00093 340100000030 non-specific DNA binding site [nucleotide binding]; other site 340100000031 salt bridge; other site 340100000032 sequence-specific DNA binding site [nucleotide binding]; other site 340100000033 HipA N-terminal domain; Region: Couple_hipA; pfam13657 340100000034 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100000035 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100000036 Isochorismatase family; Region: Isochorismatase; pfam00857 340100000037 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 340100000038 catalytic triad [active] 340100000039 dimer interface [polypeptide binding]; other site 340100000040 conserved cis-peptide bond; other site 340100000041 Pirin-related protein [General function prediction only]; Region: COG1741 340100000042 Pirin; Region: Pirin; pfam02678 340100000043 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 340100000044 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100000045 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100000046 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 340100000047 putative effector binding pocket; other site 340100000048 putative dimerization interface [polypeptide binding]; other site 340100000049 AAA domain; Region: AAA_26; pfam13500 340100000050 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 340100000051 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 340100000052 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 340100000053 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100000054 catalytic residue [active] 340100000055 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 340100000056 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 340100000057 inhibitor-cofactor binding pocket; inhibition site 340100000058 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000059 catalytic residue [active] 340100000060 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 340100000061 active site 340100000062 acylphosphatase; Provisional; Region: PRK14424 340100000063 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 340100000064 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 340100000065 phosphate binding site [ion binding]; other site 340100000066 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 340100000067 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 340100000068 LytTr DNA-binding domain; Region: LytTR; smart00850 340100000069 beta-lactam binding protein AmpH; Provisional; Region: PRK10662 340100000070 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 340100000071 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 340100000072 Beta-lactamase; Region: Beta-lactamase; pfam00144 340100000073 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 340100000074 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100000075 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 340100000076 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 340100000077 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 340100000078 putative ligand binding site [chemical binding]; other site 340100000079 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 340100000080 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 340100000081 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 340100000082 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 340100000083 NADH(P)-binding; Region: NAD_binding_10; pfam13460 340100000084 NAD binding site [chemical binding]; other site 340100000085 putative active site [active] 340100000086 substrate binding site [chemical binding]; other site 340100000087 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]; Region: COG3613 340100000088 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK00014 340100000089 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 340100000090 Proteins containing SET domain [General function prediction only]; Region: COG2940 340100000091 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 340100000092 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100000093 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 340100000094 putative DNA binding site [nucleotide binding]; other site 340100000095 putative Zn2+ binding site [ion binding]; other site 340100000096 AsnC family; Region: AsnC_trans_reg; pfam01037 340100000097 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 340100000098 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100000099 PYR/PP interface [polypeptide binding]; other site 340100000100 dimer interface [polypeptide binding]; other site 340100000101 TPP binding site [chemical binding]; other site 340100000102 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100000103 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 340100000104 TPP-binding site [chemical binding]; other site 340100000105 dimer interface [polypeptide binding]; other site 340100000106 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100000107 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100000108 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000109 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100000110 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 340100000111 substrate binding site [chemical binding]; other site 340100000112 oxyanion hole (OAH) forming residues; other site 340100000113 trimer interface [polypeptide binding]; other site 340100000114 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000115 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100000116 The 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 340100000117 dimerization interface [polypeptide binding]; other site 340100000118 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100000119 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 340100000120 NAD(P) binding site [chemical binding]; other site 340100000121 catalytic residues [active] 340100000122 catalytic residues [active] 340100000123 gluconate 5-dehydrogenase; Provisional; Region: PRK06124 340100000124 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000125 NAD(P) binding site [chemical binding]; other site 340100000126 active site 340100000127 DNA topoisomerase III; Validated; Region: PRK08173 340100000128 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 340100000129 active site 340100000130 putative interdomain interaction site [polypeptide binding]; other site 340100000131 putative metal-binding site [ion binding]; other site 340100000132 putative nucleotide binding site [chemical binding]; other site 340100000133 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 340100000134 domain I; other site 340100000135 DNA binding groove [nucleotide binding] 340100000136 phosphate binding site [ion binding]; other site 340100000137 domain II; other site 340100000138 domain III; other site 340100000139 nucleotide binding site [chemical binding]; other site 340100000140 catalytic site [active] 340100000141 domain IV; other site 340100000142 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 340100000143 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 340100000144 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 340100000145 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 340100000146 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 340100000147 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100000148 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340100000149 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 340100000150 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100000151 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 340100000152 active site 340100000153 HIGH motif; other site 340100000154 nucleotide binding site [chemical binding]; other site 340100000155 active site 340100000156 KMSKS motif; other site 340100000157 Protein of unknown function (DUF494); Region: DUF494; pfam04361 340100000158 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 340100000159 DctM-like transporters; Region: DctM; pfam06808 340100000160 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 340100000161 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 340100000162 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 340100000163 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 340100000164 dimer interface [polypeptide binding]; other site 340100000165 active site 340100000166 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100000167 substrate binding site [chemical binding]; other site 340100000168 catalytic residue [active] 340100000169 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 340100000170 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 340100000171 inhibitor-cofactor binding pocket; inhibition site 340100000172 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000173 catalytic residue [active] 340100000174 acyl-CoA synthetase; Validated; Region: PRK08162 340100000175 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 340100000176 acyl-activating enzyme (AAE) consensus motif; other site 340100000177 putative active site [active] 340100000178 AMP binding site [chemical binding]; other site 340100000179 putative CoA binding site [chemical binding]; other site 340100000180 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 340100000181 Phosphotransferase enzyme family; Region: APH; pfam01636 340100000182 putative active site [active] 340100000183 putative substrate binding site [chemical binding]; other site 340100000184 ATP binding site [chemical binding]; other site 340100000185 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100000186 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100000187 active site 340100000188 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100000189 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100000190 NAD(P) binding site [chemical binding]; other site 340100000191 active site 340100000192 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100000193 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100000194 CoA binding domain; Region: CoA_binding_2; pfam13380 340100000195 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100000196 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100000197 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100000198 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100000199 thiolase; Provisional; Region: PRK06158 340100000200 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 340100000201 active site 340100000202 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100000203 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100000204 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100000205 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 340100000206 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100000207 ATP-grasp domain; Region: ATP-grasp_4; cl17255 340100000208 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 340100000209 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 340100000210 carboxyltransferase (CT) interaction site; other site 340100000211 biotinylation site [posttranslational modification]; other site 340100000212 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 340100000213 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 340100000214 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 340100000215 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 340100000216 dimer interface [polypeptide binding]; other site 340100000217 active site 340100000218 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 340100000219 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 340100000220 isovaleryl-CoA dehydrogenase; Region: PLN02519 340100000221 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 340100000222 substrate binding site [chemical binding]; other site 340100000223 FAD binding site [chemical binding]; other site 340100000224 catalytic base [active] 340100000225 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100000226 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100000227 metal binding site [ion binding]; metal-binding site 340100000228 putative dimer interface [polypeptide binding]; other site 340100000229 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100000230 hypothetical protein; Provisional; Region: PRK02237 340100000231 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 340100000232 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 340100000233 DNA binding residues [nucleotide binding] 340100000234 putative dimer interface [polypeptide binding]; other site 340100000235 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 340100000236 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100000237 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 340100000238 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 340100000239 homodimer interface [polypeptide binding]; other site 340100000240 substrate-cofactor binding pocket; other site 340100000241 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000242 catalytic residue [active] 340100000243 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 340100000244 catalytic residues [active] 340100000245 hinge region; other site 340100000246 alpha helical domain; other site 340100000247 Sporulation related domain; Region: SPOR; pfam05036 340100000248 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 340100000249 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 340100000250 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 340100000251 active site 340100000252 HIGH motif; other site 340100000253 KMSK motif region; other site 340100000254 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 340100000255 tRNA binding surface [nucleotide binding]; other site 340100000256 anticodon binding site; other site 340100000257 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 340100000258 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 340100000259 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 340100000260 dimer interface [polypeptide binding]; other site 340100000261 conserved gate region; other site 340100000262 putative PBP binding loops; other site 340100000263 ABC-ATPase subunit interface; other site 340100000264 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 340100000265 dimer interface [polypeptide binding]; other site 340100000266 conserved gate region; other site 340100000267 putative PBP binding loops; other site 340100000268 ABC-ATPase subunit interface; other site 340100000269 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100000270 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 340100000271 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 340100000272 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 340100000273 Walker A/P-loop; other site 340100000274 ATP binding site [chemical binding]; other site 340100000275 Q-loop/lid; other site 340100000276 ABC transporter signature motif; other site 340100000277 Walker B; other site 340100000278 D-loop; other site 340100000279 H-loop/switch region; other site 340100000280 TOBE domain; Region: TOBE_2; pfam08402 340100000281 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 340100000282 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100000283 active site 340100000284 metal binding site [ion binding]; metal-binding site 340100000285 hexamer interface [polypeptide binding]; other site 340100000286 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 340100000287 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100000288 Walker A/P-loop; other site 340100000289 ATP binding site [chemical binding]; other site 340100000290 Q-loop/lid; other site 340100000291 ABC transporter signature motif; other site 340100000292 Walker B; other site 340100000293 D-loop; other site 340100000294 H-loop/switch region; other site 340100000295 TOBE domain; Region: TOBE_2; pfam08402 340100000296 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 340100000297 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 340100000298 dimer interface [polypeptide binding]; other site 340100000299 conserved gate region; other site 340100000300 putative PBP binding loops; other site 340100000301 ABC-ATPase subunit interface; other site 340100000302 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100000303 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 340100000304 dimer interface [polypeptide binding]; other site 340100000305 conserved gate region; other site 340100000306 putative PBP binding loops; other site 340100000307 ABC-ATPase subunit interface; other site 340100000308 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 340100000309 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 340100000310 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100000311 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100000312 DNA binding site [nucleotide binding] 340100000313 domain linker motif; other site 340100000314 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100000315 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100000316 Amidase; Region: Amidase; cl11426 340100000317 2-isopropylmalate synthase; Validated; Region: PRK03739 340100000318 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 340100000319 active site 340100000320 catalytic residues [active] 340100000321 metal binding site [ion binding]; metal-binding site 340100000322 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 340100000323 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 340100000324 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 340100000325 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 340100000326 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 340100000327 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 340100000328 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 340100000329 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 340100000330 heme binding site [chemical binding]; other site 340100000331 ferroxidase pore; other site 340100000332 ferroxidase diiron center [ion binding]; other site 340100000333 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 340100000334 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 340100000335 G1 box; other site 340100000336 putative GEF interaction site [polypeptide binding]; other site 340100000337 GTP/Mg2+ binding site [chemical binding]; other site 340100000338 Switch I region; other site 340100000339 G2 box; other site 340100000340 G3 box; other site 340100000341 Switch II region; other site 340100000342 G4 box; other site 340100000343 G5 box; other site 340100000344 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 340100000345 LysE type translocator; Region: LysE; cl00565 340100000346 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 340100000347 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 340100000348 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100000349 ATP binding site [chemical binding]; other site 340100000350 Mg++ binding site [ion binding]; other site 340100000351 motif III; other site 340100000352 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 340100000353 nucleotide binding region [chemical binding]; other site 340100000354 LemA family; Region: LemA; pfam04011 340100000355 Repair protein; Region: Repair_PSII; pfam04536 340100000356 sensor protein PhoQ; Provisional; Region: PRK10815 340100000357 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 340100000358 ATP binding site [chemical binding]; other site 340100000359 Mg2+ binding site [ion binding]; other site 340100000360 G-X-G motif; other site 340100000361 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100000362 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100000363 active site 340100000364 phosphorylation site [posttranslational modification] 340100000365 intermolecular recognition site; other site 340100000366 dimerization interface [polypeptide binding]; other site 340100000367 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 340100000368 DNA binding site [nucleotide binding] 340100000369 Predicted membrane protein [Function unknown]; Region: COG3212 340100000370 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 340100000371 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 340100000372 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 340100000373 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 340100000374 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 340100000375 FAD binding pocket [chemical binding]; other site 340100000376 FAD binding motif [chemical binding]; other site 340100000377 phosphate binding motif [ion binding]; other site 340100000378 beta-alpha-beta structure motif; other site 340100000379 NAD binding pocket [chemical binding]; other site 340100000380 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 340100000381 Amidohydrolase; Region: Amidohydro_4; pfam13147 340100000382 active site 340100000383 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100000384 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100000385 Walker A/P-loop; other site 340100000386 ATP binding site [chemical binding]; other site 340100000387 Q-loop/lid; other site 340100000388 ABC transporter signature motif; other site 340100000389 Walker B; other site 340100000390 D-loop; other site 340100000391 H-loop/switch region; other site 340100000392 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 340100000393 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100000394 Walker A/P-loop; other site 340100000395 ATP binding site [chemical binding]; other site 340100000396 Q-loop/lid; other site 340100000397 ABC transporter signature motif; other site 340100000398 Walker B; other site 340100000399 D-loop; other site 340100000400 H-loop/switch region; other site 340100000401 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 340100000402 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340100000403 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 340100000404 dimer interface [polypeptide binding]; other site 340100000405 conserved gate region; other site 340100000406 putative PBP binding loops; other site 340100000407 ABC-ATPase subunit interface; other site 340100000408 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100000409 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 340100000410 dimer interface [polypeptide binding]; other site 340100000411 conserved gate region; other site 340100000412 putative PBP binding loops; other site 340100000413 ABC-ATPase subunit interface; other site 340100000414 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100000415 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 340100000416 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100000417 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340100000418 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 340100000419 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100000420 50S ribosome-binding GTPase; Region: MMR_HSR1; pfam01926 340100000421 G1 box; other site 340100000422 GTP/Mg2+ binding site [chemical binding]; other site 340100000423 G2 box; other site 340100000424 Switch I region; other site 340100000425 G3 box; other site 340100000426 Switch II region; other site 340100000427 G4 box; other site 340100000428 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 340100000429 G5 box; other site 340100000430 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 340100000431 Uncharacterized conserved protein [Function unknown]; Region: COG3339 340100000432 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100000433 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100000434 EamA-like transporter family; Region: EamA; pfam00892 340100000435 Fimbrial protein; Region: Fimbrial; pfam00419 340100000436 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 340100000437 PapC N-terminal domain; Region: PapC_N; pfam13954 340100000438 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100000439 PapC C-terminal domain; Region: PapC_C; pfam13953 340100000440 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 340100000441 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 340100000442 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 340100000443 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 340100000444 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 340100000445 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 340100000446 tetramer interface [polypeptide binding]; other site 340100000447 active site 340100000448 Mg2+/Mn2+ binding site [ion binding]; other site 340100000449 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100000450 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100000451 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 340100000452 stringent starvation protein A; Provisional; Region: sspA; PRK09481 340100000453 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 340100000454 C-terminal domain interface [polypeptide binding]; other site 340100000455 putative GSH binding site (G-site) [chemical binding]; other site 340100000456 dimer interface [polypeptide binding]; other site 340100000457 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 340100000458 dimer interface [polypeptide binding]; other site 340100000459 N-terminal domain interface [polypeptide binding]; other site 340100000460 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 340100000461 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 340100000462 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 340100000463 Qi binding site; other site 340100000464 intrachain domain interface; other site 340100000465 interchain domain interface [polypeptide binding]; other site 340100000466 heme bH binding site [chemical binding]; other site 340100000467 heme bL binding site [chemical binding]; other site 340100000468 Qo binding site; other site 340100000469 interchain domain interface [polypeptide binding]; other site 340100000470 intrachain domain interface; other site 340100000471 Qi binding site; other site 340100000472 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 340100000473 Qo binding site; other site 340100000474 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 340100000475 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 340100000476 [2Fe-2S] cluster binding site [ion binding]; other site 340100000477 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 340100000478 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 340100000479 Uncharacterized conserved protein [Function unknown]; Region: COG0327 340100000480 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 340100000481 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 340100000482 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 340100000483 protein binding site [polypeptide binding]; other site 340100000484 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100000485 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 340100000486 non-specific DNA binding site [nucleotide binding]; other site 340100000487 salt bridge; other site 340100000488 sequence-specific DNA binding site [nucleotide binding]; other site 340100000489 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 340100000490 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 340100000491 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 340100000492 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 340100000493 nucleotide binding site/active site [active] 340100000494 HIT family signature motif; other site 340100000495 catalytic residue [active] 340100000496 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 340100000497 metal binding site [ion binding]; metal-binding site 340100000498 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 340100000499 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 340100000500 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 340100000501 substrate binding site [chemical binding]; other site 340100000502 glutamase interaction surface [polypeptide binding]; other site 340100000503 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 340100000504 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 340100000505 catalytic residues [active] 340100000506 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 340100000507 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 340100000508 putative active site [active] 340100000509 oxyanion strand; other site 340100000510 catalytic triad [active] 340100000511 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 340100000512 putative active site pocket [active] 340100000513 4-fold oligomerization interface [polypeptide binding]; other site 340100000514 metal binding residues [ion binding]; metal-binding site 340100000515 3-fold/trimer interface [polypeptide binding]; other site 340100000516 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 340100000517 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 340100000518 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000519 homodimer interface [polypeptide binding]; other site 340100000520 catalytic residue [active] 340100000521 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 340100000522 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 340100000523 NAD binding site [chemical binding]; other site 340100000524 dimerization interface [polypeptide binding]; other site 340100000525 product binding site; other site 340100000526 substrate binding site [chemical binding]; other site 340100000527 zinc binding site [ion binding]; other site 340100000528 catalytic residues [active] 340100000529 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 340100000530 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 340100000531 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 340100000532 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 340100000533 hinge; other site 340100000534 active site 340100000535 BolA-like protein; Region: BolA; pfam01722 340100000536 ABC-2 type transporter; Region: ABC2_membrane; cl17235 340100000537 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 340100000538 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 340100000539 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 340100000540 Walker A/P-loop; other site 340100000541 ATP binding site [chemical binding]; other site 340100000542 Q-loop/lid; other site 340100000543 ABC transporter signature motif; other site 340100000544 Walker B; other site 340100000545 D-loop; other site 340100000546 H-loop/switch region; other site 340100000547 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 340100000548 VacJ like lipoprotein; Region: VacJ; cl01073 340100000549 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 340100000550 mce related protein; Region: MCE; pfam02470 340100000551 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 340100000552 Permease; Region: Permease; pfam02405 340100000553 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 340100000554 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 340100000555 Walker A/P-loop; other site 340100000556 ATP binding site [chemical binding]; other site 340100000557 Q-loop/lid; other site 340100000558 ABC transporter signature motif; other site 340100000559 Walker B; other site 340100000560 D-loop; other site 340100000561 H-loop/switch region; other site 340100000562 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 340100000563 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000564 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100000565 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 340100000566 putative dimerization interface [polypeptide binding]; other site 340100000567 OmpW family; Region: OmpW; cl17427 340100000568 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 340100000569 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 340100000570 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 340100000571 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 340100000572 active site 340100000573 dimer interface [polypeptide binding]; other site 340100000574 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 340100000575 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 340100000576 active site 340100000577 FMN binding site [chemical binding]; other site 340100000578 substrate binding site [chemical binding]; other site 340100000579 3Fe-4S cluster binding site [ion binding]; other site 340100000580 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 340100000581 domain interface; other site 340100000582 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 340100000583 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 340100000584 substrate binding site [chemical binding]; other site 340100000585 catalytic Zn binding site [ion binding]; other site 340100000586 NAD binding site [chemical binding]; other site 340100000587 structural Zn binding site [ion binding]; other site 340100000588 dimer interface [polypeptide binding]; other site 340100000589 S-formylglutathione hydrolase; Region: PLN02442 340100000590 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 340100000591 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 340100000592 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 340100000593 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100000594 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 340100000595 DNA binding residues [nucleotide binding] 340100000596 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 340100000597 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100000598 active site 340100000599 metal binding site [ion binding]; metal-binding site 340100000600 hexamer interface [polypeptide binding]; other site 340100000601 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 340100000602 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 340100000603 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 340100000604 ligand binding site [chemical binding]; other site 340100000605 flexible hinge region; other site 340100000606 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100000607 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100000608 DNA binding site [nucleotide binding] 340100000609 domain linker motif; other site 340100000610 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 340100000611 putative ligand binding site [chemical binding]; other site 340100000612 putative dimerization interface [polypeptide binding]; other site 340100000613 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100000614 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100000615 DctM-like transporters; Region: DctM; pfam06808 340100000616 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100000617 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 340100000618 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 340100000619 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 340100000620 nudix motif; other site 340100000621 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 340100000622 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 340100000623 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 340100000624 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100000625 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 340100000626 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100000627 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 340100000628 Subunit I/III interface [polypeptide binding]; other site 340100000629 D-pathway; other site 340100000630 Subunit I/VIIc interface [polypeptide binding]; other site 340100000631 Subunit I/IV interface [polypeptide binding]; other site 340100000632 Subunit I/II interface [polypeptide binding]; other site 340100000633 Low-spin heme (heme a) binding site [chemical binding]; other site 340100000634 Subunit I/VIIa interface [polypeptide binding]; other site 340100000635 Subunit I/VIa interface [polypeptide binding]; other site 340100000636 Dimer interface; other site 340100000637 Putative water exit pathway; other site 340100000638 Binuclear center (heme a3/CuB) [ion binding]; other site 340100000639 K-pathway; other site 340100000640 Subunit I/Vb interface [polypeptide binding]; other site 340100000641 Putative proton exit pathway; other site 340100000642 Subunit I/VIb interface; other site 340100000643 Subunit I/VIc interface [polypeptide binding]; other site 340100000644 Electron transfer pathway; other site 340100000645 Subunit I/VIIIb interface [polypeptide binding]; other site 340100000646 Subunit I/VIIb interface [polypeptide binding]; other site 340100000647 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 340100000648 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 340100000649 Subunit III/VIIa interface [polypeptide binding]; other site 340100000650 Phospholipid binding site [chemical binding]; other site 340100000651 Subunit I/III interface [polypeptide binding]; other site 340100000652 Subunit III/VIb interface [polypeptide binding]; other site 340100000653 Subunit III/VIa interface; other site 340100000654 Subunit III/Vb interface [polypeptide binding]; other site 340100000655 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 340100000656 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 340100000657 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100000658 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 340100000659 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 340100000660 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 340100000661 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 340100000662 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 340100000663 Cu(I) binding site [ion binding]; other site 340100000664 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 340100000665 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 340100000666 Substrate binding site; other site 340100000667 Mg++ binding site; other site 340100000668 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 340100000669 active site 340100000670 substrate binding site [chemical binding]; other site 340100000671 CoA binding site [chemical binding]; other site 340100000672 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 340100000673 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100000674 putative substrate translocation pore; other site 340100000675 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 340100000676 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 340100000677 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340100000678 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 340100000679 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100000680 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 340100000681 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100000682 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 340100000683 putative DNA binding site [nucleotide binding]; other site 340100000684 putative Zn2+ binding site [ion binding]; other site 340100000685 AsnC family; Region: AsnC_trans_reg; pfam01037 340100000686 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 340100000687 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 340100000688 glutaminase active site [active] 340100000689 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 340100000690 dimer interface [polypeptide binding]; other site 340100000691 active site 340100000692 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 340100000693 dimer interface [polypeptide binding]; other site 340100000694 active site 340100000695 Protein of unknown function (DUF2837); Region: DUF2837; pfam10997 340100000696 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 340100000697 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 340100000698 Autotransporter beta-domain; Region: Autotransporter; pfam03797 340100000699 rod shape-determining protein MreB; Provisional; Region: PRK13927 340100000700 MreB and similar proteins; Region: MreB_like; cd10225 340100000701 nucleotide binding site [chemical binding]; other site 340100000702 Mg binding site [ion binding]; other site 340100000703 putative protofilament interaction site [polypeptide binding]; other site 340100000704 RodZ interaction site [polypeptide binding]; other site 340100000705 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 340100000706 Autotransporter beta-domain; Region: Autotransporter; smart00869 340100000707 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100000708 Transposase; Region: HTH_Tnp_1; pfam01527 340100000709 putative transposase OrfB; Reviewed; Region: PHA02517 340100000710 HTH-like domain; Region: HTH_21; pfam13276 340100000711 Integrase core domain; Region: rve; pfam00665 340100000712 Integrase core domain; Region: rve_3; pfam13683 340100000713 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100000714 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 340100000715 DNA binding site [nucleotide binding] 340100000716 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 340100000717 DNA-binding interface [nucleotide binding]; DNA binding site 340100000718 HTH-like domain; Region: HTH_21; pfam13276 340100000719 Integrase core domain; Region: rve; pfam00665 340100000720 Integrase core domain; Region: rve_3; pfam13683 340100000721 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100000722 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 340100000723 non-specific DNA binding site [nucleotide binding]; other site 340100000724 salt bridge; other site 340100000725 sequence-specific DNA binding site [nucleotide binding]; other site 340100000726 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 340100000727 DNA-binding interface [nucleotide binding]; DNA binding site 340100000728 HTH-like domain; Region: HTH_21; pfam13276 340100000729 Integrase core domain; Region: rve; pfam00665 340100000730 Integrase core domain; Region: rve_3; pfam13683 340100000731 Predicted ATPase [General function prediction only]; Region: COG4637 340100000732 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 340100000733 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 340100000734 Walker B; other site 340100000735 D-loop; other site 340100000736 H-loop/switch region; other site 340100000737 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 340100000738 putative active site [active] 340100000739 putative metal-binding site [ion binding]; other site 340100000740 HTH-like domain; Region: HTH_21; pfam13276 340100000741 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100000742 Integrase core domain; Region: rve; pfam00665 340100000743 Integrase core domain; Region: rve_3; pfam13683 340100000744 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 340100000745 DNA-binding interface [nucleotide binding]; DNA binding site 340100000746 Winged helix-turn helix; Region: HTH_29; pfam13551 340100000747 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100000748 putative transposase OrfB; Reviewed; Region: PHA02517 340100000749 HTH-like domain; Region: HTH_21; pfam13276 340100000750 Integrase core domain; Region: rve; pfam00665 340100000751 Integrase core domain; Region: rve_3; pfam13683 340100000752 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100000753 Transposase; Region: HTH_Tnp_1; pfam01527 340100000754 Homeodomain-like domain; Region: HTH_32; pfam13565 340100000755 Integrase core domain; Region: rve; pfam00665 340100000756 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100000757 Integrase core domain; Region: rve_3; pfam13683 340100000758 Transposase; Region: HTH_Tnp_1; pfam01527 340100000759 P-loop containing region of AAA domain; Region: AAA_29; cl17516 340100000760 HTH-like domain; Region: HTH_21; pfam13276 340100000761 Transposase; Region: HTH_Tnp_1; pfam01527 340100000762 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 340100000763 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 340100000764 ATP binding site [chemical binding]; other site 340100000765 putative Mg++ binding site [ion binding]; other site 340100000766 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 340100000767 nucleotide binding region [chemical binding]; other site 340100000768 ATP-binding site [chemical binding]; other site 340100000769 Restriction endonuclease; Region: Mrr_cat; pfam04471 340100000770 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 340100000771 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 340100000772 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 340100000773 ligand binding site [chemical binding]; other site 340100000774 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 340100000775 Integrase core domain; Region: rve_3; pfam13683 340100000776 Integrase core domain; Region: rve; pfam00665 340100000777 Transposase; Region: HTH_Tnp_1; cl17663 340100000778 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100000779 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 340100000780 non-specific DNA binding site [nucleotide binding]; other site 340100000781 salt bridge; other site 340100000782 sequence-specific DNA binding site [nucleotide binding]; other site 340100000783 HipA N-terminal domain; Region: Couple_hipA; cl11853 340100000784 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100000785 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100000786 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 340100000787 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340100000788 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 340100000789 Vi polysaccharide biosynthesis protein TviD; Provisional; Region: PRK15180 340100000790 Vi polysaccharide biosynthesis protein TviE; Provisional; Region: PRK15179 340100000791 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 340100000792 Vi polysaccharide export protein VexA; Provisional; Region: PRK15175 340100000793 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 340100000794 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 340100000795 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 340100000796 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100000797 Q-loop/lid; other site 340100000798 ABC transporter signature motif; other site 340100000799 Walker B; other site 340100000800 D-loop; other site 340100000801 H-loop/switch region; other site 340100000802 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 340100000803 Vi polysaccharide export protein VexE; Provisional; Region: PRK15174 340100000804 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 340100000805 TPR motif; other site 340100000806 binding surface 340100000807 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 340100000808 putative acyl-acceptor binding pocket; other site 340100000809 Amb_all domain; Region: Amb_all; smart00656 340100000810 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100000811 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 340100000812 NAD binding site [chemical binding]; other site 340100000813 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 340100000814 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100000815 DNA-binding site [nucleotide binding]; DNA binding site 340100000816 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 340100000817 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100000818 homodimer interface [polypeptide binding]; other site 340100000819 catalytic residue [active] 340100000820 Transcriptional regulator [Transcription]; Region: PaiB; COG2808 340100000821 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 340100000822 putative substrate translocation pore; other site 340100000823 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100000824 MarR family; Region: MarR_2; cl17246 340100000825 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100000826 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 340100000827 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 340100000828 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 340100000829 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 340100000830 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 340100000831 FMN-binding pocket [chemical binding]; other site 340100000832 flavin binding motif; other site 340100000833 phosphate binding motif [ion binding]; other site 340100000834 beta-alpha-beta structure motif; other site 340100000835 NAD binding pocket [chemical binding]; other site 340100000836 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 340100000837 catalytic loop [active] 340100000838 iron binding site [ion binding]; other site 340100000839 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 340100000840 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 340100000841 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100000842 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 340100000843 hydrophobic ligand binding site; other site 340100000844 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100000845 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 340100000846 active site 340100000847 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 340100000848 heterodimer interface [polypeptide binding]; other site 340100000849 multimer interface [polypeptide binding]; other site 340100000850 protocatechuate 3,4-dioxygenase, beta subunit; Region: protocat_beta; TIGR02422 340100000851 active site 340100000852 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100000853 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100000854 The 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 340100000855 dimerization interface [polypeptide binding]; other site 340100000856 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100000857 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 340100000858 tetramer interface [polypeptide binding]; other site 340100000859 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100000860 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000861 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100000862 The 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 340100000863 dimerization interface [polypeptide binding]; other site 340100000864 Histidine kinase; Region: His_kinase; pfam06580 340100000865 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100000866 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100000867 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 340100000868 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 340100000869 NADP binding site [chemical binding]; other site 340100000870 dimer interface [polypeptide binding]; other site 340100000871 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100000872 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100000873 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100000874 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100000875 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100000876 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100000877 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100000878 active site 340100000879 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100000880 Nitronate monooxygenase; Region: NMO; pfam03060 340100000881 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 340100000882 FMN binding site [chemical binding]; other site 340100000883 substrate binding site [chemical binding]; other site 340100000884 putative catalytic residue [active] 340100000885 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100000886 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 340100000887 substrate binding site [chemical binding]; other site 340100000888 oxyanion hole (OAH) forming residues; other site 340100000889 trimer interface [polypeptide binding]; other site 340100000890 RES domain; Region: RES; smart00953 340100000891 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 340100000892 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 340100000893 hypothetical protein; Validated; Region: PRK08245 340100000894 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 340100000895 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 340100000896 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 340100000897 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 340100000898 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 340100000899 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 340100000900 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 340100000901 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 340100000902 active site 340100000903 homotetramer interface [polypeptide binding]; other site 340100000904 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100000905 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 340100000906 putative ligand binding site [chemical binding]; other site 340100000907 Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like-1; cd12808 340100000908 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100000909 catalytic site [active] 340100000910 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 340100000911 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 340100000912 phosphate binding site [ion binding]; other site 340100000913 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100000914 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100000915 The 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 340100000916 dimerization interface [polypeptide binding]; other site 340100000917 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100000918 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100000919 MlrC C-terminus; Region: MlrC_C; pfam07171 340100000920 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 340100000921 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100000922 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100000923 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 340100000924 dimer interface [polypeptide binding]; other site 340100000925 conserved gate region; other site 340100000926 putative PBP binding loops; other site 340100000927 ABC-ATPase subunit interface; other site 340100000928 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100000929 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 340100000930 dimer interface [polypeptide binding]; other site 340100000931 conserved gate region; other site 340100000932 putative PBP binding loops; other site 340100000933 ABC-ATPase subunit interface; other site 340100000934 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100000935 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100000936 Walker A/P-loop; other site 340100000937 ATP binding site [chemical binding]; other site 340100000938 Q-loop/lid; other site 340100000939 ABC transporter signature motif; other site 340100000940 Walker B; other site 340100000941 D-loop; other site 340100000942 H-loop/switch region; other site 340100000943 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 340100000944 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100000945 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100000946 Walker A/P-loop; other site 340100000947 ATP binding site [chemical binding]; other site 340100000948 Q-loop/lid; other site 340100000949 ABC transporter signature motif; other site 340100000950 Walker B; other site 340100000951 D-loop; other site 340100000952 H-loop/switch region; other site 340100000953 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100000954 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 340100000955 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 340100000956 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100000957 Amidase; Region: Amidase; cl11426 340100000958 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100000959 active site 340100000960 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 340100000961 NPCBM-associated, NEW3 domain of alpha-galactosidase; Region: NPCBM_assoc; pfam10633 340100000962 NPCBM-associated, NEW3 domain of alpha-galactosidase; Region: NPCBM_assoc; pfam10633 340100000963 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100000964 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100000965 DNA-binding site [nucleotide binding]; DNA binding site 340100000966 FCD domain; Region: FCD; pfam07729 340100000967 urea carboxylase; Region: urea_carbox; TIGR02712 340100000968 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100000969 ATP-grasp domain; Region: ATP-grasp_4; cl17255 340100000970 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 340100000971 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 340100000972 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 340100000973 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 340100000974 carboxyltransferase (CT) interaction site; other site 340100000975 biotinylation site [posttranslational modification]; other site 340100000976 allophanate hydrolase; Provisional; Region: PRK08186 340100000977 Amidase; Region: Amidase; cl11426 340100000978 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100000979 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 340100000980 putative ligand binding site [chemical binding]; other site 340100000981 HEAT repeats; Region: HEAT_2; pfam13646 340100000982 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 340100000983 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100000984 TM-ABC transporter signature motif; other site 340100000985 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100000986 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 340100000987 TM-ABC transporter signature motif; other site 340100000988 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 340100000989 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100000990 Walker A/P-loop; other site 340100000991 ATP binding site [chemical binding]; other site 340100000992 Q-loop/lid; other site 340100000993 ABC transporter signature motif; other site 340100000994 Walker B; other site 340100000995 D-loop; other site 340100000996 H-loop/switch region; other site 340100000997 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 340100000998 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100000999 Walker A/P-loop; other site 340100001000 ATP binding site [chemical binding]; other site 340100001001 Q-loop/lid; other site 340100001002 ABC transporter signature motif; other site 340100001003 Walker B; other site 340100001004 D-loop; other site 340100001005 H-loop/switch region; other site 340100001006 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100001007 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100001008 MarR family; Region: MarR_2; pfam12802 340100001009 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100001010 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001011 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 340100001012 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100001013 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 340100001014 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100001015 MarR family; Region: MarR_2; pfam12802 340100001016 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 340100001017 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 340100001018 amphipathic channel; other site 340100001019 Asn-Pro-Ala signature motifs; other site 340100001020 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 340100001021 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 340100001022 putative choline sulfate-utilization transcription factor; Region: chol_sulf_TF; TIGR03418 340100001023 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001024 The 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 340100001025 dimerization interface [polypeptide binding]; other site 340100001026 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 340100001027 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 340100001028 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 340100001029 putative catalytic residue [active] 340100001030 short chain dehydrogenase; Provisional; Region: PRK06123 340100001031 classical (c) SDRs; Region: SDR_c; cd05233 340100001032 NAD(P) binding site [chemical binding]; other site 340100001033 active site 340100001034 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 340100001035 active site 340100001036 ribulose/triose binding site [chemical binding]; other site 340100001037 phosphate binding site [ion binding]; other site 340100001038 substrate (anthranilate) binding pocket [chemical binding]; other site 340100001039 product (indole) binding pocket [chemical binding]; other site 340100001040 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 340100001041 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 340100001042 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 340100001043 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 340100001044 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 340100001045 glutamine binding [chemical binding]; other site 340100001046 catalytic triad [active] 340100001047 anthranilate synthase component I; Provisional; Region: PRK13565 340100001048 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 340100001049 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 340100001050 phosphoglycolate phosphatase; Provisional; Region: PRK13222 340100001051 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 340100001052 motif II; other site 340100001053 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 340100001054 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 340100001055 substrate binding site [chemical binding]; other site 340100001056 hexamer interface [polypeptide binding]; other site 340100001057 metal binding site [ion binding]; metal-binding site 340100001058 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 340100001059 MltA specific insert domain; Region: MltA; smart00925 340100001060 3D domain; Region: 3D; pfam06725 340100001061 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608 340100001062 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 340100001063 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 340100001064 dimerization domain [polypeptide binding]; other site 340100001065 dimer interface [polypeptide binding]; other site 340100001066 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 340100001067 catalytic residues [active] 340100001068 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 340100001069 dimerization interface [polypeptide binding]; other site 340100001070 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; Region: 2-Hacid_dh; pfam00389 340100001071 NAD binding site [chemical binding]; other site 340100001072 ligand binding site [chemical binding]; other site 340100001073 catalytic site [active] 340100001074 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 340100001075 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 340100001076 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 340100001077 Ligand Binding Site [chemical binding]; other site 340100001078 Dihydroneopterin aldolase; Region: FolB; pfam02152 340100001079 active site 340100001080 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 340100001081 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 340100001082 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 340100001083 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 340100001084 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 340100001085 protein binding site [polypeptide binding]; other site 340100001086 enoyl-CoA hydratase; Provisional; Region: PRK05862 340100001087 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 340100001088 substrate binding site [chemical binding]; other site 340100001089 oxyanion hole (OAH) forming residues; other site 340100001090 trimer interface [polypeptide binding]; other site 340100001091 Uncharacterized conserved protein [Function unknown]; Region: COG5361 340100001092 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 340100001093 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 340100001094 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 340100001095 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 340100001096 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 340100001097 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 340100001098 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 340100001099 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 340100001100 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 340100001101 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 340100001102 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 340100001103 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 340100001104 beta subunit interaction interface [polypeptide binding]; other site 340100001105 Walker A motif; other site 340100001106 ATP binding site [chemical binding]; other site 340100001107 Walker B motif; other site 340100001108 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 340100001109 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 340100001110 core domain interface [polypeptide binding]; other site 340100001111 delta subunit interface [polypeptide binding]; other site 340100001112 epsilon subunit interface [polypeptide binding]; other site 340100001113 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 340100001114 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 340100001115 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 340100001116 alpha subunit interaction interface [polypeptide binding]; other site 340100001117 Walker A motif; other site 340100001118 ATP binding site [chemical binding]; other site 340100001119 Walker B motif; other site 340100001120 inhibitor binding site; inhibition site 340100001121 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 340100001122 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 340100001123 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 340100001124 gamma subunit interface [polypeptide binding]; other site 340100001125 epsilon subunit interface [polypeptide binding]; other site 340100001126 LBP interface [polypeptide binding]; other site 340100001127 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 340100001128 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 340100001129 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 340100001130 tetramer interface [polypeptide binding]; other site 340100001131 heme binding pocket [chemical binding]; other site 340100001132 NADPH binding site [chemical binding]; other site 340100001133 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 340100001134 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 340100001135 substrate binding site [chemical binding]; other site 340100001136 active site 340100001137 primosome assembly protein PriA; Validated; Region: PRK05580 340100001138 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 340100001139 ATP binding site [chemical binding]; other site 340100001140 putative Mg++ binding site [ion binding]; other site 340100001141 helicase superfamily c-terminal domain; Region: HELICc; smart00490 340100001142 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 340100001143 Part of AAA domain; Region: AAA_19; pfam13245 340100001144 Family description; Region: UvrD_C_2; pfam13538 340100001145 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100001146 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340100001147 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 340100001148 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100001149 hypothetical protein; Provisional; Region: PRK07338 340100001150 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 340100001151 metal binding site [ion binding]; metal-binding site 340100001152 dimer interface [polypeptide binding]; other site 340100001153 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 340100001154 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 340100001155 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100001156 Walker A/P-loop; other site 340100001157 ATP binding site [chemical binding]; other site 340100001158 Q-loop/lid; other site 340100001159 ABC transporter signature motif; other site 340100001160 Walker B; other site 340100001161 D-loop; other site 340100001162 H-loop/switch region; other site 340100001163 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 340100001164 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100001165 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100001166 Walker A/P-loop; other site 340100001167 ATP binding site [chemical binding]; other site 340100001168 Q-loop/lid; other site 340100001169 ABC transporter signature motif; other site 340100001170 Walker B; other site 340100001171 D-loop; other site 340100001172 H-loop/switch region; other site 340100001173 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 340100001174 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 340100001175 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 340100001176 dimer interface [polypeptide binding]; other site 340100001177 conserved gate region; other site 340100001178 putative PBP binding loops; other site 340100001179 ABC-ATPase subunit interface; other site 340100001180 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100001181 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 340100001182 dimer interface [polypeptide binding]; other site 340100001183 conserved gate region; other site 340100001184 putative PBP binding loops; other site 340100001185 ABC-ATPase subunit interface; other site 340100001186 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 340100001187 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100001188 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 340100001189 active site 340100001190 Zn binding site [ion binding]; other site 340100001191 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001192 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001193 The 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 340100001194 dimerization interface [polypeptide binding]; other site 340100001195 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 340100001196 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100001197 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 340100001198 putative substrate binding site [chemical binding]; other site 340100001199 putative ATP binding site [chemical binding]; other site 340100001200 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 340100001201 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100001202 substrate binding site [chemical binding]; other site 340100001203 oxyanion hole (OAH) forming residues; other site 340100001204 trimer interface [polypeptide binding]; other site 340100001205 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 340100001206 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100001207 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 340100001208 substrate binding site [chemical binding]; other site 340100001209 oxyanion hole (OAH) forming residues; other site 340100001210 trimer interface [polypeptide binding]; other site 340100001211 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 340100001212 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100001213 FMN binding site [chemical binding]; other site 340100001214 substrate binding site [chemical binding]; other site 340100001215 putative catalytic residue [active] 340100001216 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100001217 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100001218 YsiA-like protein, C-terminal region; Region: TetR_C_4; pfam08359 340100001219 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100001220 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100001221 active site 340100001222 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100001223 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100001224 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 340100001225 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100001226 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100001227 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100001228 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 340100001229 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100001230 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 340100001231 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 340100001232 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001233 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100001234 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100001235 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100001236 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100001237 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 340100001238 substrate binding site [chemical binding]; other site 340100001239 oxyanion hole (OAH) forming residues; other site 340100001240 trimer interface [polypeptide binding]; other site 340100001241 short chain dehydrogenase; Provisional; Region: PRK07791 340100001242 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001243 NAD(P) binding site [chemical binding]; other site 340100001244 active site 340100001245 Coenzyme A transferase; Region: CoA_trans; cl17247 340100001246 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100001247 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100001248 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 340100001249 FMN binding site [chemical binding]; other site 340100001250 substrate binding site [chemical binding]; other site 340100001251 putative catalytic residue [active] 340100001252 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 340100001253 putative active site [active] 340100001254 putative catalytic site [active] 340100001255 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100001256 thiolase; Provisional; Region: PRK06158 340100001257 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 340100001258 active site 340100001259 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 340100001260 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100001261 putative substrate translocation pore; other site 340100001262 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100001263 Coenzyme A binding pocket [chemical binding]; other site 340100001264 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 340100001265 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340100001266 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 340100001267 active site residue [active] 340100001268 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100001269 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001270 hypothetical protein; Validated; Region: PRK06201 340100001271 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 340100001272 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100001273 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100001274 DNA-binding site [nucleotide binding]; DNA binding site 340100001275 FCD domain; Region: FCD; pfam07729 340100001276 glucose-1-dehydrogenase; Provisional; Region: PRK08936 340100001277 glucose 1 dehydrogenase (GlcDH), classical (c) SDRs; Region: GlcDH_SDR_c; cd05358 340100001278 NAD binding site [chemical binding]; other site 340100001279 homodimer interface [polypeptide binding]; other site 340100001280 active site 340100001281 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 340100001282 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 340100001283 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001284 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 340100001285 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 340100001286 NAD(P) binding site [chemical binding]; other site 340100001287 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100001288 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100001289 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001290 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001291 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 340100001292 putative effector binding pocket; other site 340100001293 dimerization interface [polypeptide binding]; other site 340100001294 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 340100001295 glutamate--cysteine ligase; Provisional; Region: PRK02107 340100001296 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 340100001297 DNA binding residues [nucleotide binding] 340100001298 dimerization interface [polypeptide binding]; other site 340100001299 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001300 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001301 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 340100001302 putative dimerization interface [polypeptide binding]; other site 340100001303 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 340100001304 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 340100001305 catalytic loop [active] 340100001306 iron binding site [ion binding]; other site 340100001307 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 340100001308 Iron-sulfur protein interface; other site 340100001309 proximal heme binding site [chemical binding]; other site 340100001310 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 340100001311 Fumarase C-terminus; Region: Fumerase_C; cl00795 340100001312 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK06263 340100001313 L-aspartate oxidase; Provisional; Region: PRK06175 340100001314 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340100001315 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001316 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 340100001317 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100001318 PYR/PP interface [polypeptide binding]; other site 340100001319 dimer interface [polypeptide binding]; other site 340100001320 TPP binding site [chemical binding]; other site 340100001321 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100001322 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 340100001323 TPP-binding site; other site 340100001324 dimer interface [polypeptide binding]; other site 340100001325 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100001326 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100001327 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100001328 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 340100001329 ligand binding site [chemical binding]; other site 340100001330 NAD binding site [chemical binding]; other site 340100001331 dimerization interface [polypeptide binding]; other site 340100001332 catalytic site [active] 340100001333 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100001334 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 340100001335 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 340100001336 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100001337 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 340100001338 Walker A/P-loop; other site 340100001339 ATP binding site [chemical binding]; other site 340100001340 Q-loop/lid; other site 340100001341 ABC transporter signature motif; other site 340100001342 Walker B; other site 340100001343 D-loop; other site 340100001344 H-loop/switch region; other site 340100001345 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 340100001346 NMT1-like family; Region: NMT1_2; pfam13379 340100001347 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 340100001348 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 340100001349 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100001350 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100001351 DNA-binding site [nucleotide binding]; DNA binding site 340100001352 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 340100001353 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 340100001354 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 340100001355 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100001356 muropeptide transporter; Reviewed; Region: ampG; PRK11902 340100001357 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 340100001358 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 340100001359 Predicted membrane protein [Function unknown]; Region: COG2860 340100001360 UPF0126 domain; Region: UPF0126; pfam03458 340100001361 UPF0126 domain; Region: UPF0126; pfam03458 340100001362 glutamate dehydrogenase; Provisional; Region: PRK09414 340100001363 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 340100001364 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 340100001365 NAD(P) binding site [chemical binding]; other site 340100001366 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 340100001367 putative active site [active] 340100001368 putative catalytic site [active] 340100001369 putative DNA binding site [nucleotide binding]; other site 340100001370 putative phosphate binding site [ion binding]; other site 340100001371 metal binding site A [ion binding]; metal-binding site 340100001372 putative AP binding site [nucleotide binding]; other site 340100001373 putative metal binding site B [ion binding]; other site 340100001374 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100001375 active site 340100001376 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 340100001377 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 340100001378 GatB domain; Region: GatB_Yqey; smart00845 340100001379 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100001380 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 340100001381 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 340100001382 rod shape-determining protein MreB; Provisional; Region: PRK13927 340100001383 MreB and similar proteins; Region: MreB_like; cd10225 340100001384 nucleotide binding site [chemical binding]; other site 340100001385 Mg binding site [ion binding]; other site 340100001386 putative protofilament interaction site [polypeptide binding]; other site 340100001387 RodZ interaction site [polypeptide binding]; other site 340100001388 rod shape-determining protein MreC; Region: mreC; TIGR00219 340100001389 rod shape-determining protein MreC; Region: MreC; pfam04085 340100001390 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 340100001391 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 340100001392 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 340100001393 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 340100001394 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 340100001395 division inhibitor protein; Provisional; Region: slmA; PRK09480 340100001396 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100001397 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 340100001398 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 340100001399 motif II; other site 340100001400 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 340100001401 feedback inhibition sensing region; other site 340100001402 homohexameric interface [polypeptide binding]; other site 340100001403 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 340100001404 nucleotide binding site [chemical binding]; other site 340100001405 N-acetyl-L-glutamate binding site [chemical binding]; other site 340100001406 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 340100001407 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 340100001408 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 340100001409 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 340100001410 catalytic residues [active] 340100001411 BON domain; Region: BON; pfam04972 340100001412 BON domain; Region: BON; pfam04972 340100001413 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 340100001414 dimer interface [polypeptide binding]; other site 340100001415 active site 340100001416 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 340100001417 Predicted methyltransferases [General function prediction only]; Region: COG0313 340100001418 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 340100001419 putative SAM binding site [chemical binding]; other site 340100001420 putative homodimer interface [polypeptide binding]; other site 340100001421 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 340100001422 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340100001423 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 340100001424 DNA binding site [nucleotide binding] 340100001425 active site 340100001426 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 340100001427 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 340100001428 Sporulation related domain; Region: SPOR; pfam05036 340100001429 shikimate kinase; Reviewed; Region: aroK; PRK00131 340100001430 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 340100001431 Cytochrome c; Region: Cytochrom_C; cl11414 340100001432 Cytochrome c; Region: Cytochrom_C; cl11414 340100001433 Cytochrome c; Region: Cytochrom_C; pfam00034 340100001434 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100001435 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100001436 Cytochrome c; Region: Cytochrom_C; pfam00034 340100001437 HPr kinase/phosphorylase; Provisional; Region: PRK05428 340100001438 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 340100001439 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 340100001440 Hpr binding site; other site 340100001441 active site 340100001442 homohexamer subunit interaction site [polypeptide binding]; other site 340100001443 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 340100001444 active site 340100001445 phosphorylation site [posttranslational modification] 340100001446 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 340100001447 30S subunit binding site; other site 340100001448 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 340100001449 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 340100001450 Walker A/P-loop; other site 340100001451 ATP binding site [chemical binding]; other site 340100001452 Q-loop/lid; other site 340100001453 ABC transporter signature motif; other site 340100001454 Walker B; other site 340100001455 D-loop; other site 340100001456 H-loop/switch region; other site 340100001457 OstA-like protein; Region: OstA; pfam03968 340100001458 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 340100001459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 340100001460 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 340100001461 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 340100001462 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 340100001463 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 340100001464 putative active site [active] 340100001465 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 340100001466 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 340100001467 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100001468 ATP-grasp domain; Region: ATP-grasp; pfam02222 340100001469 Predicted transcriptional regulators [Transcription]; Region: COG1510 340100001470 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 340100001471 dimerization interface [polypeptide binding]; other site 340100001472 putative DNA binding site [nucleotide binding]; other site 340100001473 putative Zn2+ binding site [ion binding]; other site 340100001474 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 340100001475 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 340100001476 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 340100001477 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 340100001478 Membrane bound YbgT-like protein; Region: YbgT_YccB; pfam08173 340100001479 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100001480 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100001481 Walker A/P-loop; other site 340100001482 ATP binding site [chemical binding]; other site 340100001483 ABC transporter; Region: ABC_tran; pfam00005 340100001484 Q-loop/lid; other site 340100001485 ABC transporter signature motif; other site 340100001486 Walker B; other site 340100001487 D-loop; other site 340100001488 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100001489 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 340100001490 Walker A/P-loop; other site 340100001491 ATP binding site [chemical binding]; other site 340100001492 Q-loop/lid; other site 340100001493 ABC transporter signature motif; other site 340100001494 Walker B; other site 340100001495 D-loop; other site 340100001496 H-loop/switch region; other site 340100001497 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100001498 active site 340100001499 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001500 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001501 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 340100001502 putative effector binding pocket; other site 340100001503 dimerization interface [polypeptide binding]; other site 340100001504 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100001505 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 340100001506 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 340100001507 trimer interface [polypeptide binding]; other site 340100001508 eyelet of channel; other site 340100001509 threonine dehydratase; Reviewed; Region: PRK09224 340100001510 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 340100001511 tetramer interface [polypeptide binding]; other site 340100001512 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100001513 catalytic residue [active] 340100001514 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 340100001515 putative Ile/Val binding site [chemical binding]; other site 340100001516 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 340100001517 putative Ile/Val binding site [chemical binding]; other site 340100001518 Predicted membrane protein [Function unknown]; Region: COG1238 340100001519 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 340100001520 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100001521 FAD binding domain; Region: FAD_binding_4; pfam01565 340100001522 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100001523 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 340100001524 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 340100001525 Cysteine-rich domain; Region: CCG; pfam02754 340100001526 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 340100001527 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001528 enoyl-CoA hydratase; Provisional; Region: PRK09245 340100001529 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 340100001530 substrate binding site [chemical binding]; other site 340100001531 oxyanion hole (OAH) forming residues; other site 340100001532 trimer interface [polypeptide binding]; other site 340100001533 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100001534 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100001535 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100001536 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001537 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 340100001538 dimerization interface [polypeptide binding]; other site 340100001539 substrate binding pocket [chemical binding]; other site 340100001540 succinic semialdehyde dehydrogenase; Region: PLN02278 340100001541 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100001542 tetramerization interface [polypeptide binding]; other site 340100001543 NAD(P) binding site [chemical binding]; other site 340100001544 catalytic residues [active] 340100001545 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 340100001546 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100001547 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100001548 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100001549 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 340100001550 putative active site [active] 340100001551 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 340100001552 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 340100001553 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 340100001554 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 340100001555 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100001556 putative metal binding site [ion binding]; other site 340100001557 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100001558 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001559 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 340100001560 putative dimerization interface [polypeptide binding]; other site 340100001561 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 340100001562 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 340100001563 ligand binding site [chemical binding]; other site 340100001564 NAD binding site [chemical binding]; other site 340100001565 tetramer interface [polypeptide binding]; other site 340100001566 catalytic site [active] 340100001567 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 340100001568 L-serine binding site [chemical binding]; other site 340100001569 ACT domain interface; other site 340100001570 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 340100001571 PAS domain; Region: PAS; smart00091 340100001572 putative active site [active] 340100001573 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 340100001574 dimer interface [polypeptide binding]; other site 340100001575 phosphorylation site [posttranslational modification] 340100001576 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 340100001577 ATP binding site [chemical binding]; other site 340100001578 Mg2+ binding site [ion binding]; other site 340100001579 G-X-G motif; other site 340100001580 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 340100001581 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100001582 active site 340100001583 phosphorylation site [posttranslational modification] 340100001584 intermolecular recognition site; other site 340100001585 dimerization interface [polypeptide binding]; other site 340100001586 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 340100001587 DNA binding site [nucleotide binding] 340100001588 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 340100001589 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 340100001590 S-adenosylmethionine binding site [chemical binding]; other site 340100001591 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 340100001592 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 340100001593 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 340100001594 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100001595 dinuclear metal binding motif [ion binding]; other site 340100001596 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 340100001597 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 340100001598 active site 340100001599 nucleotide binding site [chemical binding]; other site 340100001600 HIGH motif; other site 340100001601 KMSKS motif; other site 340100001602 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 340100001603 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 340100001604 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 340100001605 S-adenosylmethionine binding site [chemical binding]; other site 340100001606 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 340100001607 substrate binding site [chemical binding]; other site 340100001608 dimer interface [polypeptide binding]; other site 340100001609 ATP binding site [chemical binding]; other site 340100001610 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 340100001611 ThiS interaction site; other site 340100001612 putative active site [active] 340100001613 tetramer interface [polypeptide binding]; other site 340100001614 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 340100001615 cobalamin binding residues [chemical binding]; other site 340100001616 putative BtuC binding residues; other site 340100001617 dimer interface [polypeptide binding]; other site 340100001618 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 340100001619 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 340100001620 N-terminal plug; other site 340100001621 ligand-binding site [chemical binding]; other site 340100001622 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 340100001623 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 340100001624 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 340100001625 substrate binding pocket [chemical binding]; other site 340100001626 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 340100001627 B12 binding site [chemical binding]; other site 340100001628 cobalt ligand [ion binding]; other site 340100001629 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 340100001630 Methyltransferase domain; Region: Methyltransf_31; pfam13847 340100001631 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 340100001632 S-adenosylmethionine binding site [chemical binding]; other site 340100001633 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 340100001634 salt bridge; other site 340100001635 non-specific DNA binding site [nucleotide binding]; other site 340100001636 sequence-specific DNA binding site [nucleotide binding]; other site 340100001637 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 340100001638 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100001639 minor groove reading motif; other site 340100001640 helix-hairpin-helix signature motif; other site 340100001641 substrate binding pocket [chemical binding]; other site 340100001642 active site 340100001643 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 340100001644 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 340100001645 DNA binding and oxoG recognition site [nucleotide binding] 340100001646 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 340100001647 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 340100001648 dimer interface [polypeptide binding]; other site 340100001649 PYR/PP interface [polypeptide binding]; other site 340100001650 TPP binding site [chemical binding]; other site 340100001651 substrate binding site [chemical binding]; other site 340100001652 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 340100001653 TPP-binding site [chemical binding]; other site 340100001654 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 340100001655 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13489 340100001656 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 340100001657 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 340100001658 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100001659 Walker A/P-loop; other site 340100001660 ATP binding site [chemical binding]; other site 340100001661 Q-loop/lid; other site 340100001662 ABC transporter signature motif; other site 340100001663 Walker B; other site 340100001664 D-loop; other site 340100001665 H-loop/switch region; other site 340100001666 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 340100001667 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 340100001668 substrate binding pocket [chemical binding]; other site 340100001669 membrane-bound complex binding site; other site 340100001670 hinge residues; other site 340100001671 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 340100001672 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 340100001673 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 340100001674 dimer interface [polypeptide binding]; other site 340100001675 conserved gate region; other site 340100001676 putative PBP binding loops; other site 340100001677 ABC-ATPase subunit interface; other site 340100001678 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 340100001679 dimer interface [polypeptide binding]; other site 340100001680 conserved gate region; other site 340100001681 putative PBP binding loops; other site 340100001682 ABC-ATPase subunit interface; other site 340100001683 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100001684 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100001685 Walker A/P-loop; other site 340100001686 ATP binding site [chemical binding]; other site 340100001687 Q-loop/lid; other site 340100001688 ABC transporter signature motif; other site 340100001689 Walker B; other site 340100001690 D-loop; other site 340100001691 H-loop/switch region; other site 340100001692 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001693 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100001694 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100001695 Transposase; Region: HTH_Tnp_1; cl17663 340100001696 putative transposase OrfB; Reviewed; Region: PHA02517 340100001697 HTH-like domain; Region: HTH_21; pfam13276 340100001698 Integrase core domain; Region: rve; pfam00665 340100001699 Integrase core domain; Region: rve_2; pfam13333 340100001700 salicylate hydroxylase; Provisional; Region: PRK08163 340100001701 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100001702 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 340100001703 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001704 Chorismate mutase type II; Region: CM_2; smart00830 340100001705 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 340100001706 maleylacetoacetate isomerase; Region: maiA; TIGR01262 340100001707 C-terminal domain interface [polypeptide binding]; other site 340100001708 GSH binding site (G-site) [chemical binding]; other site 340100001709 putative dimer interface [polypeptide binding]; other site 340100001710 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 340100001711 dimer interface [polypeptide binding]; other site 340100001712 N-terminal domain interface [polypeptide binding]; other site 340100001713 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 340100001714 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100001715 hypothetical protein; Provisional; Region: PRK07538 340100001716 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100001717 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 340100001718 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100001719 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 340100001720 Cupin domain; Region: Cupin_2; pfam07883 340100001721 Cupin domain; Region: Cupin_2; cl17218 340100001722 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 340100001723 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100001724 The 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 340100001725 dimerization interface [polypeptide binding]; other site 340100001726 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 340100001727 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 340100001728 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340100001729 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; pfam09937 340100001730 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100001731 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001732 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100001733 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001734 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001735 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001736 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340100001737 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100001738 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001739 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100001740 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 340100001741 HNH/ENDO VII superfamily nuclease with conserved GHE residues; Region: GH-E; pfam14410 340100001742 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 340100001743 glycerol kinase; Provisional; Region: glpK; PRK00047 340100001744 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 340100001745 N- and C-terminal domain interface [polypeptide binding]; other site 340100001746 active site 340100001747 MgATP binding site [chemical binding]; other site 340100001748 catalytic site [active] 340100001749 metal binding site [ion binding]; metal-binding site 340100001750 glycerol binding site [chemical binding]; other site 340100001751 homotetramer interface [polypeptide binding]; other site 340100001752 homodimer interface [polypeptide binding]; other site 340100001753 FBP binding site [chemical binding]; other site 340100001754 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 340100001755 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100001756 putative substrate translocation pore; other site 340100001757 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 340100001758 Pantoate-beta-alanine ligase; Region: PanC; cd00560 340100001759 pantoate--beta-alanine ligase; Region: panC; TIGR00018 340100001760 active site 340100001761 ATP-binding site [chemical binding]; other site 340100001762 pantoate-binding site; other site 340100001763 HXXH motif; other site 340100001764 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100001765 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 340100001766 DNA binding residues [nucleotide binding] 340100001767 dimerization interface [polypeptide binding]; other site 340100001768 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 340100001769 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 340100001770 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 340100001771 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 340100001772 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 340100001773 CoA-binding site [chemical binding]; other site 340100001774 ATP-binding [chemical binding]; other site 340100001775 hypothetical protein; Provisional; Region: PRK05287 340100001776 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 340100001777 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100001778 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100001779 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 340100001780 Protein export membrane protein; Region: SecD_SecF; cl14618 340100001781 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 340100001782 Protein export membrane protein; Region: SecD_SecF; cl14618 340100001783 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100001784 hypothetical protein; Provisional; Region: PRK08999 340100001785 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 340100001786 active site 340100001787 8-oxo-dGMP binding site [chemical binding]; other site 340100001788 nudix motif; other site 340100001789 metal binding site [ion binding]; metal-binding site 340100001790 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 340100001791 active site 340100001792 thiamine phosphate binding site [chemical binding]; other site 340100001793 pyrophosphate binding site [ion binding]; other site 340100001794 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 340100001795 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 340100001796 Walker A motif; other site 340100001797 ATP binding site [chemical binding]; other site 340100001798 Walker B motif; other site 340100001799 arginine finger; other site 340100001800 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 340100001801 heterotetramer interface [polypeptide binding]; other site 340100001802 active site pocket [active] 340100001803 cleavage site 340100001804 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100001805 MarR family; Region: MarR; pfam01047 340100001806 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 340100001807 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100001808 substrate binding pocket [chemical binding]; other site 340100001809 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100001810 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 340100001811 putative ligand binding site [chemical binding]; other site 340100001812 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 340100001813 TM-ABC transporter signature motif; other site 340100001814 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100001815 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 340100001816 TM-ABC transporter signature motif; other site 340100001817 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100001818 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100001819 Walker A/P-loop; other site 340100001820 ATP binding site [chemical binding]; other site 340100001821 Q-loop/lid; other site 340100001822 ABC transporter signature motif; other site 340100001823 Walker B; other site 340100001824 D-loop; other site 340100001825 H-loop/switch region; other site 340100001826 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100001827 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100001828 Walker A/P-loop; other site 340100001829 ATP binding site [chemical binding]; other site 340100001830 Q-loop/lid; other site 340100001831 ABC transporter signature motif; other site 340100001832 Walker B; other site 340100001833 D-loop; other site 340100001834 H-loop/switch region; other site 340100001835 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 340100001836 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100001837 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 340100001838 active site 340100001839 FMN binding site [chemical binding]; other site 340100001840 substrate binding site [chemical binding]; other site 340100001841 homotetramer interface [polypeptide binding]; other site 340100001842 catalytic residue [active] 340100001843 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100001844 classical (c) SDRs; Region: SDR_c; cd05233 340100001845 NAD(P) binding site [chemical binding]; other site 340100001846 active site 340100001847 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100001848 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 340100001849 substrate binding site [chemical binding]; other site 340100001850 oxyanion hole (OAH) forming residues; other site 340100001851 trimer interface [polypeptide binding]; other site 340100001852 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100001853 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100001854 active site 340100001855 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100001856 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 340100001857 acyl-activating enzyme (AAE) consensus motif; other site 340100001858 AMP binding site [chemical binding]; other site 340100001859 active site 340100001860 CoA binding site [chemical binding]; other site 340100001861 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 340100001862 active site 340100001863 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 340100001864 homotrimer interaction site [polypeptide binding]; other site 340100001865 putative active site [active] 340100001866 Protein of unknown function (DUF342); Region: DUF342; pfam03961 340100001867 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 340100001868 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 340100001869 inhibitor-cofactor binding pocket; inhibition site 340100001870 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100001871 catalytic residue [active] 340100001872 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 340100001873 thiamine phosphate binding site [chemical binding]; other site 340100001874 active site 340100001875 pyrophosphate binding site [ion binding]; other site 340100001876 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 340100001877 substrate binding site [chemical binding]; other site 340100001878 ATP binding site [chemical binding]; other site 340100001879 Rubredoxin [Energy production and conversion]; Region: COG1773 340100001880 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 340100001881 iron binding site [ion binding]; other site 340100001882 hypothetical protein; Validated; Region: PRK00228 340100001883 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 340100001884 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 340100001885 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340100001886 putative acyl-acceptor binding pocket; other site 340100001887 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 340100001888 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 340100001889 active site 340100001890 metal binding site [ion binding]; metal-binding site 340100001891 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 340100001892 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 340100001893 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 340100001894 Transglycosylase; Region: Transgly; cl17702 340100001895 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 340100001896 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 340100001897 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 340100001898 shikimate binding site; other site 340100001899 NAD(P) binding site [chemical binding]; other site 340100001900 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 340100001901 RNB domain; Region: RNB; pfam00773 340100001902 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 340100001903 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 340100001904 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100001905 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 340100001906 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100001907 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100001908 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100001909 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 340100001910 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 340100001911 catalytic residues [active] 340100001912 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 340100001913 Dehydroquinase class II; Region: DHquinase_II; pfam01220 340100001914 trimer interface [polypeptide binding]; other site 340100001915 active site 340100001916 dimer interface [polypeptide binding]; other site 340100001917 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 340100001918 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 340100001919 carboxyltransferase (CT) interaction site; other site 340100001920 biotinylation site [posttranslational modification]; other site 340100001921 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 340100001922 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100001923 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 340100001924 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 340100001925 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 340100001926 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 340100001927 S-adenosylmethionine binding site [chemical binding]; other site 340100001928 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 340100001929 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 340100001930 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 340100001931 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 340100001932 substrate binding site [chemical binding]; other site 340100001933 ATP binding site [chemical binding]; other site 340100001934 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 340100001935 YGGT family; Region: YGGT; pfam02325 340100001936 YGGT family; Region: YGGT; pfam02325 340100001937 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 340100001938 dimer interface [polypeptide binding]; other site 340100001939 putative radical transfer pathway; other site 340100001940 diiron center [ion binding]; other site 340100001941 tyrosyl radical; other site 340100001942 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 340100001943 ATP cone domain; Region: ATP-cone; pfam03477 340100001944 Class I ribonucleotide reductase; Region: RNR_I; cd01679 340100001945 active site 340100001946 dimer interface [polypeptide binding]; other site 340100001947 catalytic residues [active] 340100001948 effector binding site; other site 340100001949 R2 peptide binding site; other site 340100001950 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 340100001951 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 340100001952 dimer interface [polypeptide binding]; other site 340100001953 PYR/PP interface [polypeptide binding]; other site 340100001954 TPP binding site [chemical binding]; other site 340100001955 substrate binding site [chemical binding]; other site 340100001956 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 340100001957 TPP-binding site [chemical binding]; other site 340100001958 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 340100001959 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100001960 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 340100001961 putative DNA binding site [nucleotide binding]; other site 340100001962 putative Zn2+ binding site [ion binding]; other site 340100001963 AsnC family; Region: AsnC_trans_reg; pfam01037 340100001964 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 340100001965 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100001966 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 340100001967 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 340100001968 HIGH motif; other site 340100001969 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 340100001970 active site 340100001971 KMSKS motif; other site 340100001972 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 340100001973 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100001974 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100001975 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 340100001976 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100001977 Coenzyme A binding pocket [chemical binding]; other site 340100001978 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 340100001979 putative hydrolase; Provisional; Region: PRK11460 340100001980 peptidase PmbA; Provisional; Region: PRK11040 340100001981 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100001982 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100001983 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 340100001984 23S rRNA interface [nucleotide binding]; other site 340100001985 L3 interface [polypeptide binding]; other site 340100001986 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 340100001987 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 340100001988 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 340100001989 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 340100001990 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 340100001991 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100001992 putative substrate translocation pore; other site 340100001993 Predicted transcriptional regulators [Transcription]; Region: COG1733 340100001994 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 340100001995 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 340100001996 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 340100001997 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 340100001998 haemagglutination activity domain; Region: Haemagg_act; pfam05860 340100001999 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100002000 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100002001 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100002002 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100002003 Colicin D; Region: Colicin_D; pfam11429 340100002004 Bacterial self-protective colicin-like immunity; Region: Colicin_immun; pfam09204 340100002005 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 340100002006 Homeodomain-like domain; Region: HTH_32; pfam13565 340100002007 Integrase core domain; Region: rve; pfam00665 340100002008 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100002009 Integrase core domain; Region: rve_3; pfam13683 340100002010 Transposase; Region: HTH_Tnp_1; pfam01527 340100002011 Transposase; Region: HTH_Tnp_1; cl17663 340100002012 HTH-like domain; Region: HTH_21; pfam13276 340100002013 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100002014 Integrase core domain; Region: rve; pfam00665 340100002015 Integrase core domain; Region: rve_3; pfam13683 340100002016 Integrase core domain; Region: rve_3; pfam13683 340100002017 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 340100002018 putative peptidase; Provisional; Region: PRK11649 340100002019 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100002020 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 340100002021 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 340100002022 active site 340100002023 HIGH motif; other site 340100002024 dimer interface [polypeptide binding]; other site 340100002025 KMSKS motif; other site 340100002026 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 340100002027 RNA binding surface [nucleotide binding]; other site 340100002028 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 340100002029 substrate binding site [chemical binding]; other site 340100002030 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 340100002031 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 340100002032 dimer interface [polypeptide binding]; other site 340100002033 active site 340100002034 glycine-pyridoxal phosphate binding site [chemical binding]; other site 340100002035 folate binding site [chemical binding]; other site 340100002036 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 340100002037 ATP cone domain; Region: ATP-cone; pfam03477 340100002038 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 340100002039 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 340100002040 catalytic motif [active] 340100002041 Zn binding site [ion binding]; other site 340100002042 RibD C-terminal domain; Region: RibD_C; cl17279 340100002043 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 340100002044 Lumazine binding domain; Region: Lum_binding; pfam00677 340100002045 Lumazine binding domain; Region: Lum_binding; pfam00677 340100002046 PrkA family serine protein kinase; Provisional; Region: PRK15455 340100002047 AAA ATPase domain; Region: AAA_16; pfam13191 340100002048 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 340100002049 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 340100002050 metal ion-dependent adhesion site (MIDAS); other site 340100002051 SpoVR family protein; Provisional; Region: PRK11767 340100002052 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 340100002053 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 340100002054 DNA binding site [nucleotide binding] 340100002055 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 340100002056 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100002057 active site 340100002058 phosphorylation site [posttranslational modification] 340100002059 intermolecular recognition site; other site 340100002060 dimerization interface [polypeptide binding]; other site 340100002061 LytTr DNA-binding domain; Region: LytTR; pfam04397 340100002062 Conserved TM helix; Region: TM_helix; pfam05552 340100002063 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 340100002064 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 340100002065 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 340100002066 dimerization interface [polypeptide binding]; other site 340100002067 active site 340100002068 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 340100002069 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 340100002070 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 340100002071 NAD binding site [chemical binding]; other site 340100002072 homotetramer interface [polypeptide binding]; other site 340100002073 homodimer interface [polypeptide binding]; other site 340100002074 substrate binding site [chemical binding]; other site 340100002075 active site 340100002076 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 340100002077 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100002078 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100002079 catalytic residue [active] 340100002080 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100002081 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100002082 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 340100002083 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 340100002084 RNA/DNA hybrid binding site [nucleotide binding]; other site 340100002085 active site 340100002086 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 340100002087 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100002088 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100002089 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 340100002090 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 340100002091 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 340100002092 active site 340100002093 catalytic site [active] 340100002094 substrate binding site [chemical binding]; other site 340100002095 Protein of unknown function (DUF3251); Region: DUF3251; cl08186 340100002096 Phage capsid family; Region: Phage_capsid; pfam05065 340100002097 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 340100002098 PAS domain; Region: PAS_9; pfam13426 340100002099 putative active site [active] 340100002100 heme pocket [chemical binding]; other site 340100002101 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100002102 dimer interface [polypeptide binding]; other site 340100002103 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 340100002104 putative CheW interface [polypeptide binding]; other site 340100002105 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 340100002106 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 340100002107 Ligand binding site; other site 340100002108 Putative Catalytic site; other site 340100002109 DXD motif; other site 340100002110 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 340100002111 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 340100002112 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 340100002113 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 340100002114 putative active site [active] 340100002115 YdjC motif; other site 340100002116 Mg binding site [ion binding]; other site 340100002117 putative homodimer interface [polypeptide binding]; other site 340100002118 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 340100002119 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 340100002120 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100002121 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100002122 EamA-like transporter family; Region: EamA; pfam00892 340100002123 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 340100002124 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100002125 DNA-binding site [nucleotide binding]; DNA binding site 340100002126 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 340100002127 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100002128 homodimer interface [polypeptide binding]; other site 340100002129 catalytic residue [active] 340100002130 Putative phosphatase (DUF442); Region: DUF442; cl17385 340100002131 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 340100002132 Ligand Binding Site [chemical binding]; other site 340100002133 elongation factor G; Reviewed; Region: PRK00007 340100002134 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 340100002135 G1 box; other site 340100002136 putative GEF interaction site [polypeptide binding]; other site 340100002137 GTP/Mg2+ binding site [chemical binding]; other site 340100002138 Switch I region; other site 340100002139 G2 box; other site 340100002140 G3 box; other site 340100002141 Switch II region; other site 340100002142 G4 box; other site 340100002143 G5 box; other site 340100002144 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 340100002145 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 340100002146 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 340100002147 putative transposase OrfB; Reviewed; Region: PHA02517 340100002148 HTH-like domain; Region: HTH_21; pfam13276 340100002149 Integrase core domain; Region: rve; pfam00665 340100002150 Integrase core domain; Region: rve_2; pfam13333 340100002151 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100002152 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100002153 Transposase; Region: HTH_Tnp_1; cl17663 340100002154 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 340100002155 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 340100002156 catalytic site [active] 340100002157 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 340100002158 putative deacylase active site [active] 340100002159 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 340100002160 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 340100002161 binding surface 340100002162 TPR motif; other site 340100002163 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 340100002164 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100002165 ligand binding site [chemical binding]; other site 340100002166 translocation protein TolB; Provisional; Region: tolB; PRK02889 340100002167 TolB amino-terminal domain; Region: TolB_N; pfam04052 340100002168 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002169 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002170 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002171 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340100002172 TolA protein; Region: tolA_full; TIGR02794 340100002173 TonB C terminal; Region: TonB_2; pfam13103 340100002174 TolA protein; Region: tolA_full; TIGR02794 340100002175 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 340100002176 TolR protein; Region: tolR; TIGR02801 340100002177 TolQ protein; Region: tolQ; TIGR02796 340100002178 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 340100002179 active site 340100002180 prolyl-tRNA synthetase; Provisional; Region: PRK09194 340100002181 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 340100002182 dimer interface [polypeptide binding]; other site 340100002183 motif 1; other site 340100002184 active site 340100002185 motif 2; other site 340100002186 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 340100002187 putative deacylase active site [active] 340100002188 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 340100002189 active site 340100002190 motif 3; other site 340100002191 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 340100002192 anticodon binding site; other site 340100002193 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 340100002194 putative active site [active] 340100002195 Ap4A binding site [chemical binding]; other site 340100002196 nudix motif; other site 340100002197 putative metal binding site [ion binding]; other site 340100002198 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 340100002199 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100002200 active site 340100002201 phosphorylation site [posttranslational modification] 340100002202 intermolecular recognition site; other site 340100002203 dimerization interface [polypeptide binding]; other site 340100002204 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 340100002205 DNA binding site [nucleotide binding] 340100002206 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 340100002207 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100002208 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 340100002209 dimer interface [polypeptide binding]; other site 340100002210 phosphorylation site [posttranslational modification] 340100002211 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 340100002212 ATP binding site [chemical binding]; other site 340100002213 Mg2+ binding site [ion binding]; other site 340100002214 G-X-G motif; other site 340100002215 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100002216 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002217 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 340100002218 putative effector binding pocket; other site 340100002219 putative dimerization interface [polypeptide binding]; other site 340100002220 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 340100002221 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100002222 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100002223 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100002224 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 340100002225 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100002226 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340100002227 Cell division protein ZapA; Region: ZapA; pfam05164 340100002228 Protein of unknown function (DUF541); Region: SIMPL; cl01077 340100002229 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 340100002230 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 340100002231 Cytochrome c; Region: Cytochrom_C; cl11414 340100002232 RNA polymerase sigma factor; Provisional; Region: PRK11922 340100002233 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 340100002234 DNA binding residues [nucleotide binding] 340100002235 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 340100002236 dinuclear metal binding motif [ion binding]; other site 340100002237 Cytochrome c2 [Energy production and conversion]; Region: COG3474 340100002238 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 340100002239 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 340100002240 dimer interface [polypeptide binding]; other site 340100002241 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 340100002242 active site 340100002243 Fe binding site [ion binding]; other site 340100002244 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100002245 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 340100002246 dimerization interface [polypeptide binding]; other site 340100002247 putative DNA binding site [nucleotide binding]; other site 340100002248 putative Zn2+ binding site [ion binding]; other site 340100002249 AsnC family; Region: AsnC_trans_reg; pfam01037 340100002250 Predicted membrane protein [Function unknown]; Region: COG3671 340100002251 SWI complex, BAF60b domains; Region: SWIB; smart00151 340100002252 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100002253 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100002254 metal binding site [ion binding]; metal-binding site 340100002255 putative dimer interface [polypeptide binding]; other site 340100002256 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 340100002257 active site 340100002258 substrate binding pocket [chemical binding]; other site 340100002259 dimer interface [polypeptide binding]; other site 340100002260 ABC transporter ATPase component; Reviewed; Region: PRK11147 340100002261 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100002262 ABC transporter; Region: ABC_tran_2; pfam12848 340100002263 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100002264 cell division protein MraZ; Reviewed; Region: PRK00326 340100002265 MraZ protein; Region: MraZ; pfam02381 340100002266 MraZ protein; Region: MraZ; pfam02381 340100002267 MraW methylase family; Region: Methyltransf_5; cl17771 340100002268 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 340100002269 Cell division protein FtsL; Region: FtsL; cl11433 340100002270 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 340100002271 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 340100002272 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 340100002273 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional; Region: PRK11929 340100002274 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100002275 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002276 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100002277 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100002278 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002279 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 340100002280 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 340100002281 Mg++ binding site [ion binding]; other site 340100002282 putative catalytic motif [active] 340100002283 putative substrate binding site [chemical binding]; other site 340100002284 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 340100002285 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002286 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100002287 cell division protein FtsW; Region: ftsW; TIGR02614 340100002288 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 340100002289 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 340100002290 active site 340100002291 homodimer interface [polypeptide binding]; other site 340100002292 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 340100002293 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340100002294 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100002295 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100002296 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 340100002297 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 340100002298 ATP-grasp domain; Region: ATP-grasp_4; cl17255 340100002299 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 340100002300 Cell division protein FtsQ; Region: FtsQ; pfam03799 340100002301 cell division protein FtsA; Region: ftsA; TIGR01174 340100002302 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 340100002303 nucleotide binding site [chemical binding]; other site 340100002304 Cell division protein FtsA; Region: FtsA; pfam14450 340100002305 cell division protein FtsZ; Validated; Region: PRK09330 340100002306 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 340100002307 nucleotide binding site [chemical binding]; other site 340100002308 SulA interaction site; other site 340100002309 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 340100002310 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 340100002311 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 340100002312 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100002313 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 340100002314 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 340100002315 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 340100002316 SEC-C motif; Region: SEC-C; pfam02810 340100002317 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 340100002318 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 340100002319 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100002320 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100002321 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 340100002322 putative DNA binding site [nucleotide binding]; other site 340100002323 putative Zn2+ binding site [ion binding]; other site 340100002324 AsnC family; Region: AsnC_trans_reg; pfam01037 340100002325 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 340100002326 MgtE intracellular N domain; Region: MgtE_N; smart00924 340100002327 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 340100002328 Divalent cation transporter; Region: MgtE; cl00786 340100002329 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 340100002330 Predicted membrane protein [Function unknown]; Region: COG2855 340100002331 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002332 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 340100002333 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 340100002334 putative dimerization interface [polypeptide binding]; other site 340100002335 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100002336 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100002337 metal binding site [ion binding]; metal-binding site 340100002338 putative dimer interface [polypeptide binding]; other site 340100002339 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 340100002340 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 340100002341 acyl-activating enzyme (AAE) consensus motif; other site 340100002342 putative AMP binding site [chemical binding]; other site 340100002343 putative active site [active] 340100002344 putative CoA binding site [chemical binding]; other site 340100002345 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 340100002346 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 340100002347 active site 340100002348 dimerization interface [polypeptide binding]; other site 340100002349 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 340100002350 Uncharacterized conserved protein [Function unknown]; Region: COG4121 340100002351 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 340100002352 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 340100002353 Glycosyl hydrolases family 31; Region: Glyco_hydro_31; pfam01055 340100002354 active site 340100002355 catalytic site [active] 340100002356 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 340100002357 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 340100002358 Walker A/P-loop; other site 340100002359 ATP binding site [chemical binding]; other site 340100002360 Q-loop/lid; other site 340100002361 ABC transporter signature motif; other site 340100002362 Walker B; other site 340100002363 D-loop; other site 340100002364 H-loop/switch region; other site 340100002365 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 340100002366 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 340100002367 dimer interface [polypeptide binding]; other site 340100002368 conserved gate region; other site 340100002369 ABC-ATPase subunit interface; other site 340100002370 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 340100002371 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 340100002372 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 340100002373 active site 2 [active] 340100002374 active site 1 [active] 340100002375 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100002376 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 340100002377 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100002378 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 340100002379 putative PBP binding loops; other site 340100002380 dimer interface [polypeptide binding]; other site 340100002381 ABC-ATPase subunit interface; other site 340100002382 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 340100002383 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002384 Walker A/P-loop; other site 340100002385 ATP binding site [chemical binding]; other site 340100002386 Q-loop/lid; other site 340100002387 ABC transporter signature motif; other site 340100002388 Walker B; other site 340100002389 D-loop; other site 340100002390 H-loop/switch region; other site 340100002391 TOBE domain; Region: TOBE; pfam03459 340100002392 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002393 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002394 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 340100002395 putative dimerization interface [polypeptide binding]; other site 340100002396 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100002397 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 340100002398 active site 340100002399 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100002400 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100002401 classical (c) SDRs; Region: SDR_c; cd05233 340100002402 NAD(P) binding site [chemical binding]; other site 340100002403 active site 340100002404 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100002405 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002406 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 340100002407 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 340100002408 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 340100002409 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 340100002410 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100002411 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100002412 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100002413 classical (c) SDRs; Region: SDR_c; cd05233 340100002414 NAD(P) binding site [chemical binding]; other site 340100002415 active site 340100002416 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100002417 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100002418 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100002419 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 340100002420 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100002421 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100002422 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 340100002423 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 340100002424 putative ligand binding site [chemical binding]; other site 340100002425 NAD binding site [chemical binding]; other site 340100002426 catalytic site [active] 340100002427 NIPSNAP; Region: NIPSNAP; pfam07978 340100002428 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 340100002429 Protein of unknown function (DUF1810); Region: DUF1810; pfam08837 340100002430 ornithine cyclodeaminase; Validated; Region: PRK07589 340100002431 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 340100002432 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100002433 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 340100002434 AsnC family; Region: AsnC_trans_reg; pfam01037 340100002435 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 340100002436 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100002437 putative substrate translocation pore; other site 340100002438 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002439 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002440 LysR substrate binding domain; Region: LysR_substrate; pfam03466 340100002441 dimerization interface [polypeptide binding]; other site 340100002442 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100002443 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100002444 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 340100002445 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 340100002446 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100002447 ligand binding site [chemical binding]; other site 340100002448 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 340100002449 aromatic arch; other site 340100002450 DCoH dimer interaction site [polypeptide binding]; other site 340100002451 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 340100002452 DCoH tetramer interaction site [polypeptide binding]; other site 340100002453 substrate binding site [chemical binding]; other site 340100002454 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340100002455 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 340100002456 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 340100002457 Substrate binding site; other site 340100002458 metal-binding site 340100002459 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 340100002460 Phosphotransferase enzyme family; Region: APH; pfam01636 340100002461 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 340100002462 Organic solvent tolerance protein; Region: OstA_C; pfam04453 340100002463 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 340100002464 SurA N-terminal domain; Region: SurA_N; pfam09312 340100002465 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100002466 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100002467 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 340100002468 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 340100002469 S-adenosylmethionine binding site [chemical binding]; other site 340100002470 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 340100002471 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 340100002472 pyruvate kinase; Provisional; Region: PRK05826 340100002473 domain interfaces; other site 340100002474 active site 340100002475 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100002476 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 340100002477 active site 340100002478 putative substrate binding pocket [chemical binding]; other site 340100002479 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100002480 Response regulator receiver domain; Region: Response_reg; pfam00072 340100002481 active site 340100002482 phosphorylation site [posttranslational modification] 340100002483 intermolecular recognition site; other site 340100002484 dimerization interface [polypeptide binding]; other site 340100002485 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; cl17355 340100002486 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 340100002487 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002488 Walker B; other site 340100002489 D-loop; other site 340100002490 H-loop/switch region; other site 340100002491 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100002492 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 340100002493 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 340100002494 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100002495 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100002496 active site 340100002497 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 340100002498 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 340100002499 active site 340100002500 catalytic residues [active] 340100002501 metal binding site [ion binding]; metal-binding site 340100002502 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100002503 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 340100002504 dimer interface [polypeptide binding]; other site 340100002505 active site 340100002506 metal binding site [ion binding]; metal-binding site 340100002507 glutathione binding site [chemical binding]; other site 340100002508 tricarballylate utilization protein B; Provisional; Region: PRK15033 340100002509 tricarballylate dehydrogenase; Validated; Region: PRK08274 340100002510 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002511 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002512 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 340100002513 putative dimerization interface [polypeptide binding]; other site 340100002514 Protein of unknown function DUF45; Region: DUF45; pfam01863 340100002515 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 340100002516 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340100002517 putative acyl-acceptor binding pocket; other site 340100002518 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 340100002519 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 340100002520 active site 340100002521 motif I; other site 340100002522 motif II; other site 340100002523 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 340100002524 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 340100002525 dimer interface [polypeptide binding]; other site 340100002526 motif 1; other site 340100002527 active site 340100002528 motif 2; other site 340100002529 motif 3; other site 340100002530 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100002531 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002532 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 340100002533 dimerization interface [polypeptide binding]; other site 340100002534 substrate binding pocket [chemical binding]; other site 340100002535 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 340100002536 homotrimer interaction site [polypeptide binding]; other site 340100002537 putative active site [active] 340100002538 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 340100002539 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 340100002540 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100002541 catalytic residue [active] 340100002542 enoyl-CoA hydratase; Provisional; Region: PRK08252 340100002543 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 340100002544 substrate binding site [chemical binding]; other site 340100002545 oxyanion hole (OAH) forming residues; other site 340100002546 trimer interface [polypeptide binding]; other site 340100002547 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 340100002548 Fumarase C-terminus; Region: Fumerase_C; pfam05683 340100002549 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100002550 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100002551 Transposase; Region: HTH_Tnp_1; cl17663 340100002552 putative transposase OrfB; Reviewed; Region: PHA02517 340100002553 HTH-like domain; Region: HTH_21; pfam13276 340100002554 Integrase core domain; Region: rve; pfam00665 340100002555 Integrase core domain; Region: rve_2; pfam13333 340100002556 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 340100002557 Domain of unknown function DUF21; Region: DUF21; pfam01595 340100002558 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 340100002559 Transporter associated domain; Region: CorC_HlyC; smart01091 340100002560 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 340100002561 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100002562 Coenzyme A binding pocket [chemical binding]; other site 340100002563 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 340100002564 Uncharacterized conserved protein [Function unknown]; Region: COG5649 340100002565 ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]; Region: CcmA; COG4133 340100002566 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002567 Walker A/P-loop; other site 340100002568 ATP binding site [chemical binding]; other site 340100002569 Q-loop/lid; other site 340100002570 ABC transporter signature motif; other site 340100002571 Walker B; other site 340100002572 D-loop; other site 340100002573 H-loop/switch region; other site 340100002574 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 340100002575 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 340100002576 homodimer interaction site [polypeptide binding]; other site 340100002577 putative active site [active] 340100002578 putative catalytic site [active] 340100002579 acyl-CoA synthetase; Validated; Region: PRK06164 340100002580 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100002581 acyl-activating enzyme (AAE) consensus motif; other site 340100002582 AMP binding site [chemical binding]; other site 340100002583 active site 340100002584 CoA binding site [chemical binding]; other site 340100002585 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100002586 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100002587 Walker A/P-loop; other site 340100002588 ATP binding site [chemical binding]; other site 340100002589 Q-loop/lid; other site 340100002590 ABC transporter signature motif; other site 340100002591 Walker B; other site 340100002592 D-loop; other site 340100002593 H-loop/switch region; other site 340100002594 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100002595 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100002596 Walker A/P-loop; other site 340100002597 ATP binding site [chemical binding]; other site 340100002598 Q-loop/lid; other site 340100002599 ABC transporter signature motif; other site 340100002600 Walker B; other site 340100002601 D-loop; other site 340100002602 H-loop/switch region; other site 340100002603 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100002604 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 340100002605 TM-ABC transporter signature motif; other site 340100002606 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 340100002607 TM-ABC transporter signature motif; other site 340100002608 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100002609 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 340100002610 ligand binding site [chemical binding]; other site 340100002611 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002612 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002613 enoyl-CoA hydratase; Region: PLN02864 340100002614 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 340100002615 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 340100002616 dimer interaction site [polypeptide binding]; other site 340100002617 substrate-binding tunnel; other site 340100002618 active site 340100002619 catalytic site [active] 340100002620 substrate binding site [chemical binding]; other site 340100002621 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002622 NAD(P) binding site [chemical binding]; other site 340100002623 short chain dehydrogenase; Provisional; Region: PRK07060 340100002624 active site 340100002625 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002626 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002627 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 340100002628 putative dimerization interface [polypeptide binding]; other site 340100002629 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100002630 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 340100002631 non-specific DNA binding site [nucleotide binding]; other site 340100002632 salt bridge; other site 340100002633 sequence-specific DNA binding site [nucleotide binding]; other site 340100002634 Cupin domain; Region: Cupin_2; pfam07883 340100002635 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100002636 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 340100002637 active site 340100002638 putative substrate binding pocket [chemical binding]; other site 340100002639 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 340100002640 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100002641 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100002642 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100002643 MlrC C-terminus; Region: MlrC_C; pfam07171 340100002644 hydroxyglutarate oxidase; Provisional; Region: PRK11728 340100002645 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 340100002646 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100002647 D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction center; Region: Photo_RC; cl08220 340100002648 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 340100002649 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100002650 FMN binding site [chemical binding]; other site 340100002651 substrate binding site [chemical binding]; other site 340100002652 putative catalytic residue [active] 340100002653 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100002654 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100002655 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 340100002656 FAD binding site [chemical binding]; other site 340100002657 substrate binding site [chemical binding]; other site 340100002658 catalytic base [active] 340100002659 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 340100002660 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 340100002661 active site 340100002662 enoyl-CoA hydratase; Provisional; Region: PRK08140 340100002663 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 340100002664 substrate binding site [chemical binding]; other site 340100002665 oxyanion hole (OAH) forming residues; other site 340100002666 trimer interface [polypeptide binding]; other site 340100002667 Uncharacterized conserved protein [Function unknown]; Region: COG3777 340100002668 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 340100002669 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 340100002670 active site 2 [active] 340100002671 active site 1 [active] 340100002672 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002673 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002674 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 340100002675 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 340100002676 catalytic center binding site [active] 340100002677 ATP binding site [chemical binding]; other site 340100002678 poly(A) polymerase; Region: pcnB; TIGR01942 340100002679 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 340100002680 active site 340100002681 NTP binding site [chemical binding]; other site 340100002682 metal binding triad [ion binding]; metal-binding site 340100002683 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 340100002684 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 340100002685 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 340100002686 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 340100002687 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 340100002688 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 340100002689 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 340100002690 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 340100002691 dimerization interface [polypeptide binding]; other site 340100002692 putative ATP binding site [chemical binding]; other site 340100002693 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 340100002694 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 340100002695 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 340100002696 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 340100002697 ATP binding site [chemical binding]; other site 340100002698 Mg2+ binding site [ion binding]; other site 340100002699 G-X-G motif; other site 340100002700 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 340100002701 ATP binding site [chemical binding]; other site 340100002702 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 340100002703 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340100002704 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 340100002705 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 340100002706 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100002707 AMIN domain; Region: AMIN; pfam11741 340100002708 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 340100002709 active site 340100002710 metal binding site [ion binding]; metal-binding site 340100002711 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 340100002712 fumarate hydratase; Reviewed; Region: fumC; PRK00485 340100002713 Class II fumarases; Region: Fumarase_classII; cd01362 340100002714 active site 340100002715 tetramer interface [polypeptide binding]; other site 340100002716 Membrane transport protein; Region: Mem_trans; cl09117 340100002717 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100002718 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 340100002719 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002720 The 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 340100002721 dimerization interface [polypeptide binding]; other site 340100002722 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 340100002723 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100002724 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002725 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002726 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100002727 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100002728 active site 340100002729 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100002730 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002731 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 340100002732 putative dimerization interface [polypeptide binding]; other site 340100002733 putative substrate binding pocket [chemical binding]; other site 340100002734 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 340100002735 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 340100002736 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 340100002737 dimer interface [polypeptide binding]; other site 340100002738 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 340100002739 putative active site [active] 340100002740 putative catalytic site [active] 340100002741 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100002742 amidase; Provisional; Region: PRK06061 340100002743 Amidase; Region: Amidase; cl11426 340100002744 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100002745 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100002746 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100002747 DctM-like transporters; Region: DctM; pfam06808 340100002748 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100002749 2-methylcitrate dehydratase; Region: prpD; TIGR02330 340100002750 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100002751 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100002752 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100002753 active site 340100002754 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100002755 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100002756 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100002757 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100002758 DNA-binding site [nucleotide binding]; DNA binding site 340100002759 UTRA domain; Region: UTRA; pfam07702 340100002760 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 340100002761 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 340100002762 LysE type translocator; Region: LysE; cl00565 340100002763 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 340100002764 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 340100002765 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 340100002766 putative active site [active] 340100002767 putative substrate binding site [chemical binding]; other site 340100002768 putative cosubstrate binding site; other site 340100002769 catalytic site [active] 340100002770 Predicted dehydrogenase [General function prediction only]; Region: COG0579 340100002771 hydroxyglutarate oxidase; Provisional; Region: PRK11728 340100002772 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 340100002773 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 340100002774 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 340100002775 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 340100002776 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 340100002777 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100002778 Transposase; Region: HTH_Tnp_1; pfam01527 340100002779 putative transposase OrfB; Reviewed; Region: PHA02517 340100002780 HTH-like domain; Region: HTH_21; pfam13276 340100002781 Integrase core domain; Region: rve; pfam00665 340100002782 Integrase core domain; Region: rve_3; pfam13683 340100002783 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 340100002784 putative active site pocket [active] 340100002785 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 340100002786 putative substrate translocation pore; other site 340100002787 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100002788 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 340100002789 putative ATP binding site [chemical binding]; other site 340100002790 putative substrate interface [chemical binding]; other site 340100002791 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100002792 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100002793 DNA-binding site [nucleotide binding]; DNA binding site 340100002794 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 340100002795 acyl-CoA synthetase; Validated; Region: PRK06164 340100002796 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100002797 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100002798 AMP binding site [chemical binding]; other site 340100002799 active site 340100002800 acyl-activating enzyme (AAE) consensus motif; other site 340100002801 CoA binding site [chemical binding]; other site 340100002802 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100002803 short chain dehydrogenase; Provisional; Region: PRK07577 340100002804 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100002805 NAD(P) binding site [chemical binding]; other site 340100002806 active site 340100002807 hypothetical protein; Provisional; Region: PRK07546 340100002808 substrate-cofactor binding pocket; other site 340100002809 homodimer interface [polypeptide binding]; other site 340100002810 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 340100002811 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100002812 catalytic residue [active] 340100002813 aminodeoxychorismate synthase; Provisional; Region: PRK07508 340100002814 chorismate binding enzyme; Region: Chorismate_bind; cl10555 340100002815 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002816 Walker A/P-loop; other site 340100002817 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 340100002818 ATP binding site [chemical binding]; other site 340100002819 Q-loop/lid; other site 340100002820 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002821 ABC transporter signature motif; other site 340100002822 Walker B; other site 340100002823 D-loop; other site 340100002824 H-loop/switch region; other site 340100002825 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002826 Walker A/P-loop; other site 340100002827 ATP binding site [chemical binding]; other site 340100002828 Q-loop/lid; other site 340100002829 ABC transporter signature motif; other site 340100002830 Walker B; other site 340100002831 D-loop; other site 340100002832 H-loop/switch region; other site 340100002833 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002834 Walker A/P-loop; other site 340100002835 ATP binding site [chemical binding]; other site 340100002836 Q-loop/lid; other site 340100002837 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 340100002838 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100002839 Walker A/P-loop; other site 340100002840 ATP binding site [chemical binding]; other site 340100002841 Q-loop/lid; other site 340100002842 ABC transporter signature motif; other site 340100002843 Walker B; other site 340100002844 D-loop; other site 340100002845 H-loop/switch region; other site 340100002846 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100002847 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100002848 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100002849 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 340100002850 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 340100002851 active site 340100002852 intersubunit interface [polypeptide binding]; other site 340100002853 catalytic residue [active] 340100002854 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 340100002855 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 340100002856 substrate binding site [chemical binding]; other site 340100002857 ATP binding site [chemical binding]; other site 340100002858 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100002859 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100002860 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 340100002861 putative effector binding pocket; other site 340100002862 dimerization interface [polypeptide binding]; other site 340100002863 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 340100002864 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 340100002865 active site 340100002866 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100002867 EamA-like transporter family; Region: EamA; pfam00892 340100002868 EamA-like transporter family; Region: EamA; pfam00892 340100002869 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 340100002870 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100002871 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100002872 ABC transporter; Region: ABC_tran_2; pfam12848 340100002873 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100002874 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 340100002875 catalytic triad [active] 340100002876 conserved cis-peptide bond; other site 340100002877 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 340100002878 PAS domain; Region: PAS_9; pfam13426 340100002879 putative active site [active] 340100002880 heme pocket [chemical binding]; other site 340100002881 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 340100002882 DNA binding residues [nucleotide binding] 340100002883 dimerization interface [polypeptide binding]; other site 340100002884 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 340100002885 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 340100002886 active site 340100002887 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100002888 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 340100002889 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 340100002890 acyl-activating enzyme (AAE) consensus motif; other site 340100002891 acyl-activating enzyme (AAE) consensus motif; other site 340100002892 putative AMP binding site [chemical binding]; other site 340100002893 putative active site [active] 340100002894 putative CoA binding site [chemical binding]; other site 340100002895 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100002896 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100002897 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100002898 DctM-like transporters; Region: DctM; pfam06808 340100002899 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 340100002900 classical (c) SDRs; Region: SDR_c; cd05233 340100002901 NAD(P) binding site [chemical binding]; other site 340100002902 active site 340100002903 cell division topological specificity factor MinE; Provisional; Region: PRK13989 340100002904 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 340100002905 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 340100002906 Switch I; other site 340100002907 Switch II; other site 340100002908 septum formation inhibitor; Provisional; Region: minC; PRK00030 340100002909 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 340100002910 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 340100002911 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 340100002912 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100002913 active site 340100002914 HIGH motif; other site 340100002915 nucleotide binding site [chemical binding]; other site 340100002916 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 340100002917 KMSKS motif; other site 340100002918 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 340100002919 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 340100002920 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 340100002921 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 340100002922 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 340100002923 dimerization interface [polypeptide binding]; other site 340100002924 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 340100002925 ATP binding site [chemical binding]; other site 340100002926 Mg2+ binding site [ion binding]; other site 340100002927 G-X-G motif; other site 340100002928 osmolarity response regulator; Provisional; Region: ompR; PRK09468 340100002929 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100002930 active site 340100002931 phosphorylation site [posttranslational modification] 340100002932 intermolecular recognition site; other site 340100002933 dimerization interface [polypeptide binding]; other site 340100002934 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 340100002935 DNA binding site [nucleotide binding] 340100002936 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100002937 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 340100002938 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 340100002939 ATP binding site [chemical binding]; other site 340100002940 putative Mg++ binding site [ion binding]; other site 340100002941 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 340100002942 nucleotide binding region [chemical binding]; other site 340100002943 ATP-binding site [chemical binding]; other site 340100002944 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 340100002945 HRDC domain; Region: HRDC; pfam00570 340100002946 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 340100002947 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 340100002948 Walker A motif; other site 340100002949 ATP binding site [chemical binding]; other site 340100002950 Walker B motif; other site 340100002951 arginine finger; other site 340100002952 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 340100002953 serine racemase; Region: PLN02970 340100002954 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 340100002955 tetramer interface [polypeptide binding]; other site 340100002956 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100002957 catalytic residue [active] 340100002958 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 340100002959 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 340100002960 putative NAD(P) binding site [chemical binding]; other site 340100002961 active site 340100002962 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 340100002963 RuvA N terminal domain; Region: RuvA_N; pfam01330 340100002964 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 340100002965 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 340100002966 active site 340100002967 putative DNA-binding cleft [nucleotide binding]; other site 340100002968 dimer interface [polypeptide binding]; other site 340100002969 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 340100002970 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 340100002971 purine monophosphate binding site [chemical binding]; other site 340100002972 dimer interface [polypeptide binding]; other site 340100002973 putative catalytic residues [active] 340100002974 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 340100002975 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 340100002976 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 340100002977 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 340100002978 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 340100002979 FMN binding site [chemical binding]; other site 340100002980 active site 340100002981 catalytic residues [active] 340100002982 substrate binding site [chemical binding]; other site 340100002983 hypothetical protein; Provisional; Region: PRK06996 340100002984 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100002985 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 340100002986 proline aminopeptidase P II; Provisional; Region: PRK10879 340100002987 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 340100002988 active site 340100002989 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 340100002990 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 340100002991 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 340100002992 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; pfam09678 340100002993 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 340100002994 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 340100002995 active site 340100002996 tetramer interface; other site 340100002997 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 340100002998 Peptidase family M48; Region: Peptidase_M48; cl12018 340100002999 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 340100003000 SnoaL-like domain; Region: SnoaL_3; pfam13474 340100003001 SnoaL-like domain; Region: SnoaL_2; pfam12680 340100003002 Zinc-finger domain; Region: zf-CHCC; cl01821 340100003003 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 340100003004 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 340100003005 homodimer interface [polypeptide binding]; other site 340100003006 substrate-cofactor binding pocket; other site 340100003007 catalytic residue [active] 340100003008 AzlC protein; Region: AzlC; pfam03591 340100003009 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 340100003010 helicase 45; Provisional; Region: PTZ00424 340100003011 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 340100003012 ATP binding site [chemical binding]; other site 340100003013 Mg++ binding site [ion binding]; other site 340100003014 motif III; other site 340100003015 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 340100003016 nucleotide binding region [chemical binding]; other site 340100003017 ATP-binding site [chemical binding]; other site 340100003018 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 340100003019 catalytic residues [active] 340100003020 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 340100003021 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 340100003022 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 340100003023 putative MPT binding site; other site 340100003024 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100003025 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100003026 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100003027 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003028 Phasin protein; Region: Phasin_2; cl11491 340100003029 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 340100003030 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 340100003031 quinone interaction residues [chemical binding]; other site 340100003032 active site 340100003033 catalytic residues [active] 340100003034 FMN binding site [chemical binding]; other site 340100003035 substrate binding site [chemical binding]; other site 340100003036 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 340100003037 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 340100003038 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 340100003039 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 340100003040 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 340100003041 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 340100003042 nudix motif; other site 340100003043 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 340100003044 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100003045 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 340100003046 DNA binding residues [nucleotide binding] 340100003047 dimerization interface [polypeptide binding]; other site 340100003048 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100003049 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100003050 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 340100003051 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 340100003052 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 340100003053 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 340100003054 active site 340100003055 catalytic residues [active] 340100003056 DNA binding site [nucleotide binding] 340100003057 Int/Topo IB signature motif; other site 340100003058 TraU protein; Region: TraU; cl06067 340100003059 Protein of unknown function (DUF4031); Region: DUF4031; pfam13223 340100003060 Protein of unknown function (DUF550); Region: DUF550; pfam04447 340100003061 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100003062 substrate interaction site [chemical binding]; other site 340100003063 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100003064 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100003065 Walker A/P-loop; other site 340100003066 ATP binding site [chemical binding]; other site 340100003067 Q-loop/lid; other site 340100003068 RecT family; Region: RecT; cl04285 340100003069 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 340100003070 Amino acid synthesis; Region: AA_synth; pfam06684 340100003071 HNH endonuclease; Region: HNH_3; pfam13392 340100003072 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 340100003073 TM2 domain; Region: TM2; pfam05154 340100003074 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 340100003075 Predicted transcriptional regulator [Transcription]; Region: COG2932 340100003076 Catalytic site [active] 340100003077 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]; Region: COG4197 340100003078 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 340100003079 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100003080 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 340100003081 Terminase small subunit; Region: Terminase_2; pfam03592 340100003082 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 340100003083 Terminase-like family; Region: Terminase_6; pfam03237 340100003084 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 340100003085 Protein of unknown function (DUF1073); Region: DUF1073; pfam06381 340100003086 phage-related protein, HI1409 family; Region: phge_rel_HI1409; TIGR01555 340100003087 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 340100003088 Uncharacterized protein conserved in bacteria (DUF2213); Region: DUF2213; pfam09979 340100003089 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4834 340100003090 Uncharacterized protein conserved in bacteria (DUF2184); Region: DUF2184; pfam09950 340100003091 HeH/LEM domain; Region: HeH; pfam12949 340100003092 Protein of unknown function (DUF4054); Region: DUF4054; pfam13262 340100003093 Protein of unknown function (DUF3383); Region: DUF3383; pfam11863 340100003094 Protein of unknown function (DUF3277); Region: DUF3277; pfam11681 340100003095 tape measure domain; Region: tape_meas_nterm; TIGR02675 340100003096 Baseplate J-like protein; Region: Baseplate_J; cl01294 340100003097 Protein of unknown function (DUF2612); Region: DUF2612; pfam11041 340100003098 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 340100003099 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 340100003100 catalytic residue [active] 340100003101 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 340100003102 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 340100003103 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 340100003104 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100003105 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 340100003106 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 340100003107 DNA binding residues [nucleotide binding] 340100003108 dimer interface [polypeptide binding]; other site 340100003109 putative metal binding site [ion binding]; other site 340100003110 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 340100003111 Integrase core domain; Region: rve; pfam00665 340100003112 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 340100003113 Heavy-metal-associated domain; Region: HMA; pfam00403 340100003114 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 340100003115 HTH-like domain; Region: HTH_21; pfam13276 340100003116 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100003117 Integrase core domain; Region: rve; pfam00665 340100003118 Integrase core domain; Region: rve_3; pfam13683 340100003119 Transposase; Region: HTH_Tnp_1; cl17663 340100003120 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 340100003121 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 340100003122 DNA binding residues [nucleotide binding] 340100003123 dimer interface [polypeptide binding]; other site 340100003124 putative metal binding site [ion binding]; other site 340100003125 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100003126 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100003127 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 340100003128 ArsC family; Region: ArsC; pfam03960 340100003129 catalytic residues [active] 340100003130 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 340100003131 arsenical-resistance protein; Region: acr3; TIGR00832 340100003132 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 340100003133 Low molecular weight phosphatase family; Region: LMWPc; cd00115 340100003134 active site 340100003135 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 340100003136 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100003137 putative metal binding site [ion binding]; other site 340100003138 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 340100003139 putative DNA binding site [nucleotide binding]; other site 340100003140 putative Zn2+ binding site [ion binding]; other site 340100003141 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 340100003142 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100003143 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 340100003144 Magnesium ion binding site [ion binding]; other site 340100003145 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100003146 ParB-like nuclease domain; Region: ParBc; pfam02195 340100003147 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100003148 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 340100003149 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100003150 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100003151 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 340100003152 ssDNA binding site [nucleotide binding]; other site 340100003153 dimer interface [polypeptide binding]; other site 340100003154 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100003155 DNA topoisomerase III; Provisional; Region: PRK07726 340100003156 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 340100003157 active site 340100003158 putative interdomain interaction site [polypeptide binding]; other site 340100003159 putative metal-binding site [ion binding]; other site 340100003160 putative nucleotide binding site [chemical binding]; other site 340100003161 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 340100003162 domain I; other site 340100003163 DNA binding groove [nucleotide binding] 340100003164 phosphate binding site [ion binding]; other site 340100003165 domain II; other site 340100003166 domain III; other site 340100003167 nucleotide binding site [chemical binding]; other site 340100003168 catalytic site [active] 340100003169 domain IV; other site 340100003170 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100003171 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 340100003172 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100003173 cofactor binding site; other site 340100003174 DNA binding site [nucleotide binding] 340100003175 substrate interaction site [chemical binding]; other site 340100003176 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100003177 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 340100003178 active site 340100003179 DNA binding site [nucleotide binding] 340100003180 Int/Topo IB signature motif; other site 340100003181 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 340100003182 active site 340100003183 DNA binding site [nucleotide binding] 340100003184 Int/Topo IB signature motif; other site 340100003185 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N2; pfam13495 340100003186 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100003187 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 340100003188 active site 340100003189 DNA binding site [nucleotide binding] 340100003190 Int/Topo IB signature motif; other site 340100003191 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 340100003192 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100003193 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 340100003194 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100003195 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100003196 Domain of unknown function (DUF932); Region: DUF932; pfam06067 340100003197 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100003198 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 340100003199 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100003200 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 340100003201 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 340100003202 putative active site [active] 340100003203 putative NTP binding site [chemical binding]; other site 340100003204 putative nucleic acid binding site [nucleotide binding]; other site 340100003205 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100003206 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 340100003207 active site 340100003208 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100003209 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 340100003210 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100003211 putative active site [active] 340100003212 putative NTP binding site [chemical binding]; other site 340100003213 putative nucleic acid binding site [nucleotide binding]; other site 340100003214 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100003215 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 340100003216 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 340100003217 active site 340100003218 Methyltransferase domain; Region: Methyltransf_26; pfam13659 340100003219 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100003220 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 340100003221 nucleotide binding region [chemical binding]; other site 340100003222 ATP-binding site [chemical binding]; other site 340100003223 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100003224 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100003225 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100003226 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100003227 catalytic residue [active] 340100003228 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 340100003229 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 340100003230 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100003231 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 340100003232 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100003233 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100003234 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 340100003235 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 340100003236 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 340100003237 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 340100003238 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 340100003239 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100003240 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100003241 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100003242 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 340100003243 ParA/MinD ATPase like; Region: ParA; pfam10609 340100003244 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 340100003245 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 340100003246 catalytic residues [active] 340100003247 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100003248 MPN+ (JAMM) motif; other site 340100003249 Zinc-binding site [ion binding]; other site 340100003250 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 340100003251 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 340100003252 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100003253 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100003254 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 340100003255 RES domain; Region: RES; smart00953 340100003256 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100003257 Putative helicase; Region: TraI_2; pfam07514 340100003258 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100003259 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 340100003260 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 340100003261 Transposase; Region: HTH_Tnp_1; pfam01527 340100003262 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100003263 Transposase, Mutator family; Region: Transposase_mut; pfam00872 340100003264 inactivated transposase 340100003265 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003266 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 340100003267 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 340100003268 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 340100003269 Transposase; Region: DDE_Tnp_ISL3; pfam01610 340100003270 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 340100003271 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; cd00531 340100003272 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340100003273 Transposase; Region: HTH_Tnp_1; pfam01527 340100003274 Homeodomain-like domain; Region: HTH_32; pfam13565 340100003275 Integrase core domain; Region: rve; pfam00665 340100003276 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003277 Integrase core domain; Region: rve_3; pfam13683 340100003278 Fusaric acid resistance protein family; Region: FUSC; pfam04632 340100003279 HTH-like domain; Region: HTH_21; pfam13276 340100003280 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100003281 Integrase core domain; Region: rve; pfam00665 340100003282 Integrase core domain; Region: rve_3; pfam13683 340100003283 Transposase; Region: HTH_Tnp_1; cl17663 340100003284 Fusaric acid resistance protein family; Region: FUSC; pfam04632 340100003285 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 340100003286 Transposase; Region: DDE_Tnp_ISL3; pfam01610 340100003287 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 340100003288 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340100003289 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 340100003290 Homeodomain-like domain; Region: HTH_32; pfam13565 340100003291 Integrase core domain; Region: rve; pfam00665 340100003292 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003293 Integrase core domain; Region: rve_3; pfam13683 340100003294 Transposase; Region: HTH_Tnp_1; pfam01527 340100003295 Transposase; Region: HTH_Tnp_1; pfam01527 340100003296 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003297 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003298 active site 340100003299 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 340100003300 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 340100003301 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100003302 acyl-activating enzyme (AAE) consensus motif; other site 340100003303 active site 340100003304 AMP binding site [chemical binding]; other site 340100003305 CoA binding site [chemical binding]; other site 340100003306 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003307 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 340100003308 substrate binding site [chemical binding]; other site 340100003309 oxyanion hole (OAH) forming residues; other site 340100003310 trimer interface [polypeptide binding]; other site 340100003311 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003312 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003313 acetyl-CoA acetyltransferase; Provisional; Region: PRK06064 340100003314 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 340100003315 active site 340100003316 acyl-CoA synthetase; Validated; Region: PRK06188 340100003317 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100003318 acyl-activating enzyme (AAE) consensus motif; other site 340100003319 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 340100003320 putative AMP binding site [chemical binding]; other site 340100003321 putative active site [active] 340100003322 acyl-activating enzyme (AAE) consensus motif; other site 340100003323 putative CoA binding site [chemical binding]; other site 340100003324 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003325 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003326 NAD(P) binding site [chemical binding]; other site 340100003327 active site 340100003328 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100003329 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100003330 Walker A/P-loop; other site 340100003331 ATP binding site [chemical binding]; other site 340100003332 Q-loop/lid; other site 340100003333 ABC transporter signature motif; other site 340100003334 Walker B; other site 340100003335 D-loop; other site 340100003336 H-loop/switch region; other site 340100003337 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100003338 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100003339 acyl-activating enzyme (AAE) consensus motif; other site 340100003340 active site 340100003341 AMP binding site [chemical binding]; other site 340100003342 CoA binding site [chemical binding]; other site 340100003343 putative transposase OrfB; Reviewed; Region: PHA02517 340100003344 HTH-like domain; Region: HTH_21; pfam13276 340100003345 Integrase core domain; Region: rve; pfam00665 340100003346 Integrase core domain; Region: rve_3; pfam13683 340100003347 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100003348 Transposase; Region: HTH_Tnp_1; pfam01527 340100003349 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100003350 CoA binding site [chemical binding]; other site 340100003351 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 340100003352 TM-ABC transporter signature motif; other site 340100003353 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 340100003354 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100003355 TM-ABC transporter signature motif; other site 340100003356 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003357 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 340100003358 ligand binding site [chemical binding]; other site 340100003359 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100003360 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100003361 Walker A/P-loop; other site 340100003362 ATP binding site [chemical binding]; other site 340100003363 Q-loop/lid; other site 340100003364 ABC transporter signature motif; other site 340100003365 Walker B; other site 340100003366 D-loop; other site 340100003367 H-loop/switch region; other site 340100003368 enoyl-CoA hydratase; Validated; Region: PRK08139 340100003369 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 340100003370 substrate binding site [chemical binding]; other site 340100003371 oxyanion hole (OAH) forming residues; other site 340100003372 trimer interface [polypeptide binding]; other site 340100003373 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003374 classical (c) SDRs; Region: SDR_c; cd05233 340100003375 NAD(P) binding site [chemical binding]; other site 340100003376 active site 340100003377 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 340100003378 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100003379 FMN binding site [chemical binding]; other site 340100003380 substrate binding site [chemical binding]; other site 340100003381 putative catalytic residue [active] 340100003382 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003383 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100003384 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 340100003385 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 340100003386 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 340100003387 Homeodomain-like domain; Region: HTH_32; pfam13565 340100003388 Integrase core domain; Region: rve; pfam00665 340100003389 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003390 Integrase core domain; Region: rve_3; pfam13683 340100003391 Transposase; Region: HTH_Tnp_1; pfam01527 340100003392 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100003393 Transposase; Region: HTH_Tnp_1; pfam01527 340100003394 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 340100003395 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 340100003396 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 340100003397 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 340100003398 transposase/IS protein; Provisional; Region: PRK09183 340100003399 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 340100003400 Walker A motif; other site 340100003401 ATP binding site [chemical binding]; other site 340100003402 Walker B motif; other site 340100003403 arginine finger; other site 340100003404 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 340100003405 Integrase core domain; Region: rve; pfam00665 340100003406 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 340100003407 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 340100003408 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 340100003409 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100003410 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100003411 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 340100003412 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 340100003413 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 340100003414 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 340100003415 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100003416 ATP-grasp domain; Region: ATP-grasp_4; cl17255 340100003417 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 340100003418 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 340100003419 carboxyltransferase (CT) interaction site; other site 340100003420 biotinylation site [posttranslational modification]; other site 340100003421 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003422 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003423 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 340100003424 active site 2 [active] 340100003425 active site 1 [active] 340100003426 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003427 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100003428 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 340100003429 substrate binding site [chemical binding]; other site 340100003430 oxyanion hole (OAH) forming residues; other site 340100003431 trimer interface [polypeptide binding]; other site 340100003432 enoyl-CoA hydratase; Provisional; Region: PRK09245 340100003433 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 340100003434 substrate binding site [chemical binding]; other site 340100003435 oxyanion hole (OAH) forming residues; other site 340100003436 trimer interface [polypeptide binding]; other site 340100003437 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100003438 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100003439 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100003440 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100003441 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100003442 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 340100003443 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 340100003444 active site 340100003445 FMN binding site [chemical binding]; other site 340100003446 substrate binding site [chemical binding]; other site 340100003447 homotetramer interface [polypeptide binding]; other site 340100003448 catalytic residue [active] 340100003449 Stress responsive A/B Barrel Domain; Region: Dabb; pfam07876 340100003450 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 340100003451 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003452 NAD(P) binding site [chemical binding]; other site 340100003453 active site 340100003454 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100003455 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100003456 Walker A/P-loop; other site 340100003457 ATP binding site [chemical binding]; other site 340100003458 Q-loop/lid; other site 340100003459 ABC transporter signature motif; other site 340100003460 Walker B; other site 340100003461 D-loop; other site 340100003462 H-loop/switch region; other site 340100003463 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100003464 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100003465 Walker A/P-loop; other site 340100003466 ATP binding site [chemical binding]; other site 340100003467 Q-loop/lid; other site 340100003468 ABC transporter signature motif; other site 340100003469 Walker B; other site 340100003470 D-loop; other site 340100003471 H-loop/switch region; other site 340100003472 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100003473 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 340100003474 TM-ABC transporter signature motif; other site 340100003475 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100003476 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 340100003477 TM-ABC transporter signature motif; other site 340100003478 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003479 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 340100003480 putative ligand binding site [chemical binding]; other site 340100003481 NAD binding domain of 6-phosphogluconate dehydrogenase; Region: NAD_binding_2; pfam03446 340100003482 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100003483 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100003484 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 340100003485 substrate binding site [chemical binding]; other site 340100003486 oxyanion hole (OAH) forming residues; other site 340100003487 trimer interface [polypeptide binding]; other site 340100003488 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003489 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003490 The 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 340100003491 dimerization interface [polypeptide binding]; other site 340100003492 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 340100003493 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100003494 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 340100003495 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 340100003496 putative active site pocket [active] 340100003497 dimerization interface [polypeptide binding]; other site 340100003498 putative catalytic residue [active] 340100003499 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 340100003500 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100003501 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 340100003502 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 340100003503 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 340100003504 FMN binding site [chemical binding]; other site 340100003505 active site 340100003506 substrate binding site [chemical binding]; other site 340100003507 catalytic residue [active] 340100003508 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 340100003509 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100003510 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003511 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003512 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 340100003513 putative effector binding pocket; other site 340100003514 dimerization interface [polypeptide binding]; other site 340100003515 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 340100003516 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100003517 SnoaL-like domain; Region: SnoaL_4; pfam13577 340100003518 hypothetical protein; Provisional; Region: PRK07236 340100003519 hypothetical protein; Provisional; Region: PRK06753 340100003520 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100003521 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 340100003522 dimer interface [polypeptide binding]; other site 340100003523 putative metal binding site [ion binding]; other site 340100003524 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003525 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 340100003526 putative ligand binding site [chemical binding]; other site 340100003527 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 340100003528 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100003529 TM-ABC transporter signature motif; other site 340100003530 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100003531 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 340100003532 TM-ABC transporter signature motif; other site 340100003533 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100003534 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100003535 Walker A/P-loop; other site 340100003536 ATP binding site [chemical binding]; other site 340100003537 Q-loop/lid; other site 340100003538 ABC transporter signature motif; other site 340100003539 Walker B; other site 340100003540 D-loop; other site 340100003541 H-loop/switch region; other site 340100003542 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100003543 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100003544 Walker A/P-loop; other site 340100003545 ATP binding site [chemical binding]; other site 340100003546 Q-loop/lid; other site 340100003547 ABC transporter signature motif; other site 340100003548 Walker B; other site 340100003549 D-loop; other site 340100003550 H-loop/switch region; other site 340100003551 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003552 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100003553 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003554 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003555 The 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 340100003556 dimerization interface [polypeptide binding]; other site 340100003557 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003558 Predicted acyl esterases [General function prediction only]; Region: COG2936 340100003559 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; pfam08530 340100003560 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 340100003561 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 340100003562 putative DNA binding site [nucleotide binding]; other site 340100003563 putative Zn2+ binding site [ion binding]; other site 340100003564 AsnC family; Region: AsnC_trans_reg; pfam01037 340100003565 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100003566 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100003567 Predicted permeases [General function prediction only]; Region: COG0679 340100003568 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003569 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 340100003570 putative effector binding pocket; other site 340100003571 dimerization interface [polypeptide binding]; other site 340100003572 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100003573 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100003574 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 340100003575 Homeodomain-like domain; Region: HTH_32; pfam13565 340100003576 Integrase core domain; Region: rve; pfam00665 340100003577 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003578 Integrase core domain; Region: rve_3; pfam13683 340100003579 Transposase; Region: HTH_Tnp_1; pfam01527 340100003580 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003581 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003582 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 340100003583 putative effector binding pocket; other site 340100003584 dimerization interface [polypeptide binding]; other site 340100003585 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100003586 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 340100003587 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100003588 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100003589 Transposase; Region: HTH_Tnp_1; pfam01527 340100003590 Homeodomain-like domain; Region: HTH_32; pfam13565 340100003591 Integrase core domain; Region: rve; pfam00665 340100003592 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003593 Integrase core domain; Region: rve_3; pfam13683 340100003594 Transposase; Region: HTH_Tnp_1; pfam01527 340100003595 Homeodomain-like domain; Region: HTH_32; pfam13565 340100003596 Integrase core domain; Region: rve; pfam00665 340100003597 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100003598 Integrase core domain; Region: rve_3; pfam13683 340100003599 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003600 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100003601 CoA binding domain; Region: CoA_binding_2; pfam13380 340100003602 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100003603 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100003604 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003605 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003606 active site 340100003607 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003608 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 340100003609 substrate binding site [chemical binding]; other site 340100003610 oxyanion hole (OAH) forming residues; other site 340100003611 trimer interface [polypeptide binding]; other site 340100003612 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 340100003613 short chain dehydrogenase; Provisional; Region: PRK07576 340100003614 NAD(P) binding site [chemical binding]; other site 340100003615 substrate binding site [chemical binding]; other site 340100003616 homotetramer interface [polypeptide binding]; other site 340100003617 active site 340100003618 homodimer interface [polypeptide binding]; other site 340100003619 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003620 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003621 active site 340100003622 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100003623 CoA binding domain; Region: CoA_binding_2; pfam13380 340100003624 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100003625 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100003626 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 340100003627 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 340100003628 FMN binding site [chemical binding]; other site 340100003629 substrate binding site [chemical binding]; other site 340100003630 putative catalytic residue [active] 340100003631 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100003632 DctM-like transporters; Region: DctM; pfam06808 340100003633 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100003634 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100003635 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003636 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003637 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003638 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003639 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 340100003640 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100003641 substrate binding site [chemical binding]; other site 340100003642 oxyanion hole (OAH) forming residues; other site 340100003643 trimer interface [polypeptide binding]; other site 340100003644 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003645 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003646 enoyl-CoA hydratase; Region: PLN02864 340100003647 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 340100003648 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 340100003649 dimer interaction site [polypeptide binding]; other site 340100003650 substrate-binding tunnel; other site 340100003651 active site 340100003652 catalytic site [active] 340100003653 substrate binding site [chemical binding]; other site 340100003654 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003655 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003656 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003657 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003658 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 340100003659 active site 2 [active] 340100003660 active site 1 [active] 340100003661 thiolase; Provisional; Region: PRK06158 340100003662 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 340100003663 active site 340100003664 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]; Region: COG1545 340100003665 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 340100003666 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100003667 enoyl-CoA hydratase; Provisional; Region: PRK06688 340100003668 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 340100003669 substrate binding site [chemical binding]; other site 340100003670 oxyanion hole (OAH) forming residues; other site 340100003671 trimer interface [polypeptide binding]; other site 340100003672 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003673 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 340100003674 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 340100003675 Walker A motif; other site 340100003676 ATP binding site [chemical binding]; other site 340100003677 Walker B motif; other site 340100003678 arginine finger; other site 340100003679 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100003680 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 340100003681 CoenzymeA binding site [chemical binding]; other site 340100003682 subunit interaction site [polypeptide binding]; other site 340100003683 PHB binding site; other site 340100003684 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100003685 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 340100003686 putative ligand binding site [chemical binding]; other site 340100003687 PAS domain; Region: PAS_9; pfam13426 340100003688 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 340100003689 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 340100003690 ATP binding site [chemical binding]; other site 340100003691 Walker B motif; other site 340100003692 arginine finger; other site 340100003693 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100003694 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003695 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003696 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 340100003697 Cyclohexanecarboxylate-CoA ligase (also called cyclohex-1-ene-1-carboxylate:CoA ligase); Region: CHC_CoA_lg; cd05903 340100003698 acyl-activating enzyme (AAE) consensus motif; other site 340100003699 putative AMP binding site [chemical binding]; other site 340100003700 putative active site [active] 340100003701 putative CoA binding site [chemical binding]; other site 340100003702 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 340100003703 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 340100003704 substrate binding site [chemical binding]; other site 340100003705 oxyanion hole (OAH) forming residues; other site 340100003706 trimer interface [polypeptide binding]; other site 340100003707 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100003708 classical (c) SDRs; Region: SDR_c; cd05233 340100003709 NAD(P) binding site [chemical binding]; other site 340100003710 active site 340100003711 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100003712 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100003713 active site 340100003714 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07819 340100003715 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100003716 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100003717 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100003718 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100003719 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100003720 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 340100003721 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 340100003722 NAD(P) binding site [chemical binding]; other site 340100003723 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100003724 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 340100003725 substrate binding site [chemical binding]; other site 340100003726 oxyanion hole (OAH) forming residues; other site 340100003727 trimer interface [polypeptide binding]; other site 340100003728 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 340100003729 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 340100003730 Nucleotide-sugar transporter; Region: Nuc_sug_transp; pfam04142 340100003731 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003732 GAF domain; Region: GAF; cl17456 340100003733 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003734 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003735 The 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 340100003736 dimerization interface [polypeptide binding]; other site 340100003737 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100003738 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100003739 Predicted acyl esterases [General function prediction only]; Region: COG2936 340100003740 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; pfam08530 340100003741 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003742 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 340100003743 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003744 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 340100003745 putative dimerization interface [polypeptide binding]; other site 340100003746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100003747 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 340100003748 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 340100003749 dimer interface [polypeptide binding]; other site 340100003750 NADP binding site [chemical binding]; other site 340100003751 catalytic residues [active] 340100003752 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 340100003753 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 340100003754 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 340100003755 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100003756 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100003757 Malate/L-lactate dehydrogenases [Energy production and conversion]; Region: COG2055 340100003758 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 340100003759 Proline racemase [Amino acid transport and metabolism]; Region: COG3938 340100003760 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 340100003761 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 340100003762 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 340100003763 active site 340100003764 benzoate transport; Region: 2A0115; TIGR00895 340100003765 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 340100003766 putative substrate translocation pore; other site 340100003767 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 340100003768 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100003769 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100003770 Walker A/P-loop; other site 340100003771 ATP binding site [chemical binding]; other site 340100003772 Q-loop/lid; other site 340100003773 ABC transporter signature motif; other site 340100003774 Walker B; other site 340100003775 D-loop; other site 340100003776 H-loop/switch region; other site 340100003777 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 340100003778 dimer interface [polypeptide binding]; other site 340100003779 conserved gate region; other site 340100003780 putative PBP binding loops; other site 340100003781 ABC-ATPase subunit interface; other site 340100003782 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100003783 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 340100003784 dimer interface [polypeptide binding]; other site 340100003785 conserved gate region; other site 340100003786 putative PBP binding loops; other site 340100003787 ABC-ATPase subunit interface; other site 340100003788 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100003789 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 340100003790 substrate binding pocket [chemical binding]; other site 340100003791 membrane-bound complex binding site; other site 340100003792 hinge residues; other site 340100003793 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100003794 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 340100003795 inhibitor site; inhibition site 340100003796 active site 340100003797 dimer interface [polypeptide binding]; other site 340100003798 catalytic residue [active] 340100003799 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100003800 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100003801 DNA-binding site [nucleotide binding]; DNA binding site 340100003802 FCD domain; Region: FCD; pfam07729 340100003803 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003804 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003805 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 340100003806 dimerization interface [polypeptide binding]; other site 340100003807 substrate binding pocket [chemical binding]; other site 340100003808 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100003809 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 340100003810 non-specific DNA binding site [nucleotide binding]; other site 340100003811 salt bridge; other site 340100003812 sequence-specific DNA binding site [nucleotide binding]; other site 340100003813 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 340100003814 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003815 dimerization interface [polypeptide binding]; other site 340100003816 substrate binding pocket [chemical binding]; other site 340100003817 integrase; Provisional; Region: PRK09692 340100003818 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 340100003819 active site 340100003820 Int/Topo IB signature motif; other site 340100003821 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 340100003822 Methyltransferase domain; Region: Methyltransf_18; pfam12847 340100003823 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 340100003824 glutathionine S-transferase; Provisional; Region: PRK10542 340100003825 C-terminal domain interface [polypeptide binding]; other site 340100003826 GSH binding site (G-site) [chemical binding]; other site 340100003827 dimer interface [polypeptide binding]; other site 340100003828 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100003829 dimer interface [polypeptide binding]; other site 340100003830 substrate binding pocket (H-site) [chemical binding]; other site 340100003831 N-terminal domain interface [polypeptide binding]; other site 340100003832 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100003833 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003834 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 340100003835 dimerization interface [polypeptide binding]; other site 340100003836 substrate binding pocket [chemical binding]; other site 340100003837 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100003838 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 340100003839 C-terminal domain interface [polypeptide binding]; other site 340100003840 GSH binding site (G-site) [chemical binding]; other site 340100003841 dimer interface [polypeptide binding]; other site 340100003842 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 340100003843 N-terminal domain interface [polypeptide binding]; other site 340100003844 putative dimer interface [polypeptide binding]; other site 340100003845 active site 340100003846 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100003847 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 340100003848 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100003849 acyl-CoA synthetase; Validated; Region: PRK06188 340100003850 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 340100003851 acyl-activating enzyme (AAE) consensus motif; other site 340100003852 putative AMP binding site [chemical binding]; other site 340100003853 putative active site [active] 340100003854 putative CoA binding site [chemical binding]; other site 340100003855 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 340100003856 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 340100003857 active site 340100003858 oxalacetate binding site [chemical binding]; other site 340100003859 citrylCoA binding site [chemical binding]; other site 340100003860 coenzyme A binding site [chemical binding]; other site 340100003861 catalytic triad [active] 340100003862 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100003863 short chain dehydrogenase; Provisional; Region: PRK07577 340100003864 NAD(P) binding site [chemical binding]; other site 340100003865 active site 340100003866 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100003867 classical (c) SDRs; Region: SDR_c; cd05233 340100003868 NAD(P) binding site [chemical binding]; other site 340100003869 active site 340100003870 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003871 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100003872 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 340100003873 dimerization interface [polypeptide binding]; other site 340100003874 substrate binding pocket [chemical binding]; other site 340100003875 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 340100003876 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100003877 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 340100003878 P-loop; other site 340100003879 Magnesium ion binding site [ion binding]; other site 340100003880 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 340100003881 Magnesium ion binding site [ion binding]; other site 340100003882 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100003883 ParB-like nuclease domain; Region: ParBc; pfam02195 340100003884 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100003885 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 340100003886 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100003887 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 340100003888 DNA methylase; Region: N6_N4_Mtase; pfam01555 340100003889 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100003890 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 340100003891 ssDNA binding site [nucleotide binding]; other site 340100003892 dimer interface [polypeptide binding]; other site 340100003893 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100003894 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 340100003895 active site 340100003896 putative interdomain interaction site [polypeptide binding]; other site 340100003897 putative metal-binding site [ion binding]; other site 340100003898 putative nucleotide binding site [chemical binding]; other site 340100003899 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 340100003900 domain I; other site 340100003901 DNA binding groove [nucleotide binding] 340100003902 phosphate binding site [ion binding]; other site 340100003903 domain III; other site 340100003904 nucleotide binding site [chemical binding]; other site 340100003905 catalytic site [active] 340100003906 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100003907 Transposase; Region: HTH_Tnp_1; pfam01527 340100003908 putative transposase OrfB; Reviewed; Region: PHA02517 340100003909 HTH-like domain; Region: HTH_21; pfam13276 340100003910 Integrase core domain; Region: rve; pfam00665 340100003911 Integrase core domain; Region: rve_3; pfam13683 340100003912 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 340100003913 domain II; other site 340100003914 domain IV; other site 340100003915 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100003916 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 340100003917 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100003918 cofactor binding site; other site 340100003919 DNA binding site [nucleotide binding] 340100003920 substrate interaction site [chemical binding]; other site 340100003921 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N2; pfam13495 340100003922 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100003923 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 340100003924 active site 340100003925 DNA binding site [nucleotide binding] 340100003926 Int/Topo IB signature motif; other site 340100003927 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 340100003928 active site 340100003929 DNA binding site [nucleotide binding] 340100003930 Int/Topo IB signature motif; other site 340100003931 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100003932 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 340100003933 active site 340100003934 DNA binding site [nucleotide binding] 340100003935 Int/Topo IB signature motif; other site 340100003936 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100003937 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 340100003938 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4453 340100003939 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 340100003940 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100003941 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100003942 Domain of unknown function (DUF932); Region: DUF932; pfam06067 340100003943 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 340100003944 S-adenosylmethionine binding site [chemical binding]; other site 340100003945 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100003946 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 340100003947 ATP binding site [chemical binding]; other site 340100003948 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 340100003949 nucleotide binding region [chemical binding]; other site 340100003950 ATP-binding site [chemical binding]; other site 340100003951 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 340100003952 salt bridge; other site 340100003953 non-specific DNA binding site [nucleotide binding]; other site 340100003954 sequence-specific DNA binding site [nucleotide binding]; other site 340100003955 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 340100003956 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 340100003957 substrate-cofactor binding pocket; other site 340100003958 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100003959 catalytic residue [active] 340100003960 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100003961 Coenzyme A binding pocket [chemical binding]; other site 340100003962 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 340100003963 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 340100003964 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 340100003965 active site 340100003966 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 340100003967 dimer interface [polypeptide binding]; other site 340100003968 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 340100003969 Ligand Binding Site [chemical binding]; other site 340100003970 Molecular Tunnel; other site 340100003971 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100003972 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 340100003973 putative substrate translocation pore; other site 340100003974 hypothetical protein; Provisional; Region: PRK06847 340100003975 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100003976 FAD binding domain; Region: FAD_binding_3; pfam01494 340100003977 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100003978 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100003979 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100003980 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100003981 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100003982 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 340100003983 putative substrate translocation pore; other site 340100003984 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100003985 EamA-like transporter family; Region: EamA; pfam00892 340100003986 Membrane protein of unknown function (DUF340); Region: DUF340; pfam03956 340100003987 Biofilm formation and stress response factor; Region: BsmA; cl01794 340100003988 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100003989 Transposase; Region: HTH_Tnp_1; pfam01527 340100003990 putative transposase OrfB; Reviewed; Region: PHA02517 340100003991 HTH-like domain; Region: HTH_21; pfam13276 340100003992 Integrase core domain; Region: rve; pfam00665 340100003993 Integrase core domain; Region: rve_3; pfam13683 340100003994 Biofilm formation and stress response factor; Region: BsmA; cl01794 340100003995 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100003996 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; cl17879 340100003997 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 340100003998 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100003999 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100004000 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 340100004001 putative effector binding pocket; other site 340100004002 dimerization interface [polypeptide binding]; other site 340100004003 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100004004 Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: MukB; COG3096 340100004005 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100004006 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 340100004007 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 340100004008 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 340100004009 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100004010 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 340100004011 carbon storage regulator; Provisional; Region: PRK01712 340100004012 HipA N-terminal domain; Region: Couple_hipA; cl11853 340100004013 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100004014 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100004015 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100004016 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 340100004017 non-specific DNA binding site [nucleotide binding]; other site 340100004018 salt bridge; other site 340100004019 sequence-specific DNA binding site [nucleotide binding]; other site 340100004020 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100004021 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100004022 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 340100004023 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 340100004024 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 340100004025 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 340100004026 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 340100004027 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100004028 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 340100004029 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100004030 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100004031 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 340100004032 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 340100004033 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 340100004034 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 340100004035 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 340100004036 metal binding site [ion binding]; metal-binding site 340100004037 active site 340100004038 I-site; other site 340100004039 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 340100004040 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 340100004041 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 340100004042 catalytic residues [active] 340100004043 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 340100004044 ParB-like nuclease domain; Region: ParBc; pfam02195 340100004045 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 340100004046 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 340100004047 Active Sites [active] 340100004048 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 340100004049 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004050 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100004051 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 340100004052 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 340100004053 putative active site [active] 340100004054 heme pocket [chemical binding]; other site 340100004055 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 340100004056 putative active site [active] 340100004057 heme pocket [chemical binding]; other site 340100004058 GAF domain; Region: GAF; cl17456 340100004059 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 340100004060 metal binding site [ion binding]; metal-binding site 340100004061 active site 340100004062 I-site; other site 340100004063 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 340100004064 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 340100004065 PAS domain; Region: PAS_9; pfam13426 340100004066 putative active site [active] 340100004067 heme pocket [chemical binding]; other site 340100004068 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 340100004069 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100004070 dimer interface [polypeptide binding]; other site 340100004071 putative CheW interface [polypeptide binding]; other site 340100004072 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100004073 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100004074 The 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 340100004075 dimerization interface [polypeptide binding]; other site 340100004076 Biofilm formation and stress response factor; Region: BsmA; pfam10014 340100004077 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100004078 phosphoserine phosphatase; Provisional; Region: thrH; PRK13582 340100004079 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 340100004080 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 340100004081 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 340100004082 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100004083 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100004084 PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, Archaeoglobus fulgidus AF0591 protein and homologs; Region: PIN_VapC-Smg6-like; cd09855 340100004085 putative active site [active] 340100004086 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100004087 Putative helicase; Region: TraI_2; pfam07514 340100004088 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100004089 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 340100004090 Dynamin family; Region: Dynamin_N; pfam00350 340100004091 G1 box; other site 340100004092 GTP/Mg2+ binding site [chemical binding]; other site 340100004093 G2 box; other site 340100004094 Switch I region; other site 340100004095 G3 box; other site 340100004096 Switch II region; other site 340100004097 G4 box; other site 340100004098 G5 box; other site 340100004099 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 340100004100 G1 box; other site 340100004101 GTP/Mg2+ binding site [chemical binding]; other site 340100004102 G2 box; other site 340100004103 Switch I region; other site 340100004104 G3 box; other site 340100004105 Switch II region; other site 340100004106 G4 box; other site 340100004107 G5 box; other site 340100004108 Benzoate membrane transport protein; Region: BenE; pfam03594 340100004109 benzoate transporter; Region: benE; TIGR00843 340100004110 benzoate transport; Region: 2A0115; TIGR00895 340100004111 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 340100004112 putative substrate translocation pore; other site 340100004113 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 340100004114 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 340100004115 catalytic Zn binding site [ion binding]; other site 340100004116 NAD binding site [chemical binding]; other site 340100004117 structural Zn binding site [ion binding]; other site 340100004118 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100004119 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 340100004120 NAD(P) binding site [chemical binding]; other site 340100004121 catalytic residues [active] 340100004122 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100004123 Muconolactone delta-isomerase; Region: MIase; cl01992 340100004124 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 340100004125 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 340100004126 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 340100004127 active site 340100004128 Coenzyme A transferase; Region: CoA_trans; cl17247 340100004129 benzoate transport; Region: 2A0115; TIGR00895 340100004130 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 340100004131 putative substrate translocation pore; other site 340100004132 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 340100004133 homotrimer interaction site [polypeptide binding]; other site 340100004134 putative active site [active] 340100004135 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional; Region: benD; PRK12823 340100004136 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 340100004137 putative NAD(P) binding site [chemical binding]; other site 340100004138 active site 340100004139 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 340100004140 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 340100004141 catalytic loop [active] 340100004142 iron binding site [ion binding]; other site 340100004143 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 340100004144 FAD binding pocket [chemical binding]; other site 340100004145 FAD binding motif [chemical binding]; other site 340100004146 phosphate binding motif [ion binding]; other site 340100004147 beta-alpha-beta structure motif; other site 340100004148 NAD binding pocket [chemical binding]; other site 340100004149 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 340100004150 inter-subunit interface; other site 340100004151 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 340100004152 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 340100004153 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 340100004154 putative alpha subunit interface [polypeptide binding]; other site 340100004155 putative active site [active] 340100004156 putative substrate binding site [chemical binding]; other site 340100004157 Fe binding site [ion binding]; other site 340100004158 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 340100004159 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 340100004160 dimer interface [polypeptide binding]; other site 340100004161 active site 340100004162 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100004163 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 340100004164 octamer interface [polypeptide binding]; other site 340100004165 active site 340100004166 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100004167 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 340100004168 dimerizarion interface [polypeptide binding]; other site 340100004169 CrgA pocket; other site 340100004170 substrate binding pocket [chemical binding]; other site 340100004171 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 340100004172 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 340100004173 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 340100004174 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100004175 Transposase; Region: HTH_Tnp_1; pfam01527 340100004176 Integrase core domain; Region: rve_3; cl15866 340100004177 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100004178 Winged helix-turn helix; Region: HTH_29; pfam13551 340100004179 Homeodomain-like domain; Region: HTH_32; pfam13565 340100004180 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 340100004181 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 340100004182 catalytic residues [active] 340100004183 catalytic nucleophile [active] 340100004184 Recombinase; Region: Recombinase; pfam07508 340100004185 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 340100004186 HTH-like domain; Region: HTH_21; pfam13276 340100004187 Integrase core domain; Region: rve; pfam00665 340100004188 Probable cobalt transporter subunit (CbtA); Region: CbtA; pfam09490 340100004189 Probable cobalt transporter subunit (CbtB); Region: CbtB; cl09723 340100004190 nitrile hydratase accessory protein; Region: nitrile_acc; TIGR03889 340100004191 Nitrile hydratase beta subunit; Region: NHase_beta; pfam02211 340100004192 nitrile hydratase, beta subunit; Region: nitrile_beta; TIGR03888 340100004193 Nitrile hydratase, alpha chain; Region: NHase_alpha; pfam02979 340100004194 NHLP leader peptide domain; Region: TOMM_pelo; TIGR03793 340100004195 NHLP leader peptide domain; Region: TOMM_pelo; TIGR03793 340100004196 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100004197 Amidase; Region: Amidase; pfam01425 340100004198 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 340100004199 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 340100004200 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 340100004201 PAS domain; Region: PAS_9; pfam13426 340100004202 putative active site [active] 340100004203 heme pocket [chemical binding]; other site 340100004204 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 340100004205 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100004206 dimer interface [polypeptide binding]; other site 340100004207 putative CheW interface [polypeptide binding]; other site 340100004208 Coenzyme A transferase; Region: CoA_trans; cl17247 340100004209 Coenzyme A transferase; Region: CoA_trans; cl17247 340100004210 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100004211 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100004212 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100004213 salicylate hydroxylase; Provisional; Region: PRK08163 340100004214 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100004215 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 340100004216 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100004217 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 340100004218 Cupin domain; Region: Cupin_2; pfam07883 340100004219 Cupin domain; Region: Cupin_2; pfam07883 340100004220 benzoate transport; Region: 2A0115; TIGR00895 340100004221 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 340100004222 putative substrate translocation pore; other site 340100004223 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 340100004224 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 340100004225 Presynaptic Site I dimer interface [polypeptide binding]; other site 340100004226 catalytic residues [active] 340100004227 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340100004228 Synaptic Flat tetramer interface [polypeptide binding]; other site 340100004229 Synaptic Site I dimer interface [polypeptide binding]; other site 340100004230 DNA binding site [nucleotide binding] 340100004231 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 340100004232 DNA-binding interface [nucleotide binding]; DNA binding site 340100004233 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100004234 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 340100004235 non-specific DNA binding site [nucleotide binding]; other site 340100004236 salt bridge; other site 340100004237 sequence-specific DNA binding site [nucleotide binding]; other site 340100004238 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100004239 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 340100004240 dimerization interface [polypeptide binding]; other site 340100004241 substrate binding pocket [chemical binding]; other site 340100004242 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004243 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100004244 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 340100004245 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 340100004246 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100004247 putative substrate translocation pore; other site 340100004248 integrase; Provisional; Region: PRK09692 340100004249 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 340100004250 active site 340100004251 Int/Topo IB signature motif; other site 340100004252 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 340100004253 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100004254 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 340100004255 Magnesium ion binding site [ion binding]; other site 340100004256 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100004257 ParB-like nuclease domain; Region: ParBc; pfam02195 340100004258 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100004259 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 340100004260 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100004261 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100004262 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 340100004263 ssDNA binding site [nucleotide binding]; other site 340100004264 dimer interface [polypeptide binding]; other site 340100004265 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100004266 DNA topoisomerase III; Provisional; Region: PRK07726 340100004267 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 340100004268 active site 340100004269 putative interdomain interaction site [polypeptide binding]; other site 340100004270 putative metal-binding site [ion binding]; other site 340100004271 putative nucleotide binding site [chemical binding]; other site 340100004272 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 340100004273 domain I; other site 340100004274 DNA binding groove [nucleotide binding] 340100004275 phosphate binding site [ion binding]; other site 340100004276 domain II; other site 340100004277 domain III; other site 340100004278 nucleotide binding site [chemical binding]; other site 340100004279 catalytic site [active] 340100004280 domain IV; other site 340100004281 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100004282 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 340100004283 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100004284 cofactor binding site; other site 340100004285 DNA binding site [nucleotide binding] 340100004286 substrate interaction site [chemical binding]; other site 340100004287 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N2; pfam13495 340100004288 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100004289 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 340100004290 active site 340100004291 DNA binding site [nucleotide binding] 340100004292 Int/Topo IB signature motif; other site 340100004293 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 340100004294 active site 340100004295 DNA binding site [nucleotide binding] 340100004296 Int/Topo IB signature motif; other site 340100004297 putative transposase OrfB; Reviewed; Region: PHA02517 340100004298 HTH-like domain; Region: HTH_21; pfam13276 340100004299 Integrase core domain; Region: rve; pfam00665 340100004300 Integrase core domain; Region: rve_3; pfam13683 340100004301 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100004302 Transposase; Region: HTH_Tnp_1; pfam01527 340100004303 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 340100004304 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 340100004305 active site 340100004306 DNA binding site [nucleotide binding] 340100004307 Int/Topo IB signature motif; other site 340100004308 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340100004309 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 340100004310 putative transposase OrfB; Reviewed; Region: PHA02517 340100004311 HTH-like domain; Region: HTH_21; pfam13276 340100004312 Integrase core domain; Region: rve; pfam00665 340100004313 Integrase core domain; Region: rve_3; pfam13683 340100004314 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100004315 Transposase; Region: HTH_Tnp_1; pfam01527 340100004316 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 340100004317 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 340100004318 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 340100004319 Active Sites [active] 340100004320 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100004321 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100004322 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100004323 Methyltransferase domain; Region: Methyltransf_26; pfam13659 340100004324 S-adenosylmethionine binding site [chemical binding]; other site 340100004325 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 340100004326 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 340100004327 putative active site [active] 340100004328 putative NTP binding site [chemical binding]; other site 340100004329 putative nucleic acid binding site [nucleotide binding]; other site 340100004330 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100004331 Type II intron maturase; Region: Intron_maturas2; pfam01348 340100004332 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 340100004333 nucleotide binding region [chemical binding]; other site 340100004334 ATP-binding site [chemical binding]; other site 340100004335 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100004336 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100004337 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100004338 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100004339 catalytic residue [active] 340100004340 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 340100004341 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 340100004342 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 340100004343 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 340100004344 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100004345 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100004346 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 340100004347 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 340100004348 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 340100004349 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 340100004350 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 340100004351 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100004352 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100004353 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 340100004354 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100004355 Transposase; Region: HTH_Tnp_1; pfam01527 340100004356 putative transposase OrfB; Reviewed; Region: PHA02517 340100004357 HTH-like domain; Region: HTH_21; pfam13276 340100004358 Integrase core domain; Region: rve; pfam00665 340100004359 Integrase core domain; Region: rve_3; pfam13683 340100004360 AAA-like domain; Region: AAA_10; pfam12846 340100004361 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 340100004362 catalytic residues [active] 340100004363 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100004364 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 340100004365 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 340100004366 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 340100004367 Int/Topo IB signature motif; other site 340100004368 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 340100004369 active site 340100004370 DNA binding site [nucleotide binding] 340100004371 Int/Topo IB signature motif; other site 340100004372 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 340100004373 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 340100004374 Int/Topo IB signature motif; other site 340100004375 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 340100004376 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 340100004377 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100004378 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100004379 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 340100004380 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 340100004381 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340100004382 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 340100004383 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100004384 Putative helicase; Region: TraI_2; pfam07514 340100004385 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100004386 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100004387 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100004388 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 340100004389 classical (c) SDRs; Region: SDR_c; cd05233 340100004390 NAD(P) binding site [chemical binding]; other site 340100004391 active site 340100004392 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 340100004393 inter-subunit interface; other site 340100004394 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 340100004395 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 340100004396 Putative transposase; Region: Y2_Tnp; pfam04986 340100004397 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 340100004398 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100004399 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100004400 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 340100004401 glutathione reductase; Validated; Region: PRK06116 340100004402 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100004403 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100004404 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100004405 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100004406 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100004407 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100004408 putative N-terminal domain interface [polypeptide binding]; other site 340100004409 putative dimer interface [polypeptide binding]; other site 340100004410 putative substrate binding pocket (H-site) [chemical binding]; other site 340100004411 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100004412 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 340100004413 C-terminal domain interface [polypeptide binding]; other site 340100004414 GSH binding site (G-site) [chemical binding]; other site 340100004415 dimer interface [polypeptide binding]; other site 340100004416 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100004417 N-terminal domain interface [polypeptide binding]; other site 340100004418 dimer interface [polypeptide binding]; other site 340100004419 substrate binding pocket (H-site) [chemical binding]; other site 340100004420 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 340100004421 putative FMN binding site [chemical binding]; other site 340100004422 Stress responsive A/B Barrel Domain; Region: Dabb; smart00886 340100004423 YciI-like protein; Reviewed; Region: PRK12863 340100004424 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 340100004425 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 340100004426 inhibitor-cofactor binding pocket; inhibition site 340100004427 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100004428 catalytic residue [active] 340100004429 Putative transposase; Region: Y2_Tnp; pfam04986 340100004430 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 340100004431 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 340100004432 Ligand binding site; other site 340100004433 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 340100004434 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100004435 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 340100004436 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 340100004437 trimer interface [polypeptide binding]; other site 340100004438 active site 340100004439 substrate binding site [chemical binding]; other site 340100004440 CoA binding site [chemical binding]; other site 340100004441 Organic solute transporter Ostalpha; Region: Solute_trans_a; pfam03619 340100004442 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 340100004443 Putative transposase; Region: Y2_Tnp; pfam04986 340100004444 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 340100004445 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 340100004446 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 340100004447 LysE type translocator; Region: LysE; cl00565 340100004448 LysE type translocator; Region: LysE; cl00565 340100004449 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100004450 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100004451 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 340100004452 putative dimerization interface [polypeptide binding]; other site 340100004453 putative substrate binding pocket [chemical binding]; other site 340100004454 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 340100004455 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 340100004456 dimer interface [polypeptide binding]; other site 340100004457 active site 340100004458 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 340100004459 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100004460 octamer interface [polypeptide binding]; other site 340100004461 active site 340100004462 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100004463 Dienelactone hydrolase family; Region: DLH; pfam01738 340100004464 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 340100004465 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100004466 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 340100004467 active site 340100004468 dimer interface [polypeptide binding]; other site 340100004469 metal binding site [ion binding]; metal-binding site 340100004470 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100004471 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 340100004472 iron-sulfur cluster [ion binding]; other site 340100004473 [2Fe-2S] cluster binding site [ion binding]; other site 340100004474 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 340100004475 putative alpha subunit interface [polypeptide binding]; other site 340100004476 putative active site [active] 340100004477 putative substrate binding site [chemical binding]; other site 340100004478 Fe binding site [ion binding]; other site 340100004479 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 340100004480 inter-subunit interface; other site 340100004481 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 340100004482 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 340100004483 FMN-binding pocket [chemical binding]; other site 340100004484 flavin binding motif; other site 340100004485 phosphate binding motif [ion binding]; other site 340100004486 beta-alpha-beta structure motif; other site 340100004487 NAD binding pocket [chemical binding]; other site 340100004488 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 340100004489 catalytic loop [active] 340100004490 iron binding site [ion binding]; other site 340100004491 benzoate transport; Region: 2A0115; TIGR00895 340100004492 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 340100004493 putative substrate translocation pore; other site 340100004494 YCII-related domain; Region: YCII; cl00999 340100004495 integrase; Provisional; Region: PRK09692 340100004496 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 340100004497 active site 340100004498 Int/Topo IB signature motif; other site 340100004499 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 340100004500 FAD binding domain; Region: FAD_binding_4; pfam01565 340100004501 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 340100004502 dihydrodipicolinate reductase; Provisional; Region: PRK00048 340100004503 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 340100004504 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 340100004505 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 340100004506 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 340100004507 ferric uptake regulator; Provisional; Region: fur; PRK09462 340100004508 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 340100004509 metal binding site 2 [ion binding]; metal-binding site 340100004510 putative DNA binding helix; other site 340100004511 metal binding site 1 [ion binding]; metal-binding site 340100004512 dimer interface [polypeptide binding]; other site 340100004513 structural Zn2+ binding site [ion binding]; other site 340100004514 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 340100004515 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 340100004516 Walker A/P-loop; other site 340100004517 ATP binding site [chemical binding]; other site 340100004518 Q-loop/lid; other site 340100004519 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 340100004520 ABC transporter signature motif; other site 340100004521 Walker B; other site 340100004522 D-loop; other site 340100004523 H-loop/switch region; other site 340100004524 NAD(+)/NADH kinase family protein; Provisional; Region: ppnK; PRK02155 340100004525 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 340100004526 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 340100004527 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 340100004528 ferrochelatase; Reviewed; Region: hemH; PRK00035 340100004529 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 340100004530 C-terminal domain interface [polypeptide binding]; other site 340100004531 active site 340100004532 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 340100004533 active site 340100004534 N-terminal domain interface [polypeptide binding]; other site 340100004535 GrpE; Region: GrpE; pfam01025 340100004536 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 340100004537 dimer interface [polypeptide binding]; other site 340100004538 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 340100004539 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 340100004540 catalytic residues [active] 340100004541 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 340100004542 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 340100004543 nucleotide binding site [chemical binding]; other site 340100004544 NEF interaction site [polypeptide binding]; other site 340100004545 SBD interface [polypeptide binding]; other site 340100004546 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100004547 chaperone protein DnaJ; Provisional; Region: PRK10767 340100004548 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 340100004549 HSP70 interaction site [polypeptide binding]; other site 340100004550 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 340100004551 Zn binding sites [ion binding]; other site 340100004552 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 340100004553 dimer interface [polypeptide binding]; other site 340100004554 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100004555 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100004556 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 340100004557 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 340100004558 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 340100004559 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 340100004560 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 340100004561 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 340100004562 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100004563 Coenzyme A binding pocket [chemical binding]; other site 340100004564 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 340100004565 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 340100004566 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 340100004567 Walker A motif; other site 340100004568 ATP binding site [chemical binding]; other site 340100004569 Walker B motif; other site 340100004570 arginine finger; other site 340100004571 Cytochrome c553 [Energy production and conversion]; Region: COG2863 340100004572 Cytochrome c; Region: Cytochrom_C; cl11414 340100004573 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 340100004574 isocitrate dehydrogenase; Validated; Region: PRK07362 340100004575 isocitrate dehydrogenase; Reviewed; Region: PRK07006 340100004576 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 340100004577 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 340100004578 trimer interface [polypeptide binding]; other site 340100004579 eyelet of channel; other site 340100004580 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 340100004581 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 340100004582 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 340100004583 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100004584 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 340100004585 Smr domain; Region: Smr; pfam01713 340100004586 thioredoxin reductase; Provisional; Region: PRK10262 340100004587 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100004588 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100004589 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 340100004590 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 340100004591 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 340100004592 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 340100004593 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 340100004594 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100004595 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 340100004596 homotrimer interaction site [polypeptide binding]; other site 340100004597 putative active site [active] 340100004598 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100004599 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 340100004600 active site 340100004601 putative substrate binding pocket [chemical binding]; other site 340100004602 Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins; Region: DHR2_DOCK; cl06123 340100004603 D-aminoacylase, C-terminal region; Region: D-aminoacyl_C; pfam07908 340100004604 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 340100004605 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 340100004606 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 340100004607 putative active site [active] 340100004608 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 340100004609 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100004610 Walker A/P-loop; other site 340100004611 ATP binding site [chemical binding]; other site 340100004612 Q-loop/lid; other site 340100004613 ABC transporter signature motif; other site 340100004614 Walker B; other site 340100004615 D-loop; other site 340100004616 H-loop/switch region; other site 340100004617 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 340100004618 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100004619 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100004620 Walker A/P-loop; other site 340100004621 ATP binding site [chemical binding]; other site 340100004622 Q-loop/lid; other site 340100004623 ABC transporter signature motif; other site 340100004624 Walker B; other site 340100004625 D-loop; other site 340100004626 H-loop/switch region; other site 340100004627 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100004628 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100004629 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 340100004630 dimer interface [polypeptide binding]; other site 340100004631 conserved gate region; other site 340100004632 putative PBP binding loops; other site 340100004633 ABC-ATPase subunit interface; other site 340100004634 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100004635 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 340100004636 dimer interface [polypeptide binding]; other site 340100004637 conserved gate region; other site 340100004638 putative PBP binding loops; other site 340100004639 ABC-ATPase subunit interface; other site 340100004640 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100004641 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 340100004642 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 340100004643 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase; Region: PLPDE_III_cryptic_DSD; cd06818 340100004644 dimer interface [polypeptide binding]; other site 340100004645 active site 340100004646 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100004647 substrate binding site [chemical binding]; other site 340100004648 catalytic residue [active] 340100004649 recombination factor protein RarA; Reviewed; Region: PRK13342 340100004650 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 340100004651 Walker A motif; other site 340100004652 ATP binding site [chemical binding]; other site 340100004653 Walker B motif; other site 340100004654 arginine finger; other site 340100004655 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 340100004656 seryl-tRNA synthetase; Provisional; Region: PRK05431 340100004657 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 340100004658 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 340100004659 dimer interface [polypeptide binding]; other site 340100004660 active site 340100004661 motif 1; other site 340100004662 motif 2; other site 340100004663 motif 3; other site 340100004664 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100004665 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 340100004666 C-terminal domain interface [polypeptide binding]; other site 340100004667 GSH binding site (G-site) [chemical binding]; other site 340100004668 dimer interface [polypeptide binding]; other site 340100004669 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100004670 N-terminal domain interface [polypeptide binding]; other site 340100004671 dimer interface [polypeptide binding]; other site 340100004672 substrate binding pocket (H-site) [chemical binding]; other site 340100004673 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004674 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100004675 inner membrane protein; Provisional; Region: PRK10995 340100004676 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 340100004677 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 340100004678 Chromate transporter; Region: Chromate_transp; pfam02417 340100004679 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100004680 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 340100004681 dimerization interface [polypeptide binding]; other site 340100004682 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 340100004683 ATP binding site [chemical binding]; other site 340100004684 Mg2+ binding site [ion binding]; other site 340100004685 G-X-G motif; other site 340100004686 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100004687 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100004688 active site 340100004689 phosphorylation site [posttranslational modification] 340100004690 intermolecular recognition site; other site 340100004691 dimerization interface [polypeptide binding]; other site 340100004692 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 340100004693 DNA binding site [nucleotide binding] 340100004694 MarR family; Region: MarR_2; pfam12802 340100004695 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100004696 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 340100004697 active site 340100004698 metal binding site [ion binding]; metal-binding site 340100004699 Predicted transcriptional regulator [Transcription]; Region: COG2378 340100004700 HTH domain; Region: HTH_11; pfam08279 340100004701 WYL domain; Region: WYL; pfam13280 340100004702 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 340100004703 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 340100004704 NAD binding site [chemical binding]; other site 340100004705 homotetramer interface [polypeptide binding]; other site 340100004706 homodimer interface [polypeptide binding]; other site 340100004707 substrate binding site [chemical binding]; other site 340100004708 active site 340100004709 hypothetical protein; Validated; Region: PRK02101 340100004710 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 340100004711 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100004712 putative substrate translocation pore; other site 340100004713 Predicted membrane protein [Function unknown]; Region: COG1289 340100004714 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 340100004715 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 340100004716 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 340100004717 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100004718 PYR/PP interface [polypeptide binding]; other site 340100004719 dimer interface [polypeptide binding]; other site 340100004720 TPP binding site [chemical binding]; other site 340100004721 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100004722 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 340100004723 TPP-binding site [chemical binding]; other site 340100004724 dimer interface [polypeptide binding]; other site 340100004725 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 340100004726 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 340100004727 putative valine binding site [chemical binding]; other site 340100004728 dimer interface [polypeptide binding]; other site 340100004729 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 340100004730 ketol-acid reductoisomerase; Provisional; Region: PRK05479 340100004731 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 340100004732 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 340100004733 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 340100004734 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 340100004735 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 340100004736 16S/18S rRNA binding site [nucleotide binding]; other site 340100004737 S13e-L30e interaction site [polypeptide binding]; other site 340100004738 25S rRNA binding site [nucleotide binding]; other site 340100004739 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 340100004740 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 340100004741 RNase E interface [polypeptide binding]; other site 340100004742 trimer interface [polypeptide binding]; other site 340100004743 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 340100004744 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 340100004745 RNase E interface [polypeptide binding]; other site 340100004746 trimer interface [polypeptide binding]; other site 340100004747 active site 340100004748 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 340100004749 putative nucleic acid binding region [nucleotide binding]; other site 340100004750 G-X-X-G motif; other site 340100004751 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 340100004752 RNA binding site [nucleotide binding]; other site 340100004753 domain interface; other site 340100004754 threonine dehydratase; Provisional; Region: PRK07334 340100004755 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 340100004756 tetramer interface [polypeptide binding]; other site 340100004757 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100004758 catalytic residue [active] 340100004759 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 340100004760 PIN domain; Region: PIN_3; pfam13470 340100004761 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 340100004762 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 340100004763 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340100004764 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; pfam09937 340100004765 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100004766 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004767 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004768 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340100004769 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004770 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100004771 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340100004772 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100004773 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 340100004774 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 340100004775 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 340100004776 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100004777 dinuclear metal binding motif [ion binding]; other site 340100004778 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 340100004779 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 340100004780 NAD(P) binding site [chemical binding]; other site 340100004781 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 340100004782 triosephosphate isomerase; Provisional; Region: PRK14567 340100004783 substrate binding site [chemical binding]; other site 340100004784 dimer interface [polypeptide binding]; other site 340100004785 catalytic triad [active] 340100004786 Preprotein translocase SecG subunit; Region: SecG; pfam03840 340100004787 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 340100004788 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 340100004789 motif II; other site 340100004790 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 340100004791 dinuclear metal binding motif [ion binding]; other site 340100004792 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 340100004793 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_1; cd09319 340100004794 gating phenylalanine in ion channel; other site 340100004795 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 340100004796 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 340100004797 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 340100004798 catalytic residues [active] 340100004799 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100004800 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100004801 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 340100004802 active site 340100004803 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100004804 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100004805 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 340100004806 dimerization interface [polypeptide binding]; other site 340100004807 substrate binding pocket [chemical binding]; other site 340100004808 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100004809 Coenzyme A transferase; Region: CoA_trans; cl17247 340100004810 thiolase; Provisional; Region: PRK06158 340100004811 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 340100004812 active site 340100004813 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 340100004814 DUF35 OB-fold domain; Region: DUF35; pfam01796 340100004815 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 340100004816 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 340100004817 dimanganese center [ion binding]; other site 340100004818 Protein of unknown function (DUF763); Region: DUF763; pfam05559 340100004819 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 340100004820 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 340100004821 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100004822 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100004823 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 340100004824 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100004825 NAD(P) binding site [chemical binding]; other site 340100004826 active site 340100004827 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 340100004828 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100004829 DNA-binding site [nucleotide binding]; DNA binding site 340100004830 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100004831 FCD domain; Region: FCD; pfam07729 340100004832 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100004833 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100004834 short chain dehydrogenase; Validated; Region: PRK08589 340100004835 classical (c) SDRs; Region: SDR_c; cd05233 340100004836 NAD(P) binding site [chemical binding]; other site 340100004837 active site 340100004838 Uncharacterized protein involved in propionate catabolism [General function prediction only]; Region: PrpD; COG2079 340100004839 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100004840 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 340100004841 TM-ABC transporter signature motif; other site 340100004842 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100004843 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 340100004844 TM-ABC transporter signature motif; other site 340100004845 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100004846 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100004847 Walker A/P-loop; other site 340100004848 ATP binding site [chemical binding]; other site 340100004849 Q-loop/lid; other site 340100004850 ABC transporter signature motif; other site 340100004851 Walker B; other site 340100004852 D-loop; other site 340100004853 H-loop/switch region; other site 340100004854 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100004855 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100004856 Walker A/P-loop; other site 340100004857 ATP binding site [chemical binding]; other site 340100004858 Q-loop/lid; other site 340100004859 ABC transporter signature motif; other site 340100004860 Walker B; other site 340100004861 D-loop; other site 340100004862 H-loop/switch region; other site 340100004863 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100004864 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100004865 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100004866 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100004867 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100004868 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 340100004869 NIPSNAP; Region: NIPSNAP; pfam07978 340100004870 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100004871 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100004872 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100004873 DNA-binding site [nucleotide binding]; DNA binding site 340100004874 UTRA domain; Region: UTRA; pfam07702 340100004875 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 340100004876 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 340100004877 substrate binding site [chemical binding]; other site 340100004878 ligand binding site [chemical binding]; other site 340100004879 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 340100004880 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 340100004881 substrate binding site [chemical binding]; other site 340100004882 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 340100004883 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 340100004884 tetramer interface [polypeptide binding]; other site 340100004885 active site 340100004886 Mg2+/Mn2+ binding site [ion binding]; other site 340100004887 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 340100004888 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100004889 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 340100004890 putative substrate translocation pore; other site 340100004891 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 340100004892 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 340100004893 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 340100004894 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100004895 active site 340100004896 metal binding site [ion binding]; metal-binding site 340100004897 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 340100004898 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 340100004899 active site 340100004900 2,3-diaminopropionate biosynthesis protein SbnB; Region: dehyd_SbnB_fam; TIGR03944 340100004901 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 340100004902 CoenzymeA binding site [chemical binding]; other site 340100004903 subunit interaction site [polypeptide binding]; other site 340100004904 PHB binding site; other site 340100004905 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100004906 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100004907 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 340100004908 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 340100004909 trimer interface [polypeptide binding]; other site 340100004910 eyelet of channel; other site 340100004911 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 340100004912 NADH dehydrogenase subunit B; Validated; Region: PRK06411 340100004913 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 340100004914 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 340100004915 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 340100004916 NADH dehydrogenase subunit D; Validated; Region: PRK06075 340100004917 NADH dehydrogenase subunit E; Validated; Region: PRK07539 340100004918 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 340100004919 putative dimer interface [polypeptide binding]; other site 340100004920 [2Fe-2S] cluster binding site [ion binding]; other site 340100004921 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 340100004922 SLBB domain; Region: SLBB; pfam10531 340100004923 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 340100004924 NADH dehydrogenase subunit G; Validated; Region: PRK09129 340100004925 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 340100004926 catalytic loop [active] 340100004927 iron binding site [ion binding]; other site 340100004928 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 340100004929 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 340100004930 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 340100004931 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 340100004932 4Fe-4S binding domain; Region: Fer4; cl02805 340100004933 4Fe-4S binding domain; Region: Fer4; cl02805 340100004934 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 340100004935 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 340100004936 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 340100004937 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 340100004938 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 340100004939 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 340100004940 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 340100004941 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 340100004942 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 340100004943 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 340100004944 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 340100004945 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 340100004946 N-terminal plug; other site 340100004947 ligand-binding site [chemical binding]; other site 340100004948 phosphoserine phosphatase SerB; Region: serB; TIGR00338 340100004949 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 340100004950 motif II; other site 340100004951 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 340100004952 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 340100004953 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 340100004954 ATP binding site [chemical binding]; other site 340100004955 putative Mg++ binding site [ion binding]; other site 340100004956 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 340100004957 nucleotide binding region [chemical binding]; other site 340100004958 ATP-binding site [chemical binding]; other site 340100004959 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 340100004960 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 340100004961 substrate binding site; other site 340100004962 dimer interface; other site 340100004963 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 340100004964 homotrimer interaction site [polypeptide binding]; other site 340100004965 zinc binding site [ion binding]; other site 340100004966 CDP-binding sites; other site 340100004967 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 340100004968 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 340100004969 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100004970 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 340100004971 dimer interface [polypeptide binding]; other site 340100004972 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340100004973 catalytic triad [active] 340100004974 peroxidatic and resolving cysteines [active] 340100004975 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 340100004976 dimerization interface [polypeptide binding]; other site 340100004977 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 340100004978 dimer interface [polypeptide binding]; other site 340100004979 phosphorylation site [posttranslational modification] 340100004980 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 340100004981 ATP binding site [chemical binding]; other site 340100004982 Mg2+ binding site [ion binding]; other site 340100004983 G-X-G motif; other site 340100004984 osmolarity response regulator; Provisional; Region: ompR; PRK09468 340100004985 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100004986 active site 340100004987 phosphorylation site [posttranslational modification] 340100004988 intermolecular recognition site; other site 340100004989 dimerization interface [polypeptide binding]; other site 340100004990 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 340100004991 DNA binding site [nucleotide binding] 340100004992 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 340100004993 Glycoprotease family; Region: Peptidase_M22; pfam00814 340100004994 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 340100004995 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100004996 Coenzyme A binding pocket [chemical binding]; other site 340100004997 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 340100004998 Fe-S cluster binding site [ion binding]; other site 340100004999 active site 340100005000 lysophospholipid transporter LplT; Provisional; Region: PRK11195 340100005001 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340100005002 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 340100005003 Walker A/P-loop; other site 340100005004 ATP binding site [chemical binding]; other site 340100005005 Q-loop/lid; other site 340100005006 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 340100005007 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 340100005008 ABC transporter signature motif; other site 340100005009 Walker B; other site 340100005010 D-loop; other site 340100005011 H-loop/switch region; other site 340100005012 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 340100005013 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 340100005014 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 340100005015 nucleotide binding pocket [chemical binding]; other site 340100005016 K-X-D-G motif; other site 340100005017 catalytic site [active] 340100005018 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 340100005019 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 340100005020 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 340100005021 Dimer interface [polypeptide binding]; other site 340100005022 BRCT sequence motif; other site 340100005023 SurA N-terminal domain; Region: SurA_N_3; cl07813 340100005024 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100005025 BolA-like protein; Region: BolA; pfam01722 340100005026 intracellular septation protein A; Reviewed; Region: PRK00259 340100005027 methionine sulfoxide reductase B; Provisional; Region: PRK00222 340100005028 SelR domain; Region: SelR; pfam01641 340100005029 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 340100005030 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 340100005031 Walker A/P-loop; other site 340100005032 ATP binding site [chemical binding]; other site 340100005033 Q-loop/lid; other site 340100005034 ABC transporter signature motif; other site 340100005035 Walker B; other site 340100005036 D-loop; other site 340100005037 H-loop/switch region; other site 340100005038 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 340100005039 BioY family; Region: BioY; pfam02632 340100005040 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100005041 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 340100005042 putative ligand binding site [chemical binding]; other site 340100005043 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 340100005044 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100005045 TM-ABC transporter signature motif; other site 340100005046 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 340100005047 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100005048 TM-ABC transporter signature motif; other site 340100005049 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100005050 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100005051 Walker A/P-loop; other site 340100005052 ATP binding site [chemical binding]; other site 340100005053 Q-loop/lid; other site 340100005054 ABC transporter signature motif; other site 340100005055 Walker B; other site 340100005056 D-loop; other site 340100005057 H-loop/switch region; other site 340100005058 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100005059 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100005060 Walker A/P-loop; other site 340100005061 ATP binding site [chemical binding]; other site 340100005062 Q-loop/lid; other site 340100005063 ABC transporter signature motif; other site 340100005064 Walker B; other site 340100005065 D-loop; other site 340100005066 H-loop/switch region; other site 340100005067 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 340100005068 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 340100005069 homodimer interface [polypeptide binding]; other site 340100005070 substrate-cofactor binding pocket; other site 340100005071 catalytic residue [active] 340100005072 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 340100005073 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 340100005074 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100005075 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 340100005076 TM-ABC transporter signature motif; other site 340100005077 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 340100005078 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100005079 TM-ABC transporter signature motif; other site 340100005080 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100005081 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 340100005082 putative ligand binding site [chemical binding]; other site 340100005083 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100005084 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100005085 Walker A/P-loop; other site 340100005086 ATP binding site [chemical binding]; other site 340100005087 Q-loop/lid; other site 340100005088 ABC transporter signature motif; other site 340100005089 Walker B; other site 340100005090 D-loop; other site 340100005091 H-loop/switch region; other site 340100005092 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100005093 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100005094 Walker A/P-loop; other site 340100005095 ATP binding site [chemical binding]; other site 340100005096 Q-loop/lid; other site 340100005097 ABC transporter signature motif; other site 340100005098 Walker B; other site 340100005099 D-loop; other site 340100005100 H-loop/switch region; other site 340100005101 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 340100005102 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100005103 minor groove reading motif; other site 340100005104 helix-hairpin-helix signature motif; other site 340100005105 substrate binding pocket [chemical binding]; other site 340100005106 active site 340100005107 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 340100005108 ferredoxin; Provisional; Region: PRK08764 340100005109 Putative Fe-S cluster; Region: FeS; cl17515 340100005110 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 340100005111 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 340100005112 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 340100005113 ferredoxin-NADP reductase; Provisional; Region: PRK10926 340100005114 FAD binding pocket [chemical binding]; other site 340100005115 FAD binding motif [chemical binding]; other site 340100005116 phosphate binding motif [ion binding]; other site 340100005117 beta-alpha-beta structure motif; other site 340100005118 NAD binding pocket [chemical binding]; other site 340100005119 Ferredoxin [Energy production and conversion]; Region: COG1146 340100005120 4Fe-4S binding domain; Region: Fer4; cl02805 340100005121 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 340100005122 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 340100005123 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 340100005124 active site 340100005125 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 340100005126 homotrimer interaction site [polypeptide binding]; other site 340100005127 putative active site [active] 340100005128 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 340100005129 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 340100005130 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100005131 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 340100005132 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 340100005133 HD domain; Region: HD_4; pfam13328 340100005134 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 340100005135 synthetase active site [active] 340100005136 NTP binding site [chemical binding]; other site 340100005137 metal binding site [ion binding]; metal-binding site 340100005138 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 340100005139 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 340100005140 acetylornithine deacetylase; Provisional; Region: PRK07522 340100005141 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 340100005142 metal binding site [ion binding]; metal-binding site 340100005143 putative dimer interface [polypeptide binding]; other site 340100005144 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 340100005145 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 340100005146 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005147 catalytic residue [active] 340100005148 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 340100005149 substrate binding site [chemical binding]; other site 340100005150 active site 340100005151 catalytic residues [active] 340100005152 heterodimer interface [polypeptide binding]; other site 340100005153 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 340100005154 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 340100005155 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 340100005156 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 340100005157 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 340100005158 active site 340100005159 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 340100005160 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 340100005161 homodimer interface [polypeptide binding]; other site 340100005162 oligonucleotide binding site [chemical binding]; other site 340100005163 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 340100005164 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 340100005165 RNA binding surface [nucleotide binding]; other site 340100005166 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 340100005167 active site 340100005168 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 340100005169 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 340100005170 motif II; other site 340100005171 TMAO/DMSO reductase; Reviewed; Region: PRK05363 340100005172 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 340100005173 Moco binding site; other site 340100005174 metal coordination site [ion binding]; other site 340100005175 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 340100005176 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 340100005177 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 340100005178 amidase catalytic site [active] 340100005179 Zn binding residues [ion binding]; other site 340100005180 substrate binding site [chemical binding]; other site 340100005181 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 340100005182 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 340100005183 putative SAM binding site [chemical binding]; other site 340100005184 homodimer interface [polypeptide binding]; other site 340100005185 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 340100005186 active site 340100005187 dimer interface [polypeptide binding]; other site 340100005188 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 340100005189 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 340100005190 putative phosphate acyltransferase; Provisional; Region: PRK05331 340100005191 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 340100005192 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 340100005193 dimer interface [polypeptide binding]; other site 340100005194 active site 340100005195 CoA binding pocket [chemical binding]; other site 340100005196 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 340100005197 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 340100005198 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100005199 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340100005200 NAD(P) binding site [chemical binding]; other site 340100005201 homotetramer interface [polypeptide binding]; other site 340100005202 homodimer interface [polypeptide binding]; other site 340100005203 active site 340100005204 acyl carrier protein; Provisional; Region: acpP; PRK00982 340100005205 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 340100005206 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 340100005207 dimer interface [polypeptide binding]; other site 340100005208 active site 340100005209 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 340100005210 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100005211 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 340100005212 DNA binding residues [nucleotide binding] 340100005213 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 340100005214 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 340100005215 anti-sigma E factor; Provisional; Region: rseB; PRK09455 340100005216 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 340100005217 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 340100005218 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 340100005219 protein binding site [polypeptide binding]; other site 340100005220 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 340100005221 protein binding site [polypeptide binding]; other site 340100005222 GTP-binding protein LepA; Provisional; Region: PRK05433 340100005223 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 340100005224 G1 box; other site 340100005225 putative GEF interaction site [polypeptide binding]; other site 340100005226 GTP/Mg2+ binding site [chemical binding]; other site 340100005227 Switch I region; other site 340100005228 G2 box; other site 340100005229 G3 box; other site 340100005230 Switch II region; other site 340100005231 G4 box; other site 340100005232 G5 box; other site 340100005233 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 340100005234 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 340100005235 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 340100005236 signal peptidase I; Provisional; Region: PRK10861 340100005237 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 340100005238 Catalytic site [active] 340100005239 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 340100005240 ribonuclease III; Reviewed; Region: rnc; PRK00102 340100005241 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 340100005242 dimerization interface [polypeptide binding]; other site 340100005243 active site 340100005244 metal binding site [ion binding]; metal-binding site 340100005245 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 340100005246 GTPase Era; Reviewed; Region: era; PRK00089 340100005247 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 340100005248 G1 box; other site 340100005249 GTP/Mg2+ binding site [chemical binding]; other site 340100005250 Switch I region; other site 340100005251 G2 box; other site 340100005252 Switch II region; other site 340100005253 G3 box; other site 340100005254 G4 box; other site 340100005255 G5 box; other site 340100005256 KH domain; Region: KH_2; pfam07650 340100005257 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 340100005258 Recombination protein O N terminal; Region: RecO_N; pfam11967 340100005259 Recombination protein O C terminal; Region: RecO_C; pfam02565 340100005260 Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins; Region: PliI_like; cd09632 340100005261 dimer interface [polypeptide binding]; other site 340100005262 putative inhibitory loop; other site 340100005263 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 340100005264 YccA-like proteins; Region: YccA_like; cd10433 340100005265 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 340100005266 multifunctional aminopeptidase A; Provisional; Region: PRK00913 340100005267 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 340100005268 interface (dimer of trimers) [polypeptide binding]; other site 340100005269 Substrate-binding/catalytic site; other site 340100005270 Zn-binding sites [ion binding]; other site 340100005271 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 340100005272 Predicted permeases [General function prediction only]; Region: COG0795 340100005273 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100005274 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100005275 The 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 340100005276 dimerization interface [polypeptide binding]; other site 340100005277 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100005278 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 340100005279 putative ligand binding site [chemical binding]; other site 340100005280 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 340100005281 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 340100005282 tetrameric interface [polypeptide binding]; other site 340100005283 NAD binding site [chemical binding]; other site 340100005284 catalytic residues [active] 340100005285 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 340100005286 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100005287 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 340100005288 substrate binding site [chemical binding]; other site 340100005289 dimerization interface [polypeptide binding]; other site 340100005290 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 340100005291 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 340100005292 NlpC/P60 family; Region: NLPC_P60; pfam00877 340100005293 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 340100005294 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 340100005295 acyl-activating enzyme (AAE) consensus motif; other site 340100005296 putative AMP binding site [chemical binding]; other site 340100005297 putative active site [active] 340100005298 putative CoA binding site [chemical binding]; other site 340100005299 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 340100005300 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 340100005301 acetyl-CoA synthetase; Provisional; Region: PRK00174 340100005302 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 340100005303 active site 340100005304 CoA binding site [chemical binding]; other site 340100005305 acyl-activating enzyme (AAE) consensus motif; other site 340100005306 AMP binding site [chemical binding]; other site 340100005307 acetate binding site [chemical binding]; other site 340100005308 EamA-like transporter family; Region: EamA; pfam00892 340100005309 EamA-like transporter family; Region: EamA; pfam00892 340100005310 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 340100005311 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 340100005312 tetramer interface [polypeptide binding]; other site 340100005313 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005314 catalytic residue [active] 340100005315 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100005316 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340100005317 NAD(P) binding site [chemical binding]; other site 340100005318 active site 340100005319 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 340100005320 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 340100005321 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 340100005322 active site 340100005323 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 340100005324 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100005325 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 340100005326 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 340100005327 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 340100005328 putative active site [active] 340100005329 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 340100005330 active site 340100005331 dimer interface [polypeptide binding]; other site 340100005332 catalytic nucleophile [active] 340100005333 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 340100005334 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100005335 Walker A/P-loop; other site 340100005336 ATP binding site [chemical binding]; other site 340100005337 Q-loop/lid; other site 340100005338 ABC transporter signature motif; other site 340100005339 Walker B; other site 340100005340 D-loop; other site 340100005341 H-loop/switch region; other site 340100005342 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100005343 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100005344 Walker A/P-loop; other site 340100005345 ATP binding site [chemical binding]; other site 340100005346 Q-loop/lid; other site 340100005347 ABC transporter signature motif; other site 340100005348 Walker B; other site 340100005349 D-loop; other site 340100005350 H-loop/switch region; other site 340100005351 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 340100005352 glutathione ABC transporter substrate-binding protein GsiB; Provisional; Region: PRK15413 340100005353 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 340100005354 glutathione ABC transporter permease GsiC; Provisional; Region: PRK15081 340100005355 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 340100005356 dimer interface [polypeptide binding]; other site 340100005357 conserved gate region; other site 340100005358 putative PBP binding loops; other site 340100005359 ABC-ATPase subunit interface; other site 340100005360 glutathione ABC transporter permease GsiD; Provisional; Region: PRK15082 340100005361 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340100005362 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 340100005363 dimer interface [polypeptide binding]; other site 340100005364 conserved gate region; other site 340100005365 putative PBP binding loops; other site 340100005366 ABC-ATPase subunit interface; other site 340100005367 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 340100005368 homodimer interface [polypeptide binding]; other site 340100005369 homotetramer interface [polypeptide binding]; other site 340100005370 active site pocket [active] 340100005371 cleavage site 340100005372 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA_1; cd08663 340100005373 SxDxEG motif; other site 340100005374 active site 340100005375 metal binding site [ion binding]; metal-binding site 340100005376 homopentamer interface [polypeptide binding]; other site 340100005377 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 340100005378 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 340100005379 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 340100005380 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 340100005381 active site 340100005382 CTP synthetase; Validated; Region: pyrG; PRK05380 340100005383 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 340100005384 Catalytic site [active] 340100005385 active site 340100005386 UTP binding site [chemical binding]; other site 340100005387 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 340100005388 active site 340100005389 putative oxyanion hole; other site 340100005390 catalytic triad [active] 340100005391 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 340100005392 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340100005393 enolase; Provisional; Region: eno; PRK00077 340100005394 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 340100005395 dimer interface [polypeptide binding]; other site 340100005396 metal binding site [ion binding]; metal-binding site 340100005397 substrate binding pocket [chemical binding]; other site 340100005398 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 340100005399 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 340100005400 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 340100005401 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 340100005402 dimerization interface [polypeptide binding]; other site 340100005403 domain crossover interface; other site 340100005404 redox-dependent activation switch; other site 340100005405 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 340100005406 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 340100005407 trimer interface [polypeptide binding]; other site 340100005408 putative metal binding site [ion binding]; other site 340100005409 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 340100005410 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS); Region: MACS_like_3; cd05971 340100005411 active site 340100005412 acyl-activating enzyme (AAE) consensus motif; other site 340100005413 putative CoA binding site [chemical binding]; other site 340100005414 AMP binding site [chemical binding]; other site 340100005415 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340100005416 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 340100005417 putative active site [active] 340100005418 putative metal binding site [ion binding]; other site 340100005419 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 340100005420 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 340100005421 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 340100005422 S-adenosylmethionine binding site [chemical binding]; other site 340100005423 Predicted membrane protein [Function unknown]; Region: COG1981 340100005424 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 340100005425 2-methylcitrate dehydratase; Region: prpD; TIGR02330 340100005426 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100005427 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100005428 DNA-binding site [nucleotide binding]; DNA binding site 340100005429 FCD domain; Region: FCD; pfam07729 340100005430 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 340100005431 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 340100005432 substrate binding site [chemical binding]; other site 340100005433 ligand binding site [chemical binding]; other site 340100005434 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 340100005435 substrate binding site [chemical binding]; other site 340100005436 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 340100005437 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 340100005438 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 340100005439 dimer interface [polypeptide binding]; other site 340100005440 active site 340100005441 citrylCoA binding site [chemical binding]; other site 340100005442 oxalacetate/citrate binding site [chemical binding]; other site 340100005443 coenzyme A binding site [chemical binding]; other site 340100005444 catalytic triad [active] 340100005445 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 340100005446 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 340100005447 tetramer interface [polypeptide binding]; other site 340100005448 active site 340100005449 Mg2+/Mn2+ binding site [ion binding]; other site 340100005450 malate dehydrogenase; Provisional; Region: PRK05442 340100005451 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 340100005452 NAD(P) binding site [chemical binding]; other site 340100005453 dimer interface [polypeptide binding]; other site 340100005454 malate binding site [chemical binding]; other site 340100005455 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100005456 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100005457 DNA-binding site [nucleotide binding]; DNA binding site 340100005458 UTRA domain; Region: UTRA; pfam07702 340100005459 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 340100005460 Iron-sulfur protein interface; other site 340100005461 proximal quinone binding site [chemical binding]; other site 340100005462 SdhD (CybS) interface [polypeptide binding]; other site 340100005463 proximal heme binding site [chemical binding]; other site 340100005464 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 340100005465 SdhC subunit interface [polypeptide binding]; other site 340100005466 proximal heme binding site [chemical binding]; other site 340100005467 cardiolipin binding site; other site 340100005468 Iron-sulfur protein interface; other site 340100005469 proximal quinone binding site [chemical binding]; other site 340100005470 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 340100005471 L-aspartate oxidase; Provisional; Region: PRK06175 340100005472 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340100005473 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 340100005474 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 340100005475 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 340100005476 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 340100005477 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 340100005478 dimer interface [polypeptide binding]; other site 340100005479 active site 340100005480 citrylCoA binding site [chemical binding]; other site 340100005481 NADH binding [chemical binding]; other site 340100005482 cationic pore residues; other site 340100005483 oxalacetate/citrate binding site [chemical binding]; other site 340100005484 coenzyme A binding site [chemical binding]; other site 340100005485 catalytic triad [active] 340100005486 Predicted membrane protein (DUF2214); Region: DUF2214; pfam09980 340100005487 proline/glycine betaine transporter; Provisional; Region: PRK10642 340100005488 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 340100005489 putative substrate translocation pore; other site 340100005490 Osmosensory transporter coiled coil; Region: Osmo_CC; pfam08946 340100005491 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 340100005492 Malic enzyme, N-terminal domain; Region: malic; pfam00390 340100005493 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 340100005494 putative NAD(P) binding site [chemical binding]; other site 340100005495 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 340100005496 2-oxoacid dehydrogenase subunit E1; Provisional; Region: PRK13012 340100005497 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 340100005498 dimer interface [polypeptide binding]; other site 340100005499 TPP-binding site [chemical binding]; other site 340100005500 Transketolase, pyrimidine binding domain; Region: Transket_pyr; smart00861 340100005501 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100005502 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 340100005503 putative DNA binding site [nucleotide binding]; other site 340100005504 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100005505 dimerization interface [polypeptide binding]; other site 340100005506 putative Zn2+ binding site [ion binding]; other site 340100005507 AsnC family; Region: AsnC_trans_reg; pfam01037 340100005508 Predicted membrane protein [Function unknown]; Region: COG1297 340100005509 putative oligopeptide transporter, OPT family; Region: TIGR00733 340100005510 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 340100005511 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 340100005512 TPP-binding site [chemical binding]; other site 340100005513 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 340100005514 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 340100005515 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 340100005516 E3 interaction surface; other site 340100005517 lipoyl attachment site [posttranslational modification]; other site 340100005518 e3 binding domain; Region: E3_binding; pfam02817 340100005519 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 340100005520 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 340100005521 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100005522 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100005523 Predicted ATPase [General function prediction only]; Region: COG1485 340100005524 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 340100005525 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 340100005526 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 340100005527 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 340100005528 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 340100005529 active site 340100005530 HIGH motif; other site 340100005531 dimer interface [polypeptide binding]; other site 340100005532 KMSKS motif; other site 340100005533 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100005534 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 340100005535 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 340100005536 putative Zn2+ binding site [ion binding]; other site 340100005537 putative DNA binding site [nucleotide binding]; other site 340100005538 BON domain; Region: BON; cl02771 340100005539 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 340100005540 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 340100005541 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 340100005542 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 340100005543 RNA binding site [nucleotide binding]; other site 340100005544 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 340100005545 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 340100005546 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 340100005547 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 340100005548 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 340100005549 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 340100005550 RNA binding surface [nucleotide binding]; other site 340100005551 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 340100005552 active site 340100005553 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 340100005554 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 340100005555 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 340100005556 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 340100005557 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 340100005558 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340100005559 NAD(P) binding site [chemical binding]; other site 340100005560 homotetramer interface [polypeptide binding]; other site 340100005561 homodimer interface [polypeptide binding]; other site 340100005562 active site 340100005563 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 340100005564 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 340100005565 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 340100005566 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 340100005567 Fe2+ transport protein; Region: Iron_transport; pfam10634 340100005568 Plastocyanin [Energy production and conversion]; Region: PetE; COG3794 340100005569 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 340100005570 Iron permease FTR1 family; Region: FTR1; cl00475 340100005571 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 340100005572 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100005573 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 340100005574 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 340100005575 CsbD-like; Region: CsbD; cl17424 340100005576 cyanophycin synthetase; Provisional; Region: PRK14016 340100005577 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 340100005578 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100005579 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100005580 cyanophycin synthetase; Provisional; Region: PRK14016 340100005581 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 340100005582 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100005583 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 340100005584 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100005585 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 340100005586 Walker A/P-loop; other site 340100005587 ATP binding site [chemical binding]; other site 340100005588 Q-loop/lid; other site 340100005589 ABC transporter signature motif; other site 340100005590 Walker B; other site 340100005591 D-loop; other site 340100005592 H-loop/switch region; other site 340100005593 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 340100005594 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 340100005595 Protein of unknown function, DUF482; Region: DUF482; pfam04339 340100005596 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 340100005597 dinuclear metal binding motif [ion binding]; other site 340100005598 Transglycosylase SLT domain; Region: SLT_2; pfam13406 340100005599 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100005600 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100005601 catalytic residue [active] 340100005602 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 340100005603 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 340100005604 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 340100005605 putative active site [active] 340100005606 metal binding site [ion binding]; metal-binding site 340100005607 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100005608 LysR family transcriptional regulator; Provisional; Region: PRK14997 340100005609 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 340100005610 putative effector binding pocket; other site 340100005611 dimerization interface [polypeptide binding]; other site 340100005612 glutamate carboxypeptidase; Reviewed; Region: PRK06133 340100005613 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 340100005614 metal binding site [ion binding]; metal-binding site 340100005615 dimer interface [polypeptide binding]; other site 340100005616 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100005617 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100005618 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 340100005619 putative dimerization interface [polypeptide binding]; other site 340100005620 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100005621 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 340100005622 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100005623 Coenzyme A binding pocket [chemical binding]; other site 340100005624 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100005625 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 340100005626 methionine sulfoxide reductase A; Provisional; Region: PRK14054 340100005627 methionine sulfoxide reductase B; Provisional; Region: PRK00222 340100005628 SelR domain; Region: SelR; pfam01641 340100005629 Protein of unknown function, DUF417; Region: DUF417; cl01162 340100005630 MarR family; Region: MarR_2; pfam12802 340100005631 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100005632 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 340100005633 putative substrate translocation pore; other site 340100005634 phosphoglycolate phosphatase; Provisional; Region: PRK13222 340100005635 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 340100005636 motif II; other site 340100005637 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 340100005638 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 340100005639 S-adenosylmethionine binding site [chemical binding]; other site 340100005640 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 340100005641 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100005642 ligand binding site [chemical binding]; other site 340100005643 DNA gyrase subunit A; Validated; Region: PRK05560 340100005644 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 340100005645 CAP-like domain; other site 340100005646 active site 340100005647 primary dimer interface [polypeptide binding]; other site 340100005648 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005649 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005650 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005651 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005652 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005653 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340100005654 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 340100005655 homodimer interface [polypeptide binding]; other site 340100005656 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 340100005657 substrate-cofactor binding pocket; other site 340100005658 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005659 catalytic residue [active] 340100005660 Chorismate mutase type II; Region: CM_2; cl00693 340100005661 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 340100005662 Prephenate dehydratase; Region: PDT; pfam00800 340100005663 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 340100005664 putative L-Phe binding site [chemical binding]; other site 340100005665 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 340100005666 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 340100005667 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005668 homodimer interface [polypeptide binding]; other site 340100005669 catalytic residue [active] 340100005670 prephenate dehydrogenase; Validated; Region: PRK08507 340100005671 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 340100005672 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 340100005673 hinge; other site 340100005674 active site 340100005675 cytidylate kinase; Provisional; Region: cmk; PRK00023 340100005676 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 340100005677 CMP-binding site; other site 340100005678 The sites determining sugar specificity; other site 340100005679 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 340100005680 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 340100005681 RNA binding site [nucleotide binding]; other site 340100005682 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 340100005683 RNA binding site [nucleotide binding]; other site 340100005684 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 340100005685 RNA binding site [nucleotide binding]; other site 340100005686 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 340100005687 RNA binding site [nucleotide binding]; other site 340100005688 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 340100005689 RNA binding site [nucleotide binding]; other site 340100005690 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 340100005691 RNA binding site [nucleotide binding]; other site 340100005692 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 340100005693 IHF dimer interface [polypeptide binding]; other site 340100005694 IHF - DNA interface [nucleotide binding]; other site 340100005695 tetratricopeptide repeat protein; Provisional; Region: PRK11788 340100005696 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 340100005697 binding surface 340100005698 TPR motif; other site 340100005699 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100005700 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 340100005701 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 340100005702 putative ribose interaction site [chemical binding]; other site 340100005703 putative ADP binding site [chemical binding]; other site 340100005704 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 340100005705 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 340100005706 NADP binding site [chemical binding]; other site 340100005707 homopentamer interface [polypeptide binding]; other site 340100005708 substrate binding site [chemical binding]; other site 340100005709 active site 340100005710 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 340100005711 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 340100005712 cysteine synthase B; Region: cysM; TIGR01138 340100005713 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 340100005714 dimer interface [polypeptide binding]; other site 340100005715 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100005716 catalytic residue [active] 340100005717 Transglycosylase SLT domain; Region: SLT_2; pfam13406 340100005718 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100005719 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100005720 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 340100005721 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 340100005722 putative active site [active] 340100005723 Zn binding site [ion binding]; other site 340100005724 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 340100005725 Ligand binding site [chemical binding]; other site 340100005726 Electron transfer flavoprotein domain; Region: ETF; pfam01012 340100005727 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 340100005728 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 340100005729 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 340100005730 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 340100005731 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 340100005732 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005733 active site 340100005734 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 340100005735 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100005736 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 340100005737 dimer interface [polypeptide binding]; other site 340100005738 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340100005739 catalytic triad [active] 340100005740 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100005741 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 340100005742 membrane-bound complex binding site; other site 340100005743 hinge residues; other site 340100005744 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100005745 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 340100005746 dimer interface [polypeptide binding]; other site 340100005747 conserved gate region; other site 340100005748 putative PBP binding loops; other site 340100005749 ABC-ATPase subunit interface; other site 340100005750 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100005751 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 340100005752 dimer interface [polypeptide binding]; other site 340100005753 conserved gate region; other site 340100005754 putative PBP binding loops; other site 340100005755 ABC-ATPase subunit interface; other site 340100005756 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 340100005757 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 340100005758 Walker A/P-loop; other site 340100005759 ATP binding site [chemical binding]; other site 340100005760 Q-loop/lid; other site 340100005761 ABC transporter signature motif; other site 340100005762 Walker B; other site 340100005763 D-loop; other site 340100005764 H-loop/switch region; other site 340100005765 TOBE-like domain; Region: TOBE_3; pfam12857 340100005766 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 340100005767 Active Sites [active] 340100005768 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 340100005769 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 340100005770 Active Sites [active] 340100005771 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 340100005772 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 340100005773 CysD dimerization site [polypeptide binding]; other site 340100005774 G1 box; other site 340100005775 putative GEF interaction site [polypeptide binding]; other site 340100005776 GTP/Mg2+ binding site [chemical binding]; other site 340100005777 Switch I region; other site 340100005778 G2 box; other site 340100005779 G3 box; other site 340100005780 Switch II region; other site 340100005781 G4 box; other site 340100005782 G5 box; other site 340100005783 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 340100005784 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 340100005785 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 340100005786 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 340100005787 FeS/SAM binding site; other site 340100005788 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 340100005789 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340100005790 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 340100005791 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 340100005792 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100005793 Transposase; Region: HTH_Tnp_1; pfam01527 340100005794 putative transposase OrfB; Reviewed; Region: PHA02517 340100005795 HTH-like domain; Region: HTH_21; pfam13276 340100005796 Integrase core domain; Region: rve; pfam00665 340100005797 Integrase core domain; Region: rve_3; pfam13683 340100005798 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 340100005799 GTPase RsgA; Reviewed; Region: PRK00098 340100005800 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 340100005801 RNA binding site [nucleotide binding]; other site 340100005802 homodimer interface [polypeptide binding]; other site 340100005803 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 340100005804 GTPase/Zn-binding domain interface [polypeptide binding]; other site 340100005805 GTP/Mg2+ binding site [chemical binding]; other site 340100005806 G4 box; other site 340100005807 G5 box; other site 340100005808 G1 box; other site 340100005809 Switch I region; other site 340100005810 G2 box; other site 340100005811 G3 box; other site 340100005812 Switch II region; other site 340100005813 Peptidase family M48; Region: Peptidase_M48; pfam01435 340100005814 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 340100005815 catalytic site [active] 340100005816 putative active site [active] 340100005817 putative substrate binding site [chemical binding]; other site 340100005818 dimer interface [polypeptide binding]; other site 340100005819 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 340100005820 PaaX-like protein; Region: PaaX; pfam07848 340100005821 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 340100005822 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 340100005823 phenylacetate-CoA oxygenase subunit PaaA; Provisional; Region: paaA; PRK13778 340100005824 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 340100005825 phenylacetate-CoA oxygenase subunit PaaB; Provisional; Region: paaB; PRK13781 340100005826 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; pfam05138 340100005827 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 340100005828 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 340100005829 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 340100005830 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 340100005831 FAD binding pocket [chemical binding]; other site 340100005832 FAD binding motif [chemical binding]; other site 340100005833 phosphate binding motif [ion binding]; other site 340100005834 beta-alpha-beta structure motif; other site 340100005835 NAD(p) ribose binding residues [chemical binding]; other site 340100005836 NAD binding pocket [chemical binding]; other site 340100005837 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 340100005838 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 340100005839 catalytic loop [active] 340100005840 iron binding site [ion binding]; other site 340100005841 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 340100005842 NAD(P) binding site [chemical binding]; other site 340100005843 catalytic residues [active] 340100005844 putative transposase OrfB; Reviewed; Region: PHA02517 340100005845 HTH-like domain; Region: HTH_21; pfam13276 340100005846 Integrase core domain; Region: rve; pfam00665 340100005847 Integrase core domain; Region: rve_3; pfam13683 340100005848 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100005849 Transposase; Region: HTH_Tnp_1; pfam01527 340100005850 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 340100005851 enoyl-CoA hydratase; Provisional; Region: PRK08140 340100005852 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 340100005853 substrate binding site [chemical binding]; other site 340100005854 oxyanion hole (OAH) forming residues; other site 340100005855 trimer interface [polypeptide binding]; other site 340100005856 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 340100005857 CoenzymeA binding site [chemical binding]; other site 340100005858 subunit interaction site [polypeptide binding]; other site 340100005859 PHB binding site; other site 340100005860 Phenylacetate-CoA ligase (also known as PaaK); Region: PaaK; cd05913 340100005861 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 340100005862 active site 340100005863 AMP binding site [chemical binding]; other site 340100005864 homodimer interface [polypeptide binding]; other site 340100005865 acyl-activating enzyme (AAE) consensus motif; other site 340100005866 CoA binding site [chemical binding]; other site 340100005867 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100005868 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005869 active site 340100005870 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100005871 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005872 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100005873 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100005874 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100005875 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100005876 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100005877 DctM-like transporters; Region: DctM; pfam06808 340100005878 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100005879 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100005880 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100005881 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 340100005882 FtsX-like permease family; Region: FtsX; pfam02687 340100005883 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 340100005884 apolar tunnel; other site 340100005885 heme binding site [chemical binding]; other site 340100005886 dimerization interface [polypeptide binding]; other site 340100005887 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 340100005888 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 340100005889 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 340100005890 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 340100005891 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 340100005892 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100005893 Walker A/P-loop; other site 340100005894 ATP binding site [chemical binding]; other site 340100005895 Q-loop/lid; other site 340100005896 ABC transporter signature motif; other site 340100005897 Walker B; other site 340100005898 D-loop; other site 340100005899 H-loop/switch region; other site 340100005900 TOBE domain; Region: TOBE_2; pfam08402 340100005901 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 340100005902 dimer interface [polypeptide binding]; other site 340100005903 conserved gate region; other site 340100005904 putative PBP binding loops; other site 340100005905 ABC-ATPase subunit interface; other site 340100005906 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 340100005907 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 340100005908 dimer interface [polypeptide binding]; other site 340100005909 conserved gate region; other site 340100005910 putative PBP binding loops; other site 340100005911 ABC-ATPase subunit interface; other site 340100005912 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 340100005913 ArsC family; Region: ArsC; pfam03960 340100005914 putative catalytic residues [active] 340100005915 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 340100005916 active site 340100005917 DNA binding site [nucleotide binding] 340100005918 PhoP regulatory network protein YrbL; Region: YrbL-PhoP_reg; pfam10707 340100005919 RmuC family; Region: RmuC; pfam02646 340100005920 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100005921 active site 340100005922 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 340100005923 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100005924 active site 340100005925 dimer interface [polypeptide binding]; other site 340100005926 transcriptional regulator PhoU; Provisional; Region: PRK11115 340100005927 PhoU domain; Region: PhoU; pfam01895 340100005928 PhoU domain; Region: PhoU; pfam01895 340100005929 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 340100005930 putative active site [active] 340100005931 putative catalytic site [active] 340100005932 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100005933 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100005934 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100005935 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100005936 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100005937 The 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 340100005938 dimerization interface [polypeptide binding]; other site 340100005939 oxidative damage protection protein; Provisional; Region: PRK05408 340100005940 N-acetylglutamate synthase; Validated; Region: PRK05279 340100005941 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 340100005942 putative feedback inhibition sensing region; other site 340100005943 putative nucleotide binding site [chemical binding]; other site 340100005944 putative substrate binding site [chemical binding]; other site 340100005945 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100005946 Coenzyme A binding pocket [chemical binding]; other site 340100005947 short chain dehydrogenase; Provisional; Region: PRK08339 340100005948 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 340100005949 putative NAD(P) binding site [chemical binding]; other site 340100005950 putative active site [active] 340100005951 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 340100005952 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 340100005953 ATP binding site [chemical binding]; other site 340100005954 putative Mg++ binding site [ion binding]; other site 340100005955 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 340100005956 nucleotide binding region [chemical binding]; other site 340100005957 ATP-binding site [chemical binding]; other site 340100005958 Helicase associated domain (HA2); Region: HA2; pfam04408 340100005959 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 340100005960 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 340100005961 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 340100005962 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 340100005963 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 340100005964 metal binding triad; other site 340100005965 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 340100005966 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 340100005967 metal binding triad; other site 340100005968 TIGR02099 family protein; Region: TIGR02099 340100005969 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 340100005970 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100005971 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340100005972 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 340100005973 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100005974 transcription termination factor Rho; Provisional; Region: rho; PRK09376 340100005975 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 340100005976 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 340100005977 RNA binding site [nucleotide binding]; other site 340100005978 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 340100005979 multimer interface [polypeptide binding]; other site 340100005980 Walker A motif; other site 340100005981 ATP binding site [chemical binding]; other site 340100005982 Walker B motif; other site 340100005983 thioredoxin 2; Provisional; Region: PRK10996 340100005984 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 340100005985 catalytic residues [active] 340100005986 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 340100005987 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 340100005988 ATP binding site [chemical binding]; other site 340100005989 Mg2+ binding site [ion binding]; other site 340100005990 G-X-G motif; other site 340100005991 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 340100005992 anchoring element; other site 340100005993 dimer interface [polypeptide binding]; other site 340100005994 ATP binding site [chemical binding]; other site 340100005995 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 340100005996 active site 340100005997 metal binding site [ion binding]; metal-binding site 340100005998 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 340100005999 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 340100006000 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 340100006001 CAP-like domain; other site 340100006002 active site 340100006003 primary dimer interface [polypeptide binding]; other site 340100006004 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 340100006005 DctM-like transporters; Region: DctM; pfam06808 340100006006 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100006007 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 340100006008 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 340100006009 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 340100006010 hypothetical protein; Provisional; Region: PRK07483 340100006011 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 340100006012 inhibitor-cofactor binding pocket; inhibition site 340100006013 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006014 catalytic residue [active] 340100006015 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 340100006016 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 340100006017 putative active site [active] 340100006018 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100006019 MarR family; Region: MarR; pfam01047 340100006020 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 340100006021 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100006022 Coenzyme A binding pocket [chemical binding]; other site 340100006023 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 340100006024 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 340100006025 inhibitor-cofactor binding pocket; inhibition site 340100006026 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006027 catalytic residue [active] 340100006028 Ectoine synthase; Region: Ectoine_synth; pfam06339 340100006029 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 340100006030 2-keto-3-deoxygluconate permease; Provisional; Region: PRK05274 340100006031 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3395 340100006032 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 340100006033 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 340100006034 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100006035 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100006036 DNA-binding site [nucleotide binding]; DNA binding site 340100006037 UTRA domain; Region: UTRA; pfam07702 340100006038 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 340100006039 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 340100006040 MOSC domain; Region: MOSC; pfam03473 340100006041 multidrug efflux system protein; Provisional; Region: PRK11431 340100006042 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 340100006043 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 340100006044 catalytic loop [active] 340100006045 iron binding site [ion binding]; other site 340100006046 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 340100006047 FAD binding pocket [chemical binding]; other site 340100006048 FAD binding motif [chemical binding]; other site 340100006049 phosphate binding motif [ion binding]; other site 340100006050 beta-alpha-beta structure motif; other site 340100006051 NAD binding pocket [chemical binding]; other site 340100006052 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100006053 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100006054 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 340100006055 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 340100006056 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100006057 VirB7 interaction site; other site 340100006058 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 340100006059 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 340100006060 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100006061 Type II/IV secretion system protein; Region: T2SE; pfam00437 340100006062 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100006063 Walker A motif; other site 340100006064 ATP binding site [chemical binding]; other site 340100006065 Walker B motif; other site 340100006066 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 340100006067 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 340100006068 motif 1; other site 340100006069 active site 340100006070 motif 2; other site 340100006071 motif 3; other site 340100006072 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 340100006073 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 340100006074 CPxP motif; other site 340100006075 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 340100006076 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 340100006077 RimM N-terminal domain; Region: RimM; pfam01782 340100006078 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 340100006079 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 340100006080 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 340100006081 non-specific DNA binding site [nucleotide binding]; other site 340100006082 salt bridge; other site 340100006083 sequence-specific DNA binding site [nucleotide binding]; other site 340100006084 Cupin domain; Region: Cupin_2; pfam07883 340100006085 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 340100006086 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100006087 substrate binding pocket [chemical binding]; other site 340100006088 membrane-bound complex binding site; other site 340100006089 hinge residues; other site 340100006090 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100006091 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 340100006092 dimer interface [polypeptide binding]; other site 340100006093 conserved gate region; other site 340100006094 putative PBP binding loops; other site 340100006095 ABC-ATPase subunit interface; other site 340100006096 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100006097 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100006098 Walker A/P-loop; other site 340100006099 ATP binding site [chemical binding]; other site 340100006100 Q-loop/lid; other site 340100006101 ABC transporter signature motif; other site 340100006102 Walker B; other site 340100006103 D-loop; other site 340100006104 H-loop/switch region; other site 340100006105 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 340100006106 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 340100006107 sensor protein QseC; Provisional; Region: PRK10337 340100006108 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 340100006109 dimer interface [polypeptide binding]; other site 340100006110 phosphorylation site [posttranslational modification] 340100006111 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 340100006112 ATP binding site [chemical binding]; other site 340100006113 Mg2+ binding site [ion binding]; other site 340100006114 G-X-G motif; other site 340100006115 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100006116 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100006117 active site 340100006118 phosphorylation site [posttranslational modification] 340100006119 intermolecular recognition site; other site 340100006120 dimerization interface [polypeptide binding]; other site 340100006121 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 340100006122 DNA binding site [nucleotide binding] 340100006123 MltA-interacting protein MipA; Region: MipA; cl01504 340100006124 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 340100006125 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100006126 active site 340100006127 HIGH motif; other site 340100006128 nucleotide binding site [chemical binding]; other site 340100006129 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340100006130 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 340100006131 active site 340100006132 KMSKS motif; other site 340100006133 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 340100006134 tRNA binding surface [nucleotide binding]; other site 340100006135 anticodon binding site; other site 340100006136 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 340100006137 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 340100006138 active site 340100006139 multimer interface [polypeptide binding]; other site 340100006140 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 340100006141 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 340100006142 FeS/SAM binding site; other site 340100006143 Helix-turn-helix domain; Region: HTH_25; pfam13413 340100006144 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 340100006145 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 340100006146 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 340100006147 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 340100006148 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 340100006149 dimer interface [polypeptide binding]; other site 340100006150 motif 1; other site 340100006151 active site 340100006152 motif 2; other site 340100006153 motif 3; other site 340100006154 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 340100006155 anticodon binding site; other site 340100006156 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 340100006157 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 340100006158 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 340100006159 Trp docking motif [polypeptide binding]; other site 340100006160 active site 340100006161 GTP-binding protein Der; Reviewed; Region: PRK00093 340100006162 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 340100006163 G1 box; other site 340100006164 GTP/Mg2+ binding site [chemical binding]; other site 340100006165 Switch I region; other site 340100006166 G2 box; other site 340100006167 Switch II region; other site 340100006168 G3 box; other site 340100006169 G4 box; other site 340100006170 G5 box; other site 340100006171 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 340100006172 G1 box; other site 340100006173 GTP/Mg2+ binding site [chemical binding]; other site 340100006174 Switch I region; other site 340100006175 G2 box; other site 340100006176 G3 box; other site 340100006177 Switch II region; other site 340100006178 G4 box; other site 340100006179 G5 box; other site 340100006180 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 340100006181 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 340100006182 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006183 homodimer interface [polypeptide binding]; other site 340100006184 catalytic residue [active] 340100006185 bacterial Hfq-like; Region: Hfq; cd01716 340100006186 hexamer interface [polypeptide binding]; other site 340100006187 Sm1 motif; other site 340100006188 RNA binding site [nucleotide binding]; other site 340100006189 Sm2 motif; other site 340100006190 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 340100006191 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 340100006192 HflX GTPase family; Region: HflX; cd01878 340100006193 G1 box; other site 340100006194 GTP/Mg2+ binding site [chemical binding]; other site 340100006195 Switch I region; other site 340100006196 G2 box; other site 340100006197 G3 box; other site 340100006198 Switch II region; other site 340100006199 G4 box; other site 340100006200 G5 box; other site 340100006201 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 340100006202 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 340100006203 HflK protein; Region: hflK; TIGR01933 340100006204 HflC protein; Region: hflC; TIGR01932 340100006205 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 340100006206 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100006207 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 340100006208 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 340100006209 putative active site [active] 340100006210 putative NTP binding site [chemical binding]; other site 340100006211 putative nucleic acid binding site [nucleotide binding]; other site 340100006212 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100006213 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 340100006214 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 340100006215 active site 340100006216 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 340100006217 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 340100006218 dimer interface [polypeptide binding]; other site 340100006219 motif 1; other site 340100006220 active site 340100006221 motif 2; other site 340100006222 motif 3; other site 340100006223 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 340100006224 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 340100006225 GDP-binding site [chemical binding]; other site 340100006226 ACT binding site; other site 340100006227 IMP binding site; other site 340100006228 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 340100006229 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100006230 active site 340100006231 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 340100006232 DNA primase, catalytic core; Region: dnaG; TIGR01391 340100006233 CHC2 zinc finger; Region: zf-CHC2; pfam01807 340100006234 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 340100006235 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 340100006236 active site 340100006237 metal binding site [ion binding]; metal-binding site 340100006238 interdomain interaction site; other site 340100006239 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 340100006240 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; smart00766 340100006241 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 340100006242 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 340100006243 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 340100006244 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 340100006245 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100006246 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 340100006247 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 340100006248 DNA binding residues [nucleotide binding] 340100006249 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 340100006250 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100006251 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100006252 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100006253 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 340100006254 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 340100006255 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 340100006256 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 340100006257 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 340100006258 AsnC family; Region: AsnC_trans_reg; pfam01037 340100006259 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 340100006260 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100006261 DNA-binding site [nucleotide binding]; DNA binding site 340100006262 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 340100006263 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006264 homodimer interface [polypeptide binding]; other site 340100006265 catalytic residue [active] 340100006266 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 340100006267 aspartate carbamoyltransferase; Provisional; Region: PRK11891 340100006268 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 340100006269 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 340100006270 recombination associated protein; Reviewed; Region: rdgC; PRK00321 340100006271 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 340100006272 putative substrate translocation pore; other site 340100006273 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 340100006274 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100006275 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 340100006276 dimer interface [polypeptide binding]; other site 340100006277 phosphorylation site [posttranslational modification] 340100006278 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 340100006279 ATP binding site [chemical binding]; other site 340100006280 Mg2+ binding site [ion binding]; other site 340100006281 G-X-G motif; other site 340100006282 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100006283 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100006284 active site 340100006285 phosphorylation site [posttranslational modification] 340100006286 intermolecular recognition site; other site 340100006287 dimerization interface [polypeptide binding]; other site 340100006288 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 340100006289 DNA binding site [nucleotide binding] 340100006290 recombinase A; Provisional; Region: recA; PRK09354 340100006291 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 340100006292 hexamer interface [polypeptide binding]; other site 340100006293 Walker A motif; other site 340100006294 ATP binding site [chemical binding]; other site 340100006295 Walker B motif; other site 340100006296 RecX family; Region: RecX; cl00936 340100006297 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 340100006298 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006299 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 340100006300 putative dimerization interface [polypeptide binding]; other site 340100006301 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 340100006302 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 340100006303 THF binding site; other site 340100006304 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 340100006305 substrate binding site [chemical binding]; other site 340100006306 THF binding site; other site 340100006307 zinc-binding site [ion binding]; other site 340100006308 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 340100006309 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 340100006310 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 340100006311 CoA-ligase; Region: Ligase_CoA; pfam00549 340100006312 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 340100006313 CoA binding domain; Region: CoA_binding; smart00881 340100006314 CoA-ligase; Region: Ligase_CoA; pfam00549 340100006315 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 340100006316 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 340100006317 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 340100006318 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 340100006319 domain interfaces; other site 340100006320 active site 340100006321 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 340100006322 active site 340100006323 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed; Region: PRK06975 340100006324 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 340100006325 HemY protein N-terminus; Region: HemY_N; pfam07219 340100006326 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 340100006327 dimer interface [polypeptide binding]; other site 340100006328 substrate binding site [chemical binding]; other site 340100006329 metal binding sites [ion binding]; metal-binding site 340100006330 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 340100006331 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100006332 Predicted small secreted protein [Function unknown]; Region: COG5510 340100006333 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 340100006334 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 340100006335 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 340100006336 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100006337 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 340100006338 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 340100006339 phosphopeptide binding site; other site 340100006340 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 340100006341 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 340100006342 ATP binding site [chemical binding]; other site 340100006343 Walker A motif; other site 340100006344 hexamer interface [polypeptide binding]; other site 340100006345 Walker B motif; other site 340100006346 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 340100006347 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 340100006348 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 340100006349 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 340100006350 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 340100006351 Methyltransferase domain; Region: Methyltransf_32; pfam13679 340100006352 Methyltransferase domain; Region: Methyltransf_31; pfam13847 340100006353 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; pfam09998 340100006354 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 340100006355 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 340100006356 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 340100006357 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 340100006358 active site 340100006359 GMP synthase; Reviewed; Region: guaA; PRK00074 340100006360 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 340100006361 AMP/PPi binding site [chemical binding]; other site 340100006362 candidate oxyanion hole; other site 340100006363 catalytic triad [active] 340100006364 potential glutamine specificity residues [chemical binding]; other site 340100006365 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 340100006366 ATP Binding subdomain [chemical binding]; other site 340100006367 Ligand Binding sites [chemical binding]; other site 340100006368 Dimerization subdomain; other site 340100006369 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 340100006370 Domain of unknown function (DUF3817); Region: DUF3817; pfam12823 340100006371 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100006372 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 340100006373 conserved cys residue [active] 340100006374 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100006375 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006376 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006377 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006378 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006379 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 340100006380 putative effector binding pocket; other site 340100006381 putative dimerization interface [polypeptide binding]; other site 340100006382 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR2; cd08268 340100006383 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 340100006384 putative NAD(P) binding site [chemical binding]; other site 340100006385 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006386 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006387 The 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 340100006388 dimerization interface [polypeptide binding]; other site 340100006389 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 340100006390 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100006391 putative transposase OrfB; Reviewed; Region: PHA02517 340100006392 HTH-like domain; Region: HTH_21; pfam13276 340100006393 Integrase core domain; Region: rve; pfam00665 340100006394 Integrase core domain; Region: rve_3; pfam13683 340100006395 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100006396 Transposase; Region: HTH_Tnp_1; pfam01527 340100006397 flagellin; Validated; Region: PRK08026 340100006398 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 340100006399 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 340100006400 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 340100006401 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100006402 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 340100006403 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 340100006404 DNA binding residues [nucleotide binding] 340100006405 transcriptional activator FlhD; Provisional; Region: PRK02909 340100006406 transcriptional activator FlhC; Provisional; Region: PRK12722 340100006407 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 340100006408 flagellar motor protein MotA; Validated; Region: PRK09110 340100006409 flagellar motor protein MotB; Validated; Region: motB; PRK09041 340100006410 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 340100006411 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100006412 ligand binding site [chemical binding]; other site 340100006413 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 340100006414 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100006415 active site 340100006416 phosphorylation site [posttranslational modification] 340100006417 intermolecular recognition site; other site 340100006418 dimerization interface [polypeptide binding]; other site 340100006419 chemotaxis protein CheA; Provisional; Region: PRK10547 340100006420 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 340100006421 putative binding surface; other site 340100006422 active site 340100006423 CheY binding; Region: CheY-binding; pfam09078 340100006424 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 340100006425 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 340100006426 ATP binding site [chemical binding]; other site 340100006427 Mg2+ binding site [ion binding]; other site 340100006428 G-X-G motif; other site 340100006429 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 340100006430 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 340100006431 putative CheA interaction surface; other site 340100006432 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cd00181 340100006433 dimer interface [polypeptide binding]; other site 340100006434 ligand binding site [chemical binding]; other site 340100006435 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 340100006436 dimerization interface [polypeptide binding]; other site 340100006437 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006438 dimer interface [polypeptide binding]; other site 340100006439 putative CheW interface [polypeptide binding]; other site 340100006440 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 340100006441 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 340100006442 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 340100006443 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 340100006444 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100006445 active site 340100006446 phosphorylation site [posttranslational modification] 340100006447 intermolecular recognition site; other site 340100006448 dimerization interface [polypeptide binding]; other site 340100006449 CheB methylesterase; Region: CheB_methylest; pfam01339 340100006450 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 340100006451 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100006452 active site 340100006453 phosphorylation site [posttranslational modification] 340100006454 intermolecular recognition site; other site 340100006455 dimerization interface [polypeptide binding]; other site 340100006456 chemotaxis regulator CheZ; Provisional; Region: PRK11166 340100006457 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006458 dimer interface [polypeptide binding]; other site 340100006459 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 340100006460 putative CheW interface [polypeptide binding]; other site 340100006461 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 340100006462 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 340100006463 FHIPEP family; Region: FHIPEP; pfam00771 340100006464 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 340100006465 putative transposase OrfB; Reviewed; Region: PHA02517 340100006466 HTH-like domain; Region: HTH_21; pfam13276 340100006467 Integrase core domain; Region: rve; pfam00665 340100006468 Integrase core domain; Region: rve_3; pfam13683 340100006469 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100006470 Transposase; Region: HTH_Tnp_1; pfam01527 340100006471 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 340100006472 FHIPEP family; Region: FHIPEP; pfam00771 340100006473 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 340100006474 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 340100006475 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 340100006476 FlgN protein; Region: FlgN; pfam05130 340100006477 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 340100006478 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100006479 Transposase; Region: HTH_Tnp_1; pfam01527 340100006480 putative transposase OrfB; Reviewed; Region: PHA02517 340100006481 HTH-like domain; Region: HTH_21; pfam13276 340100006482 Integrase core domain; Region: rve; pfam00665 340100006483 Integrase core domain; Region: rve_3; pfam13683 340100006484 SAF-like; Region: SAF_2; pfam13144 340100006485 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 340100006486 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 340100006487 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 340100006488 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 340100006489 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 340100006490 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 340100006491 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 340100006492 flagellar basal body rod modification protein; Provisional; Region: flgD; PRK12633 340100006493 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 340100006494 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 340100006495 flagellar hook protein FlgE; Provisional; Region: flgE; PRK12637 340100006496 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 340100006497 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 340100006498 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 340100006499 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 340100006500 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 340100006501 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 340100006502 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12694 340100006503 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 340100006504 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 340100006505 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12700 340100006506 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 340100006507 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 340100006508 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 340100006509 flagellar rod assembly protein/muramidase FlgJ; Provisional; Region: flgJ; PRK12713 340100006510 Rod binding protein; Region: Rod-binding; cl01626 340100006511 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 340100006512 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08147 340100006513 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 340100006514 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 340100006515 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 340100006516 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 340100006517 dimerization interface [polypeptide binding]; other site 340100006518 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006519 dimer interface [polypeptide binding]; other site 340100006520 putative CheW interface [polypeptide binding]; other site 340100006521 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 340100006522 dimerization interface [polypeptide binding]; other site 340100006523 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 340100006524 dimer interface [polypeptide binding]; other site 340100006525 putative CheW interface [polypeptide binding]; other site 340100006526 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 340100006527 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 340100006528 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 340100006529 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 340100006530 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 340100006531 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 340100006532 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 340100006533 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 340100006534 Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliJ; COG2882 340100006535 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 340100006536 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 340100006537 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 340100006538 Walker A motif/ATP binding site; other site 340100006539 Walker B motif; other site 340100006540 flagellar assembly protein H; Validated; Region: fliH; PRK05687 340100006541 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 340100006542 Flagellar assembly protein FliH; Region: FliH; pfam02108 340100006543 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 340100006544 FliG C-terminal domain; Region: FliG_C; pfam01706 340100006545 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 340100006546 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 340100006547 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 340100006548 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 340100006549 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 340100006550 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 340100006551 Flagellar protein FliT; Region: FliT; pfam05400 340100006552 Flagellar protein FliS; Region: FliS; cl00654 340100006553 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 340100006554 flagellar capping protein; Reviewed; Region: fliD; PRK08032 340100006555 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 340100006556 FlaG protein; Region: FlaG; pfam03646 340100006557 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100006558 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100006559 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100006560 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100006561 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100006562 active site 340100006563 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100006564 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100006565 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100006566 Cupin domain; Region: Cupin_2; pfam07883 340100006567 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 340100006568 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340100006569 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340100006570 Sporulation related domain; Region: SPOR; pfam05036 340100006571 Colicin V production protein; Region: Colicin_V; pfam02674 340100006572 amidophosphoribosyltransferase; Provisional; Region: PRK09246 340100006573 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 340100006574 active site 340100006575 tetramer interface [polypeptide binding]; other site 340100006576 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100006577 active site 340100006578 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 340100006579 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 340100006580 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 340100006581 active site 340100006582 Int/Topo IB signature motif; other site 340100006583 DNA binding site [nucleotide binding] 340100006584 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 340100006585 Helix-turn-helix domain; Region: HTH_37; pfam13744 340100006586 Predicted ATPase [General function prediction only]; Region: COG5293 340100006587 Uncharacterized protein conserved in bacteria (DUF2326); Region: DUF2326; pfam10088 340100006588 hypothetical protein; Reviewed; Region: PRK00024 340100006589 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100006590 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 340100006591 Domain of unknown function (DUF932); Region: DUF932; pfam06067 340100006592 ParB-like nuclease domain; Region: ParBc; pfam02195 340100006593 Protein of unknown function DUF86; Region: DUF86; cl01031 340100006594 Uncharacterized conserved protein [Function unknown]; Region: COG5489 340100006595 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100006596 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 340100006597 non-specific DNA binding site [nucleotide binding]; other site 340100006598 salt bridge; other site 340100006599 sequence-specific DNA binding site [nucleotide binding]; other site 340100006600 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 340100006601 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 340100006602 Helix-turn-helix domain; Region: HTH_17; cl17695 340100006603 Replication initiator protein A; Region: RPA; pfam10134 340100006604 ParA-like protein; Provisional; Region: PHA02518 340100006605 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 340100006606 P-loop; other site 340100006607 Magnesium ion binding site [ion binding]; other site 340100006608 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 340100006609 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 340100006610 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 340100006611 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 340100006612 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 340100006613 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 340100006614 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 340100006615 dimer interface [polypeptide binding]; other site 340100006616 active site 340100006617 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 340100006618 active site 340100006619 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100006620 catalytic tetrad [active] 340100006621 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 340100006622 putative active site [active] 340100006623 putative catalytic site [active] 340100006624 putative acyltransferase; Provisional; Region: PRK05790 340100006625 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 340100006626 dimer interface [polypeptide binding]; other site 340100006627 active site 340100006628 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 340100006629 CoenzymeA binding site [chemical binding]; other site 340100006630 subunit interaction site [polypeptide binding]; other site 340100006631 PHB binding site; other site 340100006632 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100006633 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 340100006634 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 340100006635 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100006636 putative substrate translocation pore; other site 340100006637 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 340100006638 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 340100006639 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100006640 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006641 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 340100006642 dimerization interface [polypeptide binding]; other site 340100006643 substrate binding pocket [chemical binding]; other site 340100006644 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 340100006645 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 340100006646 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100006647 catalytic residue [active] 340100006648 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 340100006649 active site 1 [active] 340100006650 dimer interface [polypeptide binding]; other site 340100006651 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 340100006652 hexamer interface [polypeptide binding]; other site 340100006653 active site 2 [active] 340100006654 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 340100006655 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100006656 putative substrate translocation pore; other site 340100006657 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 340100006658 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006659 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 340100006660 dimerization interface [polypeptide binding]; other site 340100006661 substrate binding pocket [chemical binding]; other site 340100006662 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 340100006663 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100006664 Walker A motif; other site 340100006665 ATP binding site [chemical binding]; other site 340100006666 Walker B motif; other site 340100006667 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 340100006668 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 340100006669 ATP binding site [chemical binding]; other site 340100006670 Walker A motif; other site 340100006671 hexamer interface [polypeptide binding]; other site 340100006672 Walker B motif; other site 340100006673 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 340100006674 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 340100006675 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 340100006676 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 340100006677 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100006678 Walker A motif; other site 340100006679 ATP binding site [chemical binding]; other site 340100006680 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 340100006681 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 340100006682 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 340100006683 conjugal transfer protein TrbL; Provisional; Region: PRK13875 340100006684 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340100006685 conjugal transfer protein TrbF; Provisional; Region: PRK13872 340100006686 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100006687 VirB7 interaction site; other site 340100006688 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 340100006689 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 340100006690 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 340100006691 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 340100006692 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 340100006693 putative active site [active] 340100006694 catalytic site [active] 340100006695 putative metal binding site [ion binding]; other site 340100006696 SurA N-terminal domain; Region: SurA_N_3; cl07813 340100006697 periplasmic folding chaperone; Provisional; Region: PRK10788 340100006698 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100006699 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 340100006700 active site 340100006701 catalytic triad [active] 340100006702 oxyanion hole [active] 340100006703 switch loop; other site 340100006704 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 340100006705 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 340100006706 Walker A/P-loop; other site 340100006707 ATP binding site [chemical binding]; other site 340100006708 Q-loop/lid; other site 340100006709 ABC transporter signature motif; other site 340100006710 Walker B; other site 340100006711 D-loop; other site 340100006712 H-loop/switch region; other site 340100006713 Isochorismatase family; Region: Isochorismatase; pfam00857 340100006714 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 340100006715 catalytic triad [active] 340100006716 conserved cis-peptide bond; other site 340100006717 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 340100006718 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100006719 conserved cys residue [active] 340100006720 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006721 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100006722 EamA-like transporter family; Region: EamA; cl17759 340100006723 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006724 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006725 The 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 340100006726 dimerization interface [polypeptide binding]; other site 340100006727 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100006728 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100006729 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100006730 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006731 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100006732 DctM-like transporters; Region: DctM; pfam06808 340100006733 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100006734 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 340100006735 amidase; Provisional; Region: PRK07056 340100006736 Amidase; Region: Amidase; cl11426 340100006737 hypothetical protein; Provisional; Region: PRK05463 340100006738 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 340100006739 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 340100006740 trimer interface [polypeptide binding]; other site 340100006741 eyelet of channel; other site 340100006742 DctM-like transporters; Region: DctM; pfam06808 340100006743 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 340100006744 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100006745 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100006746 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006747 MarR family; Region: MarR_2; cl17246 340100006748 5-oxoprolinase; Region: PLN02666 340100006749 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340100006750 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 340100006751 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 340100006752 Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase; Region: AAT; pfam03417 340100006753 glutamine ABC transporter periplasmic protein; Reviewed; Region: glnH; PRK09495 340100006754 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 340100006755 substrate binding pocket [chemical binding]; other site 340100006756 membrane-bound complex binding site; other site 340100006757 hinge residues; other site 340100006758 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 340100006759 dimer interface [polypeptide binding]; other site 340100006760 conserved gate region; other site 340100006761 putative PBP binding loops; other site 340100006762 ABC-ATPase subunit interface; other site 340100006763 glutamine ABC transporter ATP-binding protein; Reviewed; Region: glnQ; PRK09493 340100006764 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100006765 Walker A/P-loop; other site 340100006766 ATP binding site [chemical binding]; other site 340100006767 Q-loop/lid; other site 340100006768 ABC transporter signature motif; other site 340100006769 Walker B; other site 340100006770 D-loop; other site 340100006771 H-loop/switch region; other site 340100006772 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100006773 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100006774 DNA-binding site [nucleotide binding]; DNA binding site 340100006775 FCD domain; Region: FCD; pfam07729 340100006776 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100006777 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 340100006778 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 340100006779 Zn2+ binding site [ion binding]; other site 340100006780 Mg2+ binding site [ion binding]; other site 340100006781 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 340100006782 synthetase active site [active] 340100006783 NTP binding site [chemical binding]; other site 340100006784 metal binding site [ion binding]; metal-binding site 340100006785 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 340100006786 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 340100006787 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 340100006788 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 340100006789 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 340100006790 catalytic site [active] 340100006791 G-X2-G-X-G-K; other site 340100006792 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 340100006793 classical (c) SDRs; Region: SDR_c; cd05233 340100006794 NAD(P) binding site [chemical binding]; other site 340100006795 active site 340100006796 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100006797 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 340100006798 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 340100006799 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100006800 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100006801 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 340100006802 NlpC/P60 family; Region: NLPC_P60; pfam00877 340100006803 AMP nucleosidase; Provisional; Region: PRK08292 340100006804 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 340100006805 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 340100006806 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 340100006807 non-specific DNA binding site [nucleotide binding]; other site 340100006808 salt bridge; other site 340100006809 sequence-specific DNA binding site [nucleotide binding]; other site 340100006810 HipA N-terminal domain; Region: Couple_hipA; pfam13657 340100006811 HipA-like N-terminal domain; Region: HipA_N; pfam07805 340100006812 HipA-like C-terminal domain; Region: HipA_C; pfam07804 340100006813 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006814 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006815 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 340100006816 putative dimerization interface [polypeptide binding]; other site 340100006817 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100006818 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100006819 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100006820 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 340100006821 active site 340100006822 tetramer interface; other site 340100006823 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 340100006824 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 340100006825 Low affinity iron permease; Region: Iron_permease; cl12096 340100006826 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 340100006827 GAF domain; Region: GAF; pfam01590 340100006828 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 340100006829 Walker A motif; other site 340100006830 ATP binding site [chemical binding]; other site 340100006831 Walker B motif; other site 340100006832 arginine finger; other site 340100006833 Hemerythrin-like domain; Region: Hr-like; cd12108 340100006834 Fe binding site [ion binding]; other site 340100006835 hypothetical protein; Provisional; Region: PRK11820 340100006836 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 340100006837 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 340100006838 ribonuclease PH; Reviewed; Region: rph; PRK00173 340100006839 Ribonuclease PH; Region: RNase_PH_bact; cd11362 340100006840 hexamer interface [polypeptide binding]; other site 340100006841 active site 340100006842 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100006843 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100006844 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100006845 active site 340100006846 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006847 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006848 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 340100006849 putative dimerization interface [polypeptide binding]; other site 340100006850 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 340100006851 active site 340100006852 dimerization interface [polypeptide binding]; other site 340100006853 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 340100006854 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 340100006855 FeS/SAM binding site; other site 340100006856 HemN C-terminal domain; Region: HemN_C; pfam06969 340100006857 glutamine synthetase; Provisional; Region: glnA; PRK09469 340100006858 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 340100006859 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 340100006860 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 340100006861 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 340100006862 putative active site [active] 340100006863 heme pocket [chemical binding]; other site 340100006864 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 340100006865 dimer interface [polypeptide binding]; other site 340100006866 phosphorylation site [posttranslational modification] 340100006867 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 340100006868 ATP binding site [chemical binding]; other site 340100006869 Mg2+ binding site [ion binding]; other site 340100006870 G-X-G motif; other site 340100006871 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 340100006872 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100006873 active site 340100006874 phosphorylation site [posttranslational modification] 340100006875 intermolecular recognition site; other site 340100006876 dimerization interface [polypeptide binding]; other site 340100006877 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 340100006878 Walker A motif; other site 340100006879 ATP binding site [chemical binding]; other site 340100006880 Walker B motif; other site 340100006881 arginine finger; other site 340100006882 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100006883 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 340100006884 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006885 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 340100006886 putative dimerization interface [polypeptide binding]; other site 340100006887 Pirin-related protein [General function prediction only]; Region: COG1741 340100006888 Pirin; Region: Pirin; pfam02678 340100006889 Pirin-related protein [General function prediction only]; Region: COG1741 340100006890 Pirin; Region: Pirin; pfam02678 340100006891 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 340100006892 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 340100006893 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 340100006894 Walker A/P-loop; other site 340100006895 ATP binding site [chemical binding]; other site 340100006896 Q-loop/lid; other site 340100006897 ABC transporter signature motif; other site 340100006898 Walker B; other site 340100006899 D-loop; other site 340100006900 H-loop/switch region; other site 340100006901 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 340100006902 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 340100006903 dimer interface [polypeptide binding]; other site 340100006904 conserved gate region; other site 340100006905 putative PBP binding loops; other site 340100006906 ABC-ATPase subunit interface; other site 340100006907 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 340100006908 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100006909 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 340100006910 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 340100006911 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 340100006912 FAD binding pocket [chemical binding]; other site 340100006913 FAD binding motif [chemical binding]; other site 340100006914 phosphate binding motif [ion binding]; other site 340100006915 beta-alpha-beta structure motif; other site 340100006916 NAD binding pocket [chemical binding]; other site 340100006917 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100006918 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100006919 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100006920 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100006921 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006922 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 340100006923 putative dimerization interface [polypeptide binding]; other site 340100006924 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 340100006925 homotrimer interaction site [polypeptide binding]; other site 340100006926 putative active site [active] 340100006927 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 340100006928 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 340100006929 generic binding surface II; other site 340100006930 ssDNA binding site; other site 340100006931 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 340100006932 ATP binding site [chemical binding]; other site 340100006933 putative Mg++ binding site [ion binding]; other site 340100006934 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 340100006935 nucleotide binding region [chemical binding]; other site 340100006936 ATP-binding site [chemical binding]; other site 340100006937 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 340100006938 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100006939 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 340100006940 dimerization interface [polypeptide binding]; other site 340100006941 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 340100006942 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 340100006943 dimerization interface [polypeptide binding]; other site 340100006944 DPS ferroxidase diiron center [ion binding]; other site 340100006945 ion pore; other site 340100006946 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 340100006947 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 340100006948 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100006949 NAD(P) binding site [chemical binding]; other site 340100006950 active site 340100006951 Sulfatase; Region: Sulfatase; cl17466 340100006952 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 340100006953 Chain length determinant protein; Region: Wzz; cl15801 340100006954 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 340100006955 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 340100006956 SLBB domain; Region: SLBB; pfam10531 340100006957 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 340100006958 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 340100006959 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 340100006960 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 340100006961 Walker A/P-loop; other site 340100006962 ATP binding site [chemical binding]; other site 340100006963 Q-loop/lid; other site 340100006964 ABC transporter signature motif; other site 340100006965 Walker B; other site 340100006966 D-loop; other site 340100006967 H-loop/switch region; other site 340100006968 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 340100006969 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 340100006970 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 340100006971 NAD(P) binding site [chemical binding]; other site 340100006972 homodimer interface [polypeptide binding]; other site 340100006973 substrate binding site [chemical binding]; other site 340100006974 active site 340100006975 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 340100006976 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 340100006977 inhibitor-cofactor binding pocket; inhibition site 340100006978 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100006979 catalytic residue [active] 340100006980 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 340100006981 ligand binding site; other site 340100006982 tetramer interface; other site 340100006983 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 340100006984 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 340100006985 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 340100006986 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 340100006987 pseudaminic acid synthase; Region: PseI; TIGR03586 340100006988 NeuB family; Region: NeuB; pfam03102 340100006989 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 340100006990 NeuB binding interface [polypeptide binding]; other site 340100006991 putative substrate binding site [chemical binding]; other site 340100006992 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsC; COG3563 340100006993 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 340100006994 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 340100006995 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 340100006996 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 340100006997 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 340100006998 substrate-cofactor binding pocket; other site 340100006999 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100007000 catalytic residue [active] 340100007001 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 340100007002 Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3321 340100007003 active site 340100007004 Acyl transferase domain in polyketide synthase (PKS) enzymes; Region: PKS_AT; smart00827 340100007005 Dehydratase domain in polyketide synthase (PKS) enzymes; Region: PKS_DH; smart00826 340100007006 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100007007 enoyl reductase of polyketide synthase; Region: enoyl_red; cd05195 340100007008 Enoylreductase; Region: PKS_ER; smart00829 340100007009 NAD(P) binding site [chemical binding]; other site 340100007010 beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x); Region: KR_2_FAS_SDR_x; cd08955 340100007011 KR domain; Region: KR; pfam08659 340100007012 putative NADP binding site [chemical binding]; other site 340100007013 active site 340100007014 Phosphopantetheine attachment site; Region: PKS_PP; smart00823 340100007015 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100007016 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 340100007017 dimerization interface [polypeptide binding]; other site 340100007018 ligand binding site [chemical binding]; other site 340100007019 Serine hydrolase; Region: Ser_hydrolase; pfam06821 340100007020 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100007021 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 340100007022 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 340100007023 Walker A/P-loop; other site 340100007024 ATP binding site [chemical binding]; other site 340100007025 Q-loop/lid; other site 340100007026 ABC transporter signature motif; other site 340100007027 Walker B; other site 340100007028 D-loop; other site 340100007029 H-loop/switch region; other site 340100007030 TOBE domain; Region: TOBE_2; pfam08402 340100007031 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 340100007032 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 340100007033 dimer interface [polypeptide binding]; other site 340100007034 conserved gate region; other site 340100007035 putative PBP binding loops; other site 340100007036 ABC-ATPase subunit interface; other site 340100007037 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 340100007038 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 340100007039 dimer interface [polypeptide binding]; other site 340100007040 conserved gate region; other site 340100007041 putative PBP binding loops; other site 340100007042 ABC-ATPase subunit interface; other site 340100007043 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 340100007044 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100007045 Uncharacterized member of the PurR regulon [General function prediction only]; Region: yhhQ; COG1738 340100007046 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 340100007047 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 340100007048 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100007049 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 340100007050 dimerization interface [polypeptide binding]; other site 340100007051 ligand binding site [chemical binding]; other site 340100007052 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100007053 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 340100007054 TM-ABC transporter signature motif; other site 340100007055 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 340100007056 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 340100007057 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 340100007058 TM-ABC transporter signature motif; other site 340100007059 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 340100007060 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100007061 Walker A/P-loop; other site 340100007062 ATP binding site [chemical binding]; other site 340100007063 Q-loop/lid; other site 340100007064 ABC transporter signature motif; other site 340100007065 Walker B; other site 340100007066 D-loop; other site 340100007067 H-loop/switch region; other site 340100007068 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100007069 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100007070 Walker A/P-loop; other site 340100007071 ATP binding site [chemical binding]; other site 340100007072 Q-loop/lid; other site 340100007073 ABC transporter signature motif; other site 340100007074 Walker B; other site 340100007075 D-loop; other site 340100007076 H-loop/switch region; other site 340100007077 aspartate racemase; Region: asp_race; TIGR00035 340100007078 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 340100007079 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 340100007080 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 340100007081 active site 340100007082 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 340100007083 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100007084 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100007085 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100007086 The 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 340100007087 dimerization interface [polypeptide binding]; other site 340100007088 N-carbamyl-D-amino acid amidohydrolase (DCase, class 6 nitrilases); Region: DCase; cd07569 340100007089 tetramer interface [polypeptide binding]; other site 340100007090 Predicted amidohydrolase [General function prediction only]; Region: COG0388 340100007091 active site 340100007092 catalytic triad [active] 340100007093 dimer interface [polypeptide binding]; other site 340100007094 glutathionine S-transferase; Provisional; Region: PRK10542 340100007095 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 340100007096 C-terminal domain interface [polypeptide binding]; other site 340100007097 GSH binding site (G-site) [chemical binding]; other site 340100007098 dimer interface [polypeptide binding]; other site 340100007099 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100007100 N-terminal domain interface [polypeptide binding]; other site 340100007101 dimer interface [polypeptide binding]; other site 340100007102 substrate binding pocket (H-site) [chemical binding]; other site 340100007103 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 340100007104 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 340100007105 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 340100007106 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100007107 C-terminal domain interface [polypeptide binding]; other site 340100007108 GSH binding site (G-site) [chemical binding]; other site 340100007109 dimer interface [polypeptide binding]; other site 340100007110 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100007111 N-terminal domain interface [polypeptide binding]; other site 340100007112 dimer interface [polypeptide binding]; other site 340100007113 substrate binding pocket (H-site) [chemical binding]; other site 340100007114 Protein of unknown function (DUF423); Region: DUF423; pfam04241 340100007115 Arginase family; Region: Arginase; cd09989 340100007116 active site 340100007117 Mn binding site [ion binding]; other site 340100007118 oligomer interface [polypeptide binding]; other site 340100007119 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 340100007120 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 340100007121 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 340100007122 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 340100007123 NAD(P) binding site [chemical binding]; other site 340100007124 catalytic residues [active] 340100007125 allantoate amidohydrolase; Reviewed; Region: PRK12893 340100007126 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 340100007127 active site 340100007128 metal binding site [ion binding]; metal-binding site 340100007129 dimer interface [polypeptide binding]; other site 340100007130 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100007131 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100007132 PYR/PP interface [polypeptide binding]; other site 340100007133 dimer interface [polypeptide binding]; other site 340100007134 TPP binding site [chemical binding]; other site 340100007135 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100007136 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 340100007137 TPP-binding site [chemical binding]; other site 340100007138 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 340100007139 DctM-like transporters; Region: DctM; pfam06808 340100007140 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100007141 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100007142 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100007143 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 340100007144 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100007145 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100007146 DNA-binding site [nucleotide binding]; DNA binding site 340100007147 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 340100007148 short chain dehydrogenase; Provisional; Region: PRK06701 340100007149 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 340100007150 NAD binding site [chemical binding]; other site 340100007151 metal binding site [ion binding]; metal-binding site 340100007152 active site 340100007153 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 340100007154 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 340100007155 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 340100007156 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 340100007157 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100007158 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 340100007159 putative ADP-binding pocket [chemical binding]; other site 340100007160 Predicted membrane protein [Function unknown]; Region: COG2323 340100007161 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 340100007162 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 340100007163 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 340100007164 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 340100007165 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 340100007166 dimer interface [polypeptide binding]; other site 340100007167 active site residues [active] 340100007168 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 340100007169 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100007170 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100007171 short chain dehydrogenase; Provisional; Region: PRK07109 340100007172 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 340100007173 putative NAD(P) binding site [chemical binding]; other site 340100007174 active site 340100007175 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 340100007176 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100007177 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 340100007178 Subunit I/III interface [polypeptide binding]; other site 340100007179 D-pathway; other site 340100007180 Subunit I/VIIc interface [polypeptide binding]; other site 340100007181 Subunit I/IV interface [polypeptide binding]; other site 340100007182 Subunit I/II interface [polypeptide binding]; other site 340100007183 Low-spin heme (heme a) binding site [chemical binding]; other site 340100007184 Subunit I/VIIa interface [polypeptide binding]; other site 340100007185 Subunit I/VIa interface [polypeptide binding]; other site 340100007186 Dimer interface; other site 340100007187 Putative water exit pathway; other site 340100007188 Binuclear center (heme a3/CuB) [ion binding]; other site 340100007189 K-pathway; other site 340100007190 Subunit I/Vb interface [polypeptide binding]; other site 340100007191 Putative proton exit pathway; other site 340100007192 Subunit I/VIb interface; other site 340100007193 Subunit I/VIc interface [polypeptide binding]; other site 340100007194 Electron transfer pathway; other site 340100007195 Subunit I/VIIIb interface [polypeptide binding]; other site 340100007196 Subunit I/VIIb interface [polypeptide binding]; other site 340100007197 Predicted integral membrane protein [Function unknown]; Region: COG0392 340100007198 cardiolipin synthase 2; Provisional; Region: PRK11263 340100007199 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 340100007200 putative active site [active] 340100007201 catalytic site [active] 340100007202 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 340100007203 putative active site [active] 340100007204 catalytic site [active] 340100007205 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 340100007206 putative catalytic site [active] 340100007207 putative metal binding site [ion binding]; other site 340100007208 putative phosphate binding site [ion binding]; other site 340100007209 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 340100007210 GAF domain; Region: GAF; pfam01590 340100007211 PAS domain S-box; Region: sensory_box; TIGR00229 340100007212 PAS domain; Region: PAS; smart00091 340100007213 PAS domain S-box; Region: sensory_box; TIGR00229 340100007214 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 340100007215 putative active site [active] 340100007216 heme pocket [chemical binding]; other site 340100007217 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100007218 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 340100007219 dimer interface [polypeptide binding]; other site 340100007220 phosphorylation site [posttranslational modification] 340100007221 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 340100007222 ATP binding site [chemical binding]; other site 340100007223 Mg2+ binding site [ion binding]; other site 340100007224 G-X-G motif; other site 340100007225 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 340100007226 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100007227 active site 340100007228 phosphorylation site [posttranslational modification] 340100007229 intermolecular recognition site; other site 340100007230 dimerization interface [polypeptide binding]; other site 340100007231 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 340100007232 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 340100007233 active site 340100007234 catalytic site [active] 340100007235 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 340100007236 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 340100007237 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 340100007238 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 340100007239 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 340100007240 catalytic site [active] 340100007241 active site 340100007242 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 340100007243 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 340100007244 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 340100007245 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 340100007246 active site 340100007247 catalytic site [active] 340100007248 glycogen branching enzyme; Provisional; Region: PRK05402 340100007249 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 340100007250 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 340100007251 active site 340100007252 catalytic site [active] 340100007253 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 340100007254 trehalose synthase; Region: treS_nterm; TIGR02456 340100007255 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 340100007256 active site 340100007257 catalytic site [active] 340100007258 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 340100007259 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 340100007260 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 340100007261 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 340100007262 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 340100007263 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 340100007264 active site 340100007265 homodimer interface [polypeptide binding]; other site 340100007266 catalytic site [active] 340100007267 acceptor binding site [chemical binding]; other site 340100007268 glycogen synthase; Provisional; Region: glgA; PRK00654 340100007269 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 340100007270 ADP-binding pocket [chemical binding]; other site 340100007271 homodimer interface [polypeptide binding]; other site 340100007272 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 340100007273 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100007274 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 340100007275 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 340100007276 Walker A motif; other site 340100007277 ATP binding site [chemical binding]; other site 340100007278 Walker B motif; other site 340100007279 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100007280 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 340100007281 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100007282 active site 340100007283 phosphorylation site [posttranslational modification] 340100007284 intermolecular recognition site; other site 340100007285 dimerization interface [polypeptide binding]; other site 340100007286 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 340100007287 Walker A motif; other site 340100007288 ATP binding site [chemical binding]; other site 340100007289 Walker B motif; other site 340100007290 arginine finger; other site 340100007291 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100007292 thiamine pyrophosphate protein; Provisional; Region: PRK08273 340100007293 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 340100007294 PYR/PP interface [polypeptide binding]; other site 340100007295 dimer interface [polypeptide binding]; other site 340100007296 tetramer interface [polypeptide binding]; other site 340100007297 TPP binding site [chemical binding]; other site 340100007298 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100007299 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 340100007300 TPP-binding site [chemical binding]; other site 340100007301 adhesin; Provisional; Region: PRK09752 340100007302 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 340100007303 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 340100007304 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100007305 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100007306 Walker A/P-loop; other site 340100007307 ATP binding site [chemical binding]; other site 340100007308 Q-loop/lid; other site 340100007309 ABC transporter signature motif; other site 340100007310 Walker B; other site 340100007311 D-loop; other site 340100007312 H-loop/switch region; other site 340100007313 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 340100007314 Response regulator receiver domain; Region: Response_reg; pfam00072 340100007315 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100007316 active site 340100007317 phosphorylation site [posttranslational modification] 340100007318 intermolecular recognition site; other site 340100007319 dimerization interface [polypeptide binding]; other site 340100007320 BON domain; Region: BON; pfam04972 340100007321 PRC-barrel domain; Region: PRC; pfam05239 340100007322 short chain dehydrogenase; Provisional; Region: PRK08219 340100007323 classical (c) SDRs; Region: SDR_c; cd05233 340100007324 NAD(P) binding site [chemical binding]; other site 340100007325 active site 340100007326 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 340100007327 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 340100007328 active site 340100007329 motif I; other site 340100007330 motif II; other site 340100007331 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340100007332 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 340100007333 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 340100007334 putative active site [active] 340100007335 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 340100007336 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 340100007337 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 340100007338 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340100007339 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 340100007340 active site 340100007341 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340100007342 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 340100007343 putative active site [active] 340100007344 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100007345 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 340100007346 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340100007347 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 340100007348 NAD binding site [chemical binding]; other site 340100007349 putative substrate binding site 2 [chemical binding]; other site 340100007350 putative substrate binding site 1 [chemical binding]; other site 340100007351 active site 340100007352 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 340100007353 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340100007354 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 340100007355 Probable Catalytic site; other site 340100007356 metal-binding site 340100007357 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 340100007358 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 340100007359 active site 340100007360 DNA binding site [nucleotide binding] 340100007361 Int/Topo IB signature motif; other site 340100007362 catalytic residues [active] 340100007363 Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only]; Region: CinA; COG1546 340100007364 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100007365 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 340100007366 Protein of unknown function (DUF3182); Region: DUF3182; pfam11379 340100007367 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 340100007368 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100007369 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 340100007370 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100007371 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 340100007372 substrate binding pocket [chemical binding]; other site 340100007373 membrane-bound complex binding site; other site 340100007374 hinge residues; other site 340100007375 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 340100007376 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 340100007377 active site 340100007378 dimer interface [polypeptide binding]; other site 340100007379 non-prolyl cis peptide bond; other site 340100007380 insertion regions; other site 340100007381 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 340100007382 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 340100007383 ABC-ATPase subunit interface; other site 340100007384 putative PBP binding loops; other site 340100007385 putative mechanosensitive channel protein; Provisional; Region: PRK11465 340100007386 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100007387 Predicted metal-binding protein [General function prediction only]; Region: COG3019 340100007388 hypothetical protein; Provisional; Region: PRK07079 340100007389 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_2; cd05679 340100007390 metal binding site [ion binding]; metal-binding site 340100007391 putative dimer interface [polypeptide binding]; other site 340100007392 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100007393 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100007394 Walker A/P-loop; other site 340100007395 ATP binding site [chemical binding]; other site 340100007396 Q-loop/lid; other site 340100007397 ABC transporter signature motif; other site 340100007398 Walker B; other site 340100007399 D-loop; other site 340100007400 H-loop/switch region; other site 340100007401 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100007402 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100007403 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100007404 Walker A/P-loop; other site 340100007405 ATP binding site [chemical binding]; other site 340100007406 Q-loop/lid; other site 340100007407 ABC transporter signature motif; other site 340100007408 Walker B; other site 340100007409 D-loop; other site 340100007410 H-loop/switch region; other site 340100007411 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100007412 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340100007413 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100007414 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 340100007415 dimer interface [polypeptide binding]; other site 340100007416 conserved gate region; other site 340100007417 putative PBP binding loops; other site 340100007418 ABC-ATPase subunit interface; other site 340100007419 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100007420 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 340100007421 dimer interface [polypeptide binding]; other site 340100007422 conserved gate region; other site 340100007423 putative PBP binding loops; other site 340100007424 ABC-ATPase subunit interface; other site 340100007425 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100007426 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 340100007427 Beta-lactamase; Region: Beta-lactamase; pfam00144 340100007428 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 340100007429 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 340100007430 active site 340100007431 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 340100007432 Ligand Binding Site [chemical binding]; other site 340100007433 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100007434 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 340100007435 substrate binding pocket [chemical binding]; other site 340100007436 membrane-bound complex binding site; other site 340100007437 hinge residues; other site 340100007438 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 340100007439 dimer interface [polypeptide binding]; other site 340100007440 conserved gate region; other site 340100007441 putative PBP binding loops; other site 340100007442 ABC-ATPase subunit interface; other site 340100007443 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 340100007444 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100007445 Walker A/P-loop; other site 340100007446 ATP binding site [chemical binding]; other site 340100007447 Q-loop/lid; other site 340100007448 ABC transporter signature motif; other site 340100007449 Walker B; other site 340100007450 D-loop; other site 340100007451 H-loop/switch region; other site 340100007452 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 340100007453 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 340100007454 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 340100007455 active site 340100007456 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 340100007457 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100007458 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 340100007459 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 340100007460 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 340100007461 arginine deiminase; Provisional; Region: PRK01388 340100007462 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 340100007463 Spore germination protein; Region: Spore_permease; cl17796 340100007464 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 340100007465 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 340100007466 putative amphipathic alpha helix; other site 340100007467 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100007468 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100007469 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 340100007470 putative dimerization interface [polypeptide binding]; other site 340100007471 Sulfatase; Region: Sulfatase; cl17466 340100007472 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 340100007473 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100007474 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100007475 tetramerization interface [polypeptide binding]; other site 340100007476 NAD(P) binding site [chemical binding]; other site 340100007477 catalytic residues [active] 340100007478 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100007479 Integrase core domain; Region: rve_3; pfam13683 340100007480 HTH-like domain; Region: HTH_21; pfam13276 340100007481 Integrase core domain; Region: rve; pfam00665 340100007482 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100007483 Transposase; Region: HTH_Tnp_1; pfam01527 340100007484 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 340100007485 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100007486 C-terminal domain interface [polypeptide binding]; other site 340100007487 GSH binding site (G-site) [chemical binding]; other site 340100007488 dimer interface [polypeptide binding]; other site 340100007489 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100007490 dimer interface [polypeptide binding]; other site 340100007491 N-terminal domain interface [polypeptide binding]; other site 340100007492 substrate binding pocket (H-site) [chemical binding]; other site 340100007493 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100007494 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100007495 The 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 340100007496 dimerization interface [polypeptide binding]; other site 340100007497 acetylornithine deacetylase; Provisional; Region: PRK06837 340100007498 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like2; cd03895 340100007499 metal binding site [ion binding]; metal-binding site 340100007500 dimer interface [polypeptide binding]; other site 340100007501 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 340100007502 TOMM system kinase/cyclase fusion protein; Region: TOMM_kin_cyc; TIGR03903 340100007503 AAA ATPase domain; Region: AAA_16; pfam13191 340100007504 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 340100007505 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 340100007506 Protein of unknown function (DUF770); Region: DUF770; pfam05591 340100007507 type VI secretion protein, EvpB/VC_A0108 family; Region: VI_chp_2; TIGR03355 340100007508 Protein of unknown function (DUF877); Region: DUF877; pfam05943 340100007509 type VI secretion system effector, Hcp1 family; Region: VI_effect_Hcp1; TIGR03344 340100007510 type VI secretion system lysozyme-like protein; Region: VI_zyme; TIGR03357 340100007511 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 340100007512 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 340100007513 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 340100007514 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 340100007515 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 340100007516 Clp amino terminal domain; Region: Clp_N; pfam02861 340100007517 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 340100007518 Walker A motif; other site 340100007519 ATP binding site [chemical binding]; other site 340100007520 Walker B motif; other site 340100007521 arginine finger; other site 340100007522 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 340100007523 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 340100007524 Walker A motif; other site 340100007525 ATP binding site [chemical binding]; other site 340100007526 Walker B motif; other site 340100007527 arginine finger; other site 340100007528 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 340100007529 Rhs element Vgr protein; Region: vgr_GE; TIGR01646 340100007530 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 340100007531 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340100007532 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; pfam09937 340100007533 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100007534 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100007535 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100007536 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340100007537 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340100007538 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 340100007539 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 340100007540 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 340100007541 type VI secretion protein, VC_A0114 family; Region: VI_chp_4; TIGR03353 340100007542 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 340100007543 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 340100007544 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 340100007545 Protein of unknown function DUF72; Region: DUF72; pfam01904 340100007546 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 340100007547 dimer interface [polypeptide binding]; other site 340100007548 phosphorylation site [posttranslational modification] 340100007549 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 340100007550 ATP binding site [chemical binding]; other site 340100007551 Mg2+ binding site [ion binding]; other site 340100007552 G-X-G motif; other site 340100007553 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100007554 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100007555 active site 340100007556 phosphorylation site [posttranslational modification] 340100007557 intermolecular recognition site; other site 340100007558 dimerization interface [polypeptide binding]; other site 340100007559 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 340100007560 DNA binding site [nucleotide binding] 340100007561 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 340100007562 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 340100007563 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 340100007564 Moco binding site; other site 340100007565 metal coordination site [ion binding]; other site 340100007566 methionine sulfoxide reductase B; Provisional; Region: PRK00222 340100007567 SelR domain; Region: SelR; pfam01641 340100007568 methionine sulfoxide reductase A; Provisional; Region: PRK13014 340100007569 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 340100007570 metal-binding site 340100007571 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 340100007572 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 340100007573 XdhC Rossmann domain; Region: XdhC_C; pfam13478 340100007574 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100007575 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100007576 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100007577 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100007578 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100007579 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100007580 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100007581 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100007582 Cytochrome c; Region: Cytochrom_C; pfam00034 340100007583 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 340100007584 Ligand Binding Site [chemical binding]; other site 340100007585 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 340100007586 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 340100007587 active site 340100007588 Zn binding site [ion binding]; other site 340100007589 DoxX; Region: DoxX; pfam07681 340100007590 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100007591 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 340100007592 catalytic triad [active] 340100007593 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 340100007594 ArsC family; Region: ArsC; pfam03960 340100007595 catalytic residues [active] 340100007596 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100007597 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100007598 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 340100007599 TPR repeat; Region: TPR_11; pfam13414 340100007600 binding surface 340100007601 TPR motif; other site 340100007602 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 340100007603 catalytic residues [active] 340100007604 dimer interface [polypeptide binding]; other site 340100007605 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100007606 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 340100007607 dimerization interface [polypeptide binding]; other site 340100007608 putative DNA binding site [nucleotide binding]; other site 340100007609 putative Zn2+ binding site [ion binding]; other site 340100007610 AsnC family; Region: AsnC_trans_reg; pfam01037 340100007611 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100007612 EamA-like transporter family; Region: EamA; pfam00892 340100007613 EamA-like transporter family; Region: EamA; pfam00892 340100007614 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100007615 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 340100007616 C-terminal domain interface [polypeptide binding]; other site 340100007617 GSH binding site (G-site) [chemical binding]; other site 340100007618 dimer interface [polypeptide binding]; other site 340100007619 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 340100007620 N-terminal domain interface [polypeptide binding]; other site 340100007621 putative dimer interface [polypeptide binding]; other site 340100007622 active site 340100007623 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 340100007624 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 340100007625 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 340100007626 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 340100007627 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 340100007628 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 340100007629 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 340100007630 NAD(P) binding site [chemical binding]; other site 340100007631 agmatinase; Region: agmatinase; TIGR01230 340100007632 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 340100007633 putative active site [active] 340100007634 putative metal binding site [ion binding]; other site 340100007635 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100007636 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100007637 Walker A/P-loop; other site 340100007638 ATP binding site [chemical binding]; other site 340100007639 Q-loop/lid; other site 340100007640 ABC transporter signature motif; other site 340100007641 Walker B; other site 340100007642 D-loop; other site 340100007643 H-loop/switch region; other site 340100007644 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100007645 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 340100007646 dimer interface [polypeptide binding]; other site 340100007647 conserved gate region; other site 340100007648 putative PBP binding loops; other site 340100007649 ABC-ATPase subunit interface; other site 340100007650 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 340100007651 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100007652 substrate binding pocket [chemical binding]; other site 340100007653 membrane-bound complex binding site; other site 340100007654 hinge residues; other site 340100007655 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100007656 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 340100007657 putative DNA binding site [nucleotide binding]; other site 340100007658 putative Zn2+ binding site [ion binding]; other site 340100007659 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100007660 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 340100007661 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 340100007662 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 340100007663 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 340100007664 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 340100007665 active site 340100007666 DNA polymerase III subunit delta'; Validated; Region: PRK06964 340100007667 DNA polymerase III subunit delta'; Validated; Region: PRK08485 340100007668 thymidylate kinase; Validated; Region: tmk; PRK00698 340100007669 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 340100007670 TMP-binding site; other site 340100007671 ATP-binding site [chemical binding]; other site 340100007672 YceG-like family; Region: YceG; pfam02618 340100007673 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 340100007674 dimerization interface [polypeptide binding]; other site 340100007675 putative global regulator; Reviewed; Region: PRK09559 340100007676 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 340100007677 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 340100007678 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 340100007679 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 340100007680 CoenzymeA binding site [chemical binding]; other site 340100007681 subunit interaction site [polypeptide binding]; other site 340100007682 PHB binding site; other site 340100007683 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100007684 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 340100007685 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 340100007686 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 340100007687 substrate binding site [chemical binding]; other site 340100007688 oxyanion hole (OAH) forming residues; other site 340100007689 trimer interface [polypeptide binding]; other site 340100007690 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 340100007691 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100007692 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100007693 active site 340100007694 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 340100007695 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 340100007696 putative coenzyme Q binding site [chemical binding]; other site 340100007697 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 340100007698 SmpB-tmRNA interface; other site 340100007699 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 340100007700 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 340100007701 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 340100007702 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 340100007703 catalytic triad [active] 340100007704 phosphoenolpyruvate synthase; Validated; Region: PRK06464 340100007705 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 340100007706 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 340100007707 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 340100007708 PEP synthetase regulatory protein; Provisional; Region: PRK05339 340100007709 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 340100007710 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 340100007711 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 340100007712 RNA/DNA hybrid binding site [nucleotide binding]; other site 340100007713 active site 340100007714 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 340100007715 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 340100007716 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 340100007717 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 340100007718 active site 340100007719 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 340100007720 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 340100007721 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 340100007722 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 340100007723 trimer interface [polypeptide binding]; other site 340100007724 active site 340100007725 UDP-GlcNAc binding site [chemical binding]; other site 340100007726 lipid binding site [chemical binding]; lipid-binding site 340100007727 periplasmic chaperone; Provisional; Region: PRK10780 340100007728 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 340100007729 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 340100007730 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 340100007731 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 340100007732 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 340100007733 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 340100007734 Surface antigen; Region: Bac_surface_Ag; pfam01103 340100007735 zinc metallopeptidase RseP; Provisional; Region: PRK10779 340100007736 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 340100007737 active site 340100007738 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 340100007739 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 340100007740 putative substrate binding region [chemical binding]; other site 340100007741 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 340100007742 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 340100007743 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 340100007744 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 340100007745 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 340100007746 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 340100007747 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14836 340100007748 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 340100007749 catalytic residue [active] 340100007750 putative FPP diphosphate binding site; other site 340100007751 putative FPP binding hydrophobic cleft; other site 340100007752 dimer interface [polypeptide binding]; other site 340100007753 putative IPP diphosphate binding site; other site 340100007754 ribosome recycling factor; Reviewed; Region: frr; PRK00083 340100007755 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 340100007756 hinge region; other site 340100007757 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 340100007758 putative nucleotide binding site [chemical binding]; other site 340100007759 uridine monophosphate binding site [chemical binding]; other site 340100007760 homohexameric interface [polypeptide binding]; other site 340100007761 elongation factor Ts; Provisional; Region: tsf; PRK09377 340100007762 UBA/TS-N domain; Region: UBA; pfam00627 340100007763 Elongation factor TS; Region: EF_TS; pfam00889 340100007764 Elongation factor TS; Region: EF_TS; pfam00889 340100007765 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 340100007766 rRNA interaction site [nucleotide binding]; other site 340100007767 S8 interaction site; other site 340100007768 putative laminin-1 binding site; other site 340100007769 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 340100007770 active site 340100007771 PII uridylyl-transferase; Provisional; Region: PRK03059 340100007772 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 340100007773 metal binding triad; other site 340100007774 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 340100007775 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 340100007776 Zn2+ binding site [ion binding]; other site 340100007777 Mg2+ binding site [ion binding]; other site 340100007778 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 340100007779 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 340100007780 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 340100007781 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100007782 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100007783 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 340100007784 catalytic triad [active] 340100007785 dimer interface [polypeptide binding]; other site 340100007786 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100007787 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 340100007788 metal-binding site [ion binding] 340100007789 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 340100007790 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 340100007791 metal-binding site [ion binding] 340100007792 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340100007793 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 340100007794 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 340100007795 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 340100007796 DNA binding residues [nucleotide binding] 340100007797 dimer interface [polypeptide binding]; other site 340100007798 copper binding site [ion binding]; other site 340100007799 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 340100007800 TRAM domain; Region: TRAM; cl01282 340100007801 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100007802 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100007803 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 340100007804 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 340100007805 active site 340100007806 catalytic site [active] 340100007807 substrate binding site [chemical binding]; other site 340100007808 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 340100007809 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 340100007810 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100007811 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100007812 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 340100007813 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 340100007814 S-adenosylmethionine binding site [chemical binding]; other site 340100007815 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 340100007816 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 340100007817 UGMP family protein; Validated; Region: PRK09604 340100007818 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 340100007819 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 340100007820 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 340100007821 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 340100007822 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 340100007823 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 340100007824 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 340100007825 catalytic residues [active] 340100007826 Uncharacterized conserved protein [Function unknown]; Region: COG1739 340100007827 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 340100007828 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 340100007829 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 340100007830 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 340100007831 substrate binding pocket [chemical binding]; other site 340100007832 membrane-bound complex binding site; other site 340100007833 hinge residues; other site 340100007834 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 340100007835 dimer interface [polypeptide binding]; other site 340100007836 conserved gate region; other site 340100007837 putative PBP binding loops; other site 340100007838 ABC-ATPase subunit interface; other site 340100007839 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100007840 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 340100007841 substrate binding pocket [chemical binding]; other site 340100007842 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100007843 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 340100007844 Walker A/P-loop; other site 340100007845 ATP binding site [chemical binding]; other site 340100007846 Q-loop/lid; other site 340100007847 ABC transporter signature motif; other site 340100007848 Walker B; other site 340100007849 D-loop; other site 340100007850 H-loop/switch region; other site 340100007851 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 340100007852 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100007853 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100007854 ABC transporter; Region: ABC_tran_2; pfam12848 340100007855 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100007856 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100007857 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100007858 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 340100007859 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100007860 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100007861 enoyl-CoA hydratase; Provisional; Region: PRK05995 340100007862 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 340100007863 substrate binding site [chemical binding]; other site 340100007864 oxyanion hole (OAH) forming residues; other site 340100007865 trimer interface [polypeptide binding]; other site 340100007866 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 340100007867 dimer interface [polypeptide binding]; other site 340100007868 catalytic triad [active] 340100007869 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 340100007870 nucleoside/Zn binding site; other site 340100007871 dimer interface [polypeptide binding]; other site 340100007872 catalytic motif [active] 340100007873 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 340100007874 motif II; other site 340100007875 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12671 340100007876 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 340100007877 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 340100007878 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 340100007879 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 340100007880 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 340100007881 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 340100007882 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 340100007883 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 340100007884 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 340100007885 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100007886 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100007887 AAA domain; Region: AAA_23; pfam13476 340100007888 Walker A/P-loop; other site 340100007889 ATP binding site [chemical binding]; other site 340100007890 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 340100007891 active site 340100007892 metal binding site [ion binding]; metal-binding site 340100007893 DNA binding site [nucleotide binding] 340100007894 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100007895 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100007896 hydroxyglutarate oxidase; Provisional; Region: PRK11728 340100007897 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 340100007898 putative DNA binding site [nucleotide binding]; other site 340100007899 putative Zn2+ binding site [ion binding]; other site 340100007900 AsnC family; Region: AsnC_trans_reg; pfam01037 340100007901 Protein of unknown function (DUF502); Region: DUF502; pfam04367 340100007902 transglutaminase; Provisional; Region: tgl; PRK03187 340100007903 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100007904 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 340100007905 Predicted small integral membrane protein (DUF2160); Region: DUF2160; pfam09928 340100007906 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 340100007907 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 340100007908 dimer interface [polypeptide binding]; other site 340100007909 conserved gate region; other site 340100007910 putative PBP binding loops; other site 340100007911 ABC-ATPase subunit interface; other site 340100007912 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 340100007913 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 340100007914 dimer interface [polypeptide binding]; other site 340100007915 putative PBP binding loops; other site 340100007916 ABC-ATPase subunit interface; other site 340100007917 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 340100007918 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 340100007919 Walker A/P-loop; other site 340100007920 ATP binding site [chemical binding]; other site 340100007921 Q-loop/lid; other site 340100007922 ABC transporter signature motif; other site 340100007923 Walker B; other site 340100007924 D-loop; other site 340100007925 H-loop/switch region; other site 340100007926 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 340100007927 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100007928 Walker A/P-loop; other site 340100007929 ATP binding site [chemical binding]; other site 340100007930 Q-loop/lid; other site 340100007931 ABC transporter signature motif; other site 340100007932 Walker B; other site 340100007933 D-loop; other site 340100007934 H-loop/switch region; other site 340100007935 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 340100007936 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 340100007937 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 340100007938 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 340100007939 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100007940 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100007941 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 340100007942 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100007943 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100007944 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340100007945 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 340100007946 Walker A/P-loop; other site 340100007947 ATP binding site [chemical binding]; other site 340100007948 Q-loop/lid; other site 340100007949 ABC transporter signature motif; other site 340100007950 Walker B; other site 340100007951 D-loop; other site 340100007952 H-loop/switch region; other site 340100007953 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 340100007954 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 340100007955 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 340100007956 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 340100007957 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100007958 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 340100007959 putative deacylase active site [active] 340100007960 NRDE protein; Region: NRDE; cl01315 340100007961 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 340100007962 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 340100007963 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 340100007964 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 340100007965 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 340100007966 active site 340100007967 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100007968 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100007969 class II aldolase/adducin domain protein; Provisional; Region: PRK07090 340100007970 intersubunit interface [polypeptide binding]; other site 340100007971 active site 340100007972 Zn2+ binding site [ion binding]; other site 340100007973 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 340100007974 sequence-specific DNA binding site [nucleotide binding]; other site 340100007975 salt bridge; other site 340100007976 Cupin domain; Region: Cupin_2; pfam07883 340100007977 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100007978 MarR family; Region: MarR_2; pfam12802 340100007979 Fusaric acid resistance protein family; Region: FUSC; pfam04632 340100007980 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 340100007981 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 340100007982 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 340100007983 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100007984 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100007985 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 340100007986 putative hydrolase; Provisional; Region: PRK11460 340100007987 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 340100007988 Uncharacterized conserved protein [Function unknown]; Region: COG4544 340100007989 DNA Polymerase Y-family; Region: PolY_like; cd03468 340100007990 active site 340100007991 DNA binding site [nucleotide binding] 340100007992 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 340100007993 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 340100007994 putative active site [active] 340100007995 putative PHP Thumb interface [polypeptide binding]; other site 340100007996 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 340100007997 generic binding surface II; other site 340100007998 generic binding surface I; other site 340100007999 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 340100008000 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 340100008001 hydroxyglutarate oxidase; Provisional; Region: PRK11728 340100008002 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100008003 Transcriptional regulator; Region: Rrf2; cl17282 340100008004 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 340100008005 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 340100008006 heme-binding site [chemical binding]; other site 340100008007 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 340100008008 FAD binding pocket [chemical binding]; other site 340100008009 FAD binding motif [chemical binding]; other site 340100008010 phosphate binding motif [ion binding]; other site 340100008011 beta-alpha-beta structure motif; other site 340100008012 NAD binding pocket [chemical binding]; other site 340100008013 Heme binding pocket [chemical binding]; other site 340100008014 Yqey-like protein; Region: YqeY; pfam09424 340100008015 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 340100008016 active site 340100008017 DNA polymerase IV; Validated; Region: PRK02406 340100008018 DNA binding site [nucleotide binding] 340100008019 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 340100008020 CoenzymeA binding site [chemical binding]; other site 340100008021 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 340100008022 subunit interaction site [polypeptide binding]; other site 340100008023 PHB binding site; other site 340100008024 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 340100008025 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 340100008026 Transglycosylase; Region: Transgly; pfam00912 340100008027 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 340100008028 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 340100008029 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 340100008030 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 340100008031 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 340100008032 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100008033 active site 340100008034 catalytic tetrad [active] 340100008035 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100008036 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 340100008037 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 340100008038 Walker A/P-loop; other site 340100008039 ATP binding site [chemical binding]; other site 340100008040 Q-loop/lid; other site 340100008041 ABC transporter signature motif; other site 340100008042 Walker B; other site 340100008043 D-loop; other site 340100008044 H-loop/switch region; other site 340100008045 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 340100008046 iron-sulfur cluster [ion binding]; other site 340100008047 [2Fe-2S] cluster binding site [ion binding]; other site 340100008048 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 340100008049 dimerization interface [polypeptide binding]; other site 340100008050 putative active cleft [active] 340100008051 coproporphyrinogen III oxidase; Validated; Region: PRK05628 340100008052 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100008053 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 340100008054 dimer interface [polypeptide binding]; other site 340100008055 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100008056 metal binding site [ion binding]; metal-binding site 340100008057 MarR family; Region: MarR_2; cl17246 340100008058 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 340100008059 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 340100008060 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 340100008061 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 340100008062 tetramer interface [polypeptide binding]; other site 340100008063 catalytic Zn binding site [ion binding]; other site 340100008064 NADP binding site [chemical binding]; other site 340100008065 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 340100008066 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 340100008067 DNA binding residues [nucleotide binding] 340100008068 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 340100008069 IHF - DNA interface [nucleotide binding]; other site 340100008070 IHF dimer interface [polypeptide binding]; other site 340100008071 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 340100008072 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 340100008073 putative tRNA-binding site [nucleotide binding]; other site 340100008074 B3/4 domain; Region: B3_4; pfam03483 340100008075 tRNA synthetase B5 domain; Region: B5; smart00874 340100008076 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 340100008077 dimer interface [polypeptide binding]; other site 340100008078 motif 1; other site 340100008079 motif 3; other site 340100008080 motif 2; other site 340100008081 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 340100008082 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 340100008083 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 340100008084 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 340100008085 dimer interface [polypeptide binding]; other site 340100008086 motif 1; other site 340100008087 active site 340100008088 motif 2; other site 340100008089 motif 3; other site 340100008090 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 340100008091 23S rRNA binding site [nucleotide binding]; other site 340100008092 L21 binding site [polypeptide binding]; other site 340100008093 L13 binding site [polypeptide binding]; other site 340100008094 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 340100008095 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 340100008096 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 340100008097 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 340100008098 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 340100008099 Membrane fusogenic activity; Region: BMFP; pfam04380 340100008100 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 340100008101 Nitrogen regulatory protein P-II; Region: P-II; smart00938 340100008102 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 340100008103 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100008104 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100008105 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 340100008106 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100008107 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 340100008108 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100008109 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100008110 Walker A/P-loop; other site 340100008111 ATP binding site [chemical binding]; other site 340100008112 Q-loop/lid; other site 340100008113 ABC transporter signature motif; other site 340100008114 Walker B; other site 340100008115 D-loop; other site 340100008116 H-loop/switch region; other site 340100008117 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100008118 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100008119 Walker A/P-loop; other site 340100008120 ATP binding site [chemical binding]; other site 340100008121 Q-loop/lid; other site 340100008122 ABC transporter signature motif; other site 340100008123 Walker B; other site 340100008124 D-loop; other site 340100008125 H-loop/switch region; other site 340100008126 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100008127 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 340100008128 TM-ABC transporter signature motif; other site 340100008129 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100008130 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 340100008131 TM-ABC transporter signature motif; other site 340100008132 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100008133 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 340100008134 dimerization interface [polypeptide binding]; other site 340100008135 ligand binding site [chemical binding]; other site 340100008136 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 340100008137 Predicted transcriptional regulator [Transcription]; Region: COG3905 340100008138 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 340100008139 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 340100008140 Glutamate binding site [chemical binding]; other site 340100008141 NAD binding site [chemical binding]; other site 340100008142 catalytic residues [active] 340100008143 Protein of unknown function (DUF330); Region: DUF330; pfam03886 340100008144 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 340100008145 mce related protein; Region: MCE; pfam02470 340100008146 mce related protein; Region: MCE; pfam02470 340100008147 mce related protein; Region: MCE; pfam02470 340100008148 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 340100008149 Paraquat-inducible protein A; Region: PqiA; pfam04403 340100008150 Paraquat-inducible protein A; Region: PqiA; pfam04403 340100008151 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 340100008152 Clp amino terminal domain; Region: Clp_N; pfam02861 340100008153 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 340100008154 Walker A motif; other site 340100008155 ATP binding site [chemical binding]; other site 340100008156 Walker B motif; other site 340100008157 arginine finger; other site 340100008158 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 340100008159 Walker A motif; other site 340100008160 ATP binding site [chemical binding]; other site 340100008161 Walker B motif; other site 340100008162 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 340100008163 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 340100008164 Transglycosylase; Region: Transgly; pfam00912 340100008165 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 340100008166 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 340100008167 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 340100008168 MG2 domain; Region: A2M_N; pfam01835 340100008169 Alpha-2-macroglobulin family; Region: A2M; pfam00207 340100008170 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 340100008171 surface patch; other site 340100008172 thioester region; other site 340100008173 specificity defining residues; other site 340100008174 ATP-dependent Clp protease adaptor protein ClpS; Reviewed; Region: clpS; PRK00033 340100008175 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 340100008176 DNA-binding site [nucleotide binding]; DNA binding site 340100008177 RNA-binding motif; other site 340100008178 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 340100008179 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 340100008180 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 340100008181 dimer interface [polypeptide binding]; other site 340100008182 active site 340100008183 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 340100008184 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 340100008185 putative ion selectivity filter; other site 340100008186 putative pore gating glutamate residue; other site 340100008187 putative H+/Cl- coupling transport residue; other site 340100008188 superoxide dismutase; Provisional; Region: PRK10543 340100008189 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 340100008190 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 340100008191 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 340100008192 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 340100008193 generic binding surface II; other site 340100008194 generic binding surface I; other site 340100008195 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 340100008196 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 340100008197 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 340100008198 Uncharacterized conserved protein [Function unknown]; Region: COG2835 340100008199 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 340100008200 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 340100008201 Ligand binding site; other site 340100008202 oligomer interface; other site 340100008203 adenylate kinase; Reviewed; Region: adk; PRK00279 340100008204 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 340100008205 AMP-binding site [chemical binding]; other site 340100008206 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 340100008207 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 340100008208 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 340100008209 NAD binding site [chemical binding]; other site 340100008210 homodimer interface [polypeptide binding]; other site 340100008211 homotetramer interface [polypeptide binding]; other site 340100008212 active site 340100008213 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 340100008214 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 340100008215 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 340100008216 FecR protein; Region: FecR; pfam04773 340100008217 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 340100008218 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional; Region: PRK10558 340100008219 dihydroxy-acid dehydratase; Validated; Region: PRK06131 340100008220 Malate/L-lactate dehydrogenases [Energy production and conversion]; Region: COG2055 340100008221 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100008222 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008223 DNA-binding site [nucleotide binding]; DNA binding site 340100008224 FCD domain; Region: FCD; pfam07729 340100008225 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 340100008226 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 340100008227 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100008228 inhibitor site; inhibition site 340100008229 active site 340100008230 dimer interface [polypeptide binding]; other site 340100008231 catalytic residue [active] 340100008232 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100008233 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100008234 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 340100008235 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 340100008236 putative ligand binding site [chemical binding]; other site 340100008237 NAD binding site [chemical binding]; other site 340100008238 catalytic site [active] 340100008239 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 340100008240 ornithine carbamoyltransferase; Provisional; Region: PRK00779 340100008241 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 340100008242 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 340100008243 argininosuccinate synthase; Validated; Region: PRK05370 340100008244 argininosuccinate synthase; Provisional; Region: PRK13820 340100008245 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 340100008246 potassium uptake protein; Region: kup; TIGR00794 340100008247 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100008248 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 340100008249 dimer interface [polypeptide binding]; other site 340100008250 phosphorylation site [posttranslational modification] 340100008251 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 340100008252 ATP binding site [chemical binding]; other site 340100008253 G-X-G motif; other site 340100008254 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100008255 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100008256 active site 340100008257 phosphorylation site [posttranslational modification] 340100008258 intermolecular recognition site; other site 340100008259 dimerization interface [polypeptide binding]; other site 340100008260 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 340100008261 DNA binding site [nucleotide binding] 340100008262 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 340100008263 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 340100008264 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 340100008265 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 340100008266 Rdx family; Region: Rdx; cl01407 340100008267 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100008268 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 340100008269 ATP binding site [chemical binding]; other site 340100008270 G-X-G motif; other site 340100008271 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 340100008272 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100008273 active site 340100008274 phosphorylation site [posttranslational modification] 340100008275 intermolecular recognition site; other site 340100008276 dimerization interface [polypeptide binding]; other site 340100008277 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100008278 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 340100008279 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 340100008280 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 340100008281 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100008282 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 340100008283 D-pathway; other site 340100008284 Putative ubiquinol binding site [chemical binding]; other site 340100008285 Low-spin heme (heme b) binding site [chemical binding]; other site 340100008286 Putative water exit pathway; other site 340100008287 Binuclear center (heme o3/CuB) [ion binding]; other site 340100008288 K-pathway; other site 340100008289 Putative proton exit pathway; other site 340100008290 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 340100008291 Subunit I/III interface [polypeptide binding]; other site 340100008292 Subunit III/IV interface [polypeptide binding]; other site 340100008293 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 340100008294 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 340100008295 IHF dimer interface [polypeptide binding]; other site 340100008296 IHF - DNA interface [nucleotide binding]; other site 340100008297 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 340100008298 hypothetical protein; Provisional; Region: PRK05939 340100008299 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 340100008300 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100008301 catalytic residue [active] 340100008302 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 340100008303 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 340100008304 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 340100008305 ribonuclease R; Region: RNase_R; TIGR02063 340100008306 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 340100008307 RNB domain; Region: RNB; pfam00773 340100008308 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 340100008309 RNA binding site [nucleotide binding]; other site 340100008310 DTW domain; Region: DTW; cl01221 340100008311 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100008312 Coenzyme A binding pocket [chemical binding]; other site 340100008313 Predicted permeases [General function prediction only]; Region: COG0679 340100008314 arsenical pump membrane protein; Provisional; Region: PRK15445 340100008315 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 340100008316 transmembrane helices; other site 340100008317 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 340100008318 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 340100008319 active site 340100008320 FMN binding site [chemical binding]; other site 340100008321 substrate binding site [chemical binding]; other site 340100008322 3Fe-4S cluster binding site [ion binding]; other site 340100008323 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 340100008324 PLD-like domain; Region: PLDc_2; pfam13091 340100008325 putative active site [active] 340100008326 catalytic site [active] 340100008327 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 340100008328 PLD-like domain; Region: PLDc_2; pfam13091 340100008329 putative active site [active] 340100008330 catalytic site [active] 340100008331 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 340100008332 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 340100008333 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 340100008334 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 340100008335 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 340100008336 Protein of unknown function (DUF3053); Region: DUF3053; pfam11254 340100008337 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 340100008338 Cytochrome C' Region: Cytochrom_C_2; pfam01322 340100008339 adenylosuccinate lyase; Provisional; Region: PRK09285 340100008340 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 340100008341 tetramer interface [polypeptide binding]; other site 340100008342 active site 340100008343 putative glutathione S-transferase; Provisional; Region: PRK10357 340100008344 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 340100008345 putative C-terminal domain interface [polypeptide binding]; other site 340100008346 putative GSH binding site (G-site) [chemical binding]; other site 340100008347 putative dimer interface [polypeptide binding]; other site 340100008348 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 340100008349 dimer interface [polypeptide binding]; other site 340100008350 N-terminal domain interface [polypeptide binding]; other site 340100008351 putative substrate binding pocket (H-site) [chemical binding]; other site 340100008352 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100008353 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 340100008354 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 340100008355 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100008356 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100008357 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 340100008358 dimerization interface [polypeptide binding]; other site 340100008359 substrate binding pocket [chemical binding]; other site 340100008360 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100008361 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 340100008362 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 340100008363 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 340100008364 ligand binding site [chemical binding]; other site 340100008365 homodimer interface [polypeptide binding]; other site 340100008366 NAD(P) binding site [chemical binding]; other site 340100008367 trimer interface B [polypeptide binding]; other site 340100008368 trimer interface A [polypeptide binding]; other site 340100008369 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 340100008370 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 340100008371 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 340100008372 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 340100008373 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 340100008374 Cysteine-rich domain; Region: CCG; pfam02754 340100008375 Cysteine-rich domain; Region: CCG; pfam02754 340100008376 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 340100008377 FAD binding domain; Region: FAD_binding_4; pfam01565 340100008378 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 340100008379 FAD binding domain; Region: FAD_binding_4; pfam01565 340100008380 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100008381 FAD binding domain; Region: FAD_binding_4; pfam01565 340100008382 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 340100008383 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340100008384 protease TldD; Provisional; Region: tldD; PRK10735 340100008385 nitrilase; Region: PLN02798 340100008386 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 340100008387 putative active site [active] 340100008388 catalytic triad [active] 340100008389 dimer interface [polypeptide binding]; other site 340100008390 H-NS histone family; Region: Histone_HNS; pfam00816 340100008391 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 340100008392 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 340100008393 aminopeptidase N; Provisional; Region: pepN; PRK14015 340100008394 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 340100008395 active site 340100008396 Zn binding site [ion binding]; other site 340100008397 fructose-1,6-bisphosphatase family protein; Region: PLN02628 340100008398 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 340100008399 AMP binding site [chemical binding]; other site 340100008400 metal binding site [ion binding]; metal-binding site 340100008401 active site 340100008402 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 340100008403 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 340100008404 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 340100008405 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008406 catalytic residue [active] 340100008407 homoserine dehydrogenase; Provisional; Region: PRK06349 340100008408 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 340100008409 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 340100008410 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 340100008411 aminotransferase; Validated; Region: PRK08175 340100008412 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 340100008413 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008414 homodimer interface [polypeptide binding]; other site 340100008415 catalytic residue [active] 340100008416 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 340100008417 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100008418 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 340100008419 catalytic triad [active] 340100008420 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 340100008421 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 340100008422 putative active site [active] 340100008423 PhoH-like protein; Region: PhoH; pfam02562 340100008424 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 340100008425 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 340100008426 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 340100008427 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 340100008428 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 340100008429 hypothetical protein; Provisional; Region: PRK07907 340100008430 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 340100008431 metal binding site [ion binding]; metal-binding site 340100008432 putative dimer interface [polypeptide binding]; other site 340100008433 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100008434 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 340100008435 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 340100008436 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 340100008437 dimerization interface [polypeptide binding]; other site 340100008438 ATP binding site [chemical binding]; other site 340100008439 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 340100008440 dimerization interface [polypeptide binding]; other site 340100008441 ATP binding site [chemical binding]; other site 340100008442 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 340100008443 putative active site [active] 340100008444 catalytic triad [active] 340100008445 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 340100008446 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 340100008447 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 340100008448 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 340100008449 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 340100008450 active site 340100008451 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 340100008452 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 340100008453 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 340100008454 ComEC family competence protein; Provisional; Region: PRK11539 340100008455 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 340100008456 Competence protein; Region: Competence; pfam03772 340100008457 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 340100008458 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 340100008459 active site 340100008460 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 340100008461 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 340100008462 Walker A/P-loop; other site 340100008463 ATP binding site [chemical binding]; other site 340100008464 Q-loop/lid; other site 340100008465 ABC transporter signature motif; other site 340100008466 Walker B; other site 340100008467 D-loop; other site 340100008468 H-loop/switch region; other site 340100008469 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 340100008470 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 340100008471 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 340100008472 DHH family; Region: DHH; pfam01368 340100008473 DHHA1 domain; Region: DHHA1; pfam02272 340100008474 peptide chain release factor 2; Validated; Region: prfB; PRK00578 340100008475 This domain is found in peptide chain release factors; Region: PCRF; smart00937 340100008476 RF-1 domain; Region: RF-1; pfam00472 340100008477 short chain dehydrogenase; Provisional; Region: PRK07023 340100008478 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008479 NAD(P) binding site [chemical binding]; other site 340100008480 active site 340100008481 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 340100008482 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 340100008483 dimer interface [polypeptide binding]; other site 340100008484 putative anticodon binding site; other site 340100008485 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 340100008486 motif 1; other site 340100008487 active site 340100008488 motif 2; other site 340100008489 motif 3; other site 340100008490 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 340100008491 substrate binding site [chemical binding]; other site 340100008492 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 340100008493 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 340100008494 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 340100008495 catalytic loop [active] 340100008496 iron binding site [ion binding]; other site 340100008497 chaperone protein HscA; Provisional; Region: hscA; PRK05183 340100008498 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 340100008499 nucleotide binding site [chemical binding]; other site 340100008500 putative NEF/HSP70 interaction site [polypeptide binding]; other site 340100008501 SBD interface [polypeptide binding]; other site 340100008502 co-chaperone HscB; Provisional; Region: hscB; PRK03578 340100008503 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 340100008504 HSP70 interaction site [polypeptide binding]; other site 340100008505 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 340100008506 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 340100008507 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 340100008508 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 340100008509 trimerization site [polypeptide binding]; other site 340100008510 active site 340100008511 cysteine desulfurase; Provisional; Region: PRK14012 340100008512 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 340100008513 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100008514 catalytic residue [active] 340100008515 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 340100008516 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100008517 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 340100008518 Low molecular weight phosphatase family; Region: LMWPc; cd00115 340100008519 active site 340100008520 excinuclease ABC subunit B; Provisional; Region: PRK05298 340100008521 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 340100008522 ATP binding site [chemical binding]; other site 340100008523 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 340100008524 nucleotide binding region [chemical binding]; other site 340100008525 ATP-binding site [chemical binding]; other site 340100008526 Ultra-violet resistance protein B; Region: UvrB; pfam12344 340100008527 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 340100008528 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 340100008529 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008530 homodimer interface [polypeptide binding]; other site 340100008531 catalytic residue [active] 340100008532 LexA repressor; Validated; Region: PRK00215 340100008533 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 340100008534 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 340100008535 Catalytic site [active] 340100008536 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100008537 active site 340100008538 catalytic residues [active] 340100008539 metal binding site [ion binding]; metal-binding site 340100008540 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100008541 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008542 DNA-binding site [nucleotide binding]; DNA binding site 340100008543 FCD domain; Region: FCD; pfam07729 340100008544 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100008545 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100008546 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100008547 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100008548 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100008549 DctM-like transporters; Region: DctM; pfam06808 340100008550 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100008551 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 340100008552 Found in ATP-dependent protease La (LON); Region: LON; smart00464 340100008553 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 340100008554 Walker A motif; other site 340100008555 ATP binding site [chemical binding]; other site 340100008556 Walker B motif; other site 340100008557 arginine finger; other site 340100008558 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 340100008559 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 340100008560 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 340100008561 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 340100008562 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 340100008563 Walker A motif; other site 340100008564 ATP binding site [chemical binding]; other site 340100008565 Walker B motif; other site 340100008566 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 340100008567 Clp protease; Region: CLP_protease; pfam00574 340100008568 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 340100008569 oligomer interface [polypeptide binding]; other site 340100008570 active site residues [active] 340100008571 trigger factor; Provisional; Region: tig; PRK01490 340100008572 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 340100008573 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 340100008574 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 340100008575 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 340100008576 DNA-binding site [nucleotide binding]; DNA binding site 340100008577 RNA-binding motif; other site 340100008578 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 340100008579 DNA-binding site [nucleotide binding]; DNA binding site 340100008580 RNA-binding motif; other site 340100008581 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 340100008582 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 340100008583 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100008584 homodimer interface [polypeptide binding]; other site 340100008585 catalytic residue [active] 340100008586 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 340100008587 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 340100008588 trimer interface [polypeptide binding]; other site 340100008589 active site 340100008590 substrate binding site [chemical binding]; other site 340100008591 CoA binding site [chemical binding]; other site 340100008592 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 340100008593 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 340100008594 metal binding site [ion binding]; metal-binding site 340100008595 dimer interface [polypeptide binding]; other site 340100008596 HemK family putative methylases; Region: hemK_fam; TIGR00536 340100008597 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 340100008598 S-adenosylmethionine binding site [chemical binding]; other site 340100008599 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100008600 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 340100008601 Walker A/P-loop; other site 340100008602 ATP binding site [chemical binding]; other site 340100008603 Q-loop/lid; other site 340100008604 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100008605 ABC transporter; Region: ABC_tran_2; pfam12848 340100008606 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 340100008607 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008608 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100008609 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 340100008610 substrate binding pocket [chemical binding]; other site 340100008611 dimerization interface [polypeptide binding]; other site 340100008612 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100008613 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 340100008614 iron-sulfur cluster [ion binding]; other site 340100008615 [2Fe-2S] cluster binding site [ion binding]; other site 340100008616 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 340100008617 putative alpha subunit interface [polypeptide binding]; other site 340100008618 putative active site [active] 340100008619 putative substrate binding site [chemical binding]; other site 340100008620 Fe binding site [ion binding]; other site 340100008621 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 340100008622 inter-subunit interface; other site 340100008623 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 340100008624 [2Fe-2S] cluster binding site [ion binding]; other site 340100008625 Chorismate mutase type II; Region: CM_2; cl00693 340100008626 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 340100008627 Part of AAA domain; Region: AAA_19; pfam13245 340100008628 Family description; Region: UvrD_C_2; pfam13538 340100008629 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 340100008630 Fatty acid desaturase; Region: FA_desaturase; pfam00487 340100008631 Di-iron ligands [ion binding]; other site 340100008632 Transposase; Region: DDE_Tnp_ISL3; pfam01610 340100008633 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 340100008634 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 340100008635 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 340100008636 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 340100008637 active site 340100008638 substrate binding site [chemical binding]; other site 340100008639 cosubstrate binding site; other site 340100008640 catalytic site [active] 340100008641 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 340100008642 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 340100008643 active site 340100008644 Riboflavin kinase; Region: Flavokinase; smart00904 340100008645 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 340100008646 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100008647 active site 340100008648 HIGH motif; other site 340100008649 nucleotide binding site [chemical binding]; other site 340100008650 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340100008651 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 340100008652 active site 340100008653 KMSKS motif; other site 340100008654 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 340100008655 tRNA binding surface [nucleotide binding]; other site 340100008656 anticodon binding site; other site 340100008657 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 340100008658 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 340100008659 lipoprotein signal peptidase; Provisional; Region: PRK14787 340100008660 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 340100008661 Flavoprotein; Region: Flavoprotein; pfam02441 340100008662 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 340100008663 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100008664 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 340100008665 putative DNA binding site [nucleotide binding]; other site 340100008666 putative Zn2+ binding site [ion binding]; other site 340100008667 AsnC family; Region: AsnC_trans_reg; pfam01037 340100008668 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 340100008669 dUTPase; Region: dUTPase_2; pfam08761 340100008670 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins; Region: NTP-PPase_dUTPase; cd11527 340100008671 active site 340100008672 homodimer interface [polypeptide binding]; other site 340100008673 metal binding site [ion binding]; metal-binding site 340100008674 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100008675 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100008676 Walker A/P-loop; other site 340100008677 ATP binding site [chemical binding]; other site 340100008678 Q-loop/lid; other site 340100008679 ABC transporter signature motif; other site 340100008680 Walker B; other site 340100008681 D-loop; other site 340100008682 H-loop/switch region; other site 340100008683 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 340100008684 dimer interface [polypeptide binding]; other site 340100008685 conserved gate region; other site 340100008686 putative PBP binding loops; other site 340100008687 ABC-ATPase subunit interface; other site 340100008688 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 340100008689 dimer interface [polypeptide binding]; other site 340100008690 conserved gate region; other site 340100008691 putative PBP binding loops; other site 340100008692 ABC-ATPase subunit interface; other site 340100008693 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100008694 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 340100008695 substrate binding pocket [chemical binding]; other site 340100008696 membrane-bound complex binding site; other site 340100008697 hinge residues; other site 340100008698 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100008699 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 340100008700 putative ligand binding site [chemical binding]; other site 340100008701 ornithine cyclodeaminase; Validated; Region: PRK06141 340100008702 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 340100008703 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 340100008704 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 340100008705 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 340100008706 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 340100008707 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 340100008708 dimerization domain swap beta strand [polypeptide binding]; other site 340100008709 regulatory protein interface [polypeptide binding]; other site 340100008710 active site 340100008711 regulatory phosphorylation site [posttranslational modification]; other site 340100008712 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; cl00025 340100008713 active pocket/dimerization site; other site 340100008714 active site 340100008715 phosphorylation site [posttranslational modification] 340100008716 glutathione synthetase; Provisional; Region: PRK05246 340100008717 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 340100008718 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 340100008719 translation initiation factor IF-3; Region: infC; TIGR00168 340100008720 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 340100008721 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 340100008722 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 340100008723 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 340100008724 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 340100008725 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 340100008726 active site 340100008727 dimer interface [polypeptide binding]; other site 340100008728 motif 1; other site 340100008729 motif 2; other site 340100008730 motif 3; other site 340100008731 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 340100008732 anticodon binding site; other site 340100008733 Response regulator receiver domain; Region: Response_reg; pfam00072 340100008734 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100008735 active site 340100008736 phosphorylation site [posttranslational modification] 340100008737 intermolecular recognition site; other site 340100008738 dimerization interface [polypeptide binding]; other site 340100008739 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 340100008740 DNA binding residues [nucleotide binding] 340100008741 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008742 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100008743 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 340100008744 putative effector binding pocket; other site 340100008745 putative dimerization interface [polypeptide binding]; other site 340100008746 short chain dehydrogenase; Provisional; Region: PRK12744 340100008747 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100008748 NAD(P) binding site [chemical binding]; other site 340100008749 active site 340100008750 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 340100008751 O-Antigen ligase; Region: Wzy_C; pfam04932 340100008752 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 340100008753 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 340100008754 DNA-binding site [nucleotide binding]; DNA binding site 340100008755 RNA-binding motif; other site 340100008756 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 340100008757 active site 340100008758 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 340100008759 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 340100008760 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 340100008761 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100008762 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 340100008763 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 340100008764 dimerization interface 3.5A [polypeptide binding]; other site 340100008765 active site 340100008766 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100008767 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 340100008768 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 340100008769 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 340100008770 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100008771 Walker A/P-loop; other site 340100008772 ATP binding site [chemical binding]; other site 340100008773 Q-loop/lid; other site 340100008774 ABC transporter signature motif; other site 340100008775 Walker B; other site 340100008776 D-loop; other site 340100008777 H-loop/switch region; other site 340100008778 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 340100008779 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100008780 Walker A/P-loop; other site 340100008781 ATP binding site [chemical binding]; other site 340100008782 Q-loop/lid; other site 340100008783 ABC transporter signature motif; other site 340100008784 Walker B; other site 340100008785 D-loop; other site 340100008786 H-loop/switch region; other site 340100008787 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100008788 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100008789 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 340100008790 dimer interface [polypeptide binding]; other site 340100008791 conserved gate region; other site 340100008792 putative PBP binding loops; other site 340100008793 ABC-ATPase subunit interface; other site 340100008794 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100008795 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 340100008796 dimer interface [polypeptide binding]; other site 340100008797 conserved gate region; other site 340100008798 putative PBP binding loops; other site 340100008799 ABC-ATPase subunit interface; other site 340100008800 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 340100008801 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100008802 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 340100008803 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100008804 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008805 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100008806 The 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 340100008807 dimerization interface [polypeptide binding]; other site 340100008808 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 340100008809 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 340100008810 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 340100008811 Type II transport protein GspH; Region: GspH; pfam12019 340100008812 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 340100008813 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 340100008814 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 340100008815 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 340100008816 type II secretion system protein J; Region: gspJ; TIGR01711 340100008817 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 340100008818 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 340100008819 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 340100008820 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 340100008821 type II secretion system protein E; Region: type_II_gspE; TIGR02533 340100008822 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 340100008823 Walker A motif; other site 340100008824 ATP binding site [chemical binding]; other site 340100008825 Walker B motif; other site 340100008826 type II secretion system protein D; Region: type_II_gspD; TIGR02517 340100008827 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340100008828 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340100008829 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340100008830 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100008831 type II secretion system protein F; Region: GspF; TIGR02120 340100008832 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 340100008833 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 340100008834 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 340100008835 Nitrogen regulatory protein P-II; Region: P-II; smart00938 340100008836 NAD synthetase; Provisional; Region: PRK13981 340100008837 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 340100008838 multimer interface [polypeptide binding]; other site 340100008839 active site 340100008840 catalytic triad [active] 340100008841 protein interface 1 [polypeptide binding]; other site 340100008842 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 340100008843 homodimer interface [polypeptide binding]; other site 340100008844 NAD binding pocket [chemical binding]; other site 340100008845 ATP binding pocket [chemical binding]; other site 340100008846 Mg binding site [ion binding]; other site 340100008847 active-site loop [active] 340100008848 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 340100008849 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100008850 argininosuccinate lyase; Provisional; Region: PRK00855 340100008851 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 340100008852 active sites [active] 340100008853 tetramer interface [polypeptide binding]; other site 340100008854 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 340100008855 putative FMN binding site [chemical binding]; other site 340100008856 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 340100008857 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 340100008858 DNA binding residues [nucleotide binding] 340100008859 dimer interface [polypeptide binding]; other site 340100008860 putative metal binding site [ion binding]; other site 340100008861 Heavy-metal-associated domain; Region: HMA; pfam00403 340100008862 metal-binding site [ion binding] 340100008863 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 340100008864 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340100008865 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 340100008866 active site 340100008867 motif I; other site 340100008868 motif II; other site 340100008869 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100008870 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 340100008871 substrate binding pocket [chemical binding]; other site 340100008872 membrane-bound complex binding site; other site 340100008873 hinge residues; other site 340100008874 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100008875 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 340100008876 dimer interface [polypeptide binding]; other site 340100008877 conserved gate region; other site 340100008878 putative PBP binding loops; other site 340100008879 ABC-ATPase subunit interface; other site 340100008880 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100008881 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100008882 Walker A/P-loop; other site 340100008883 ATP binding site [chemical binding]; other site 340100008884 Q-loop/lid; other site 340100008885 ABC transporter signature motif; other site 340100008886 Walker B; other site 340100008887 D-loop; other site 340100008888 H-loop/switch region; other site 340100008889 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100008890 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 340100008891 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 340100008892 active site 340100008893 citrylCoA binding site [chemical binding]; other site 340100008894 oxalacetate binding site [chemical binding]; other site 340100008895 coenzyme A binding site [chemical binding]; other site 340100008896 catalytic triad [active] 340100008897 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100008898 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100008899 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 340100008900 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100008901 The 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 340100008902 dimerization interface [polypeptide binding]; other site 340100008903 integrase; Provisional; Region: PRK09692 340100008904 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 340100008905 active site 340100008906 Int/Topo IB signature motif; other site 340100008907 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 340100008908 Uncharacterized conserved protein [Function unknown]; Region: COG4983 340100008909 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 340100008910 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 340100008911 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 340100008912 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 340100008913 putative catalytic site [active] 340100008914 putative phosphate binding site [ion binding]; other site 340100008915 active site 340100008916 metal binding site A [ion binding]; metal-binding site 340100008917 DNA binding site [nucleotide binding] 340100008918 putative AP binding site [nucleotide binding]; other site 340100008919 putative metal binding site B [ion binding]; other site 340100008920 putative inner membrane protein; Provisional; Region: PRK11099 340100008921 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 340100008922 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 340100008923 active site residue [active] 340100008924 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 340100008925 active site residue [active] 340100008926 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 340100008927 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100008928 Predicted transcriptional regulator [Transcription]; Region: COG1959 340100008929 Transcriptional regulator; Region: Rrf2; pfam02082 340100008930 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100008931 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 340100008932 putative substrate translocation pore; other site 340100008933 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 340100008934 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100008935 catalytic residue [active] 340100008936 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 340100008937 dimer interface [polypeptide binding]; other site 340100008938 pyridoxamine kinase; Validated; Region: PRK05756 340100008939 pyridoxal binding site [chemical binding]; other site 340100008940 ATP binding site [chemical binding]; other site 340100008941 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 340100008942 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 340100008943 Walker A/P-loop; other site 340100008944 ATP binding site [chemical binding]; other site 340100008945 Q-loop/lid; other site 340100008946 ABC transporter signature motif; other site 340100008947 Walker B; other site 340100008948 D-loop; other site 340100008949 H-loop/switch region; other site 340100008950 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 340100008951 putative dimer interface [polypeptide binding]; other site 340100008952 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100008953 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100008954 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 340100008955 putative substrate translocation pore; other site 340100008956 Uncharacterized conserved protein [Function unknown]; Region: COG3422 340100008957 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 340100008958 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100008959 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 340100008960 active site pocket [active] 340100008961 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100008962 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100008963 DNA-binding site [nucleotide binding]; DNA binding site 340100008964 UTRA domain; Region: UTRA; pfam07702 340100008965 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 340100008966 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 340100008967 dimer interface [polypeptide binding]; other site 340100008968 conserved gate region; other site 340100008969 putative PBP binding loops; other site 340100008970 ABC-ATPase subunit interface; other site 340100008971 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100008972 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 340100008973 Walker A/P-loop; other site 340100008974 ATP binding site [chemical binding]; other site 340100008975 Q-loop/lid; other site 340100008976 ABC transporter signature motif; other site 340100008977 Walker B; other site 340100008978 D-loop; other site 340100008979 H-loop/switch region; other site 340100008980 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 340100008981 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 340100008982 membrane-bound complex binding site; other site 340100008983 choline dehydrogenase; Validated; Region: PRK02106 340100008984 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 340100008985 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100008986 dihydroxy-acid dehydratase; Validated; Region: PRK06131 340100008987 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100008988 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100008989 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 340100008990 putative dimerization interface [polypeptide binding]; other site 340100008991 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100008992 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 340100008993 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100008994 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 340100008995 putative active site [active] 340100008996 Methyltransferase domain; Region: Methyltransf_23; pfam13489 340100008997 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 340100008998 S-adenosylmethionine binding site [chemical binding]; other site 340100008999 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 340100009000 active site 340100009001 substrate-binding site [chemical binding]; other site 340100009002 metal-binding site [ion binding] 340100009003 GTP binding site [chemical binding]; other site 340100009004 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 340100009005 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 340100009006 cation binding site [ion binding]; other site 340100009007 allantoate amidohydrolase; Reviewed; Region: PRK12890 340100009008 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 340100009009 active site 340100009010 metal binding site [ion binding]; metal-binding site 340100009011 dimer interface [polypeptide binding]; other site 340100009012 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 340100009013 catalytic residues [active] 340100009014 EamA-like transporter family; Region: EamA; pfam00892 340100009015 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 340100009016 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 340100009017 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 340100009018 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 340100009019 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009020 DNA-binding site [nucleotide binding]; DNA binding site 340100009021 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 340100009022 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009023 homodimer interface [polypeptide binding]; other site 340100009024 catalytic residue [active] 340100009025 glutathione reductase; Validated; Region: PRK06116 340100009026 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100009027 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100009028 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100009029 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100009030 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100009031 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340100009032 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 340100009033 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100009034 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 340100009035 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340100009036 4-hydroxybenzoyl-CoA reductase, gamma subunit; Region: 4hydroxCoAred; TIGR03193 340100009037 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 340100009038 catalytic loop [active] 340100009039 iron binding site [ion binding]; other site 340100009040 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100009041 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100009042 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100009043 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 340100009044 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100009045 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100009046 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 340100009047 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009048 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100009049 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 340100009050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3826 340100009051 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 340100009052 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 340100009053 dimer interface [polypeptide binding]; other site 340100009054 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100009055 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 340100009056 putative substrate translocation pore; other site 340100009057 Bacterial protein of unknown function (DUF937); Region: DUF937; pfam06078 340100009058 putative transporter; Provisional; Region: PRK11660 340100009059 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 340100009060 Sulfate transporter family; Region: Sulfate_transp; pfam00916 340100009061 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 340100009062 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 340100009063 ZIP Zinc transporter; Region: Zip; pfam02535 340100009064 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 340100009065 Uncharacterized conserved protein [Function unknown]; Region: COG1432 340100009066 LabA_like proteins; Region: LabA_like; cd06167 340100009067 putative metal binding site [ion binding]; other site 340100009068 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 340100009069 YCII-related domain; Region: YCII; cl00999 340100009070 YCII-related domain; Region: YCII; cl00999 340100009071 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 340100009072 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100009073 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 340100009074 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100009075 Domain of unknown function (DUF4168); Region: DUF4168; pfam13767 340100009076 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 340100009077 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340100009078 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100009079 ligand binding site [chemical binding]; other site 340100009080 Domain of unknown function (DUF4281); Region: DUF4281; pfam14108 340100009081 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100009082 WHG domain; Region: WHG; pfam13305 340100009083 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100009084 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009085 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100009086 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100009087 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100009088 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 340100009089 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100009090 Walker A/P-loop; other site 340100009091 ATP binding site [chemical binding]; other site 340100009092 Q-loop/lid; other site 340100009093 ABC transporter signature motif; other site 340100009094 Walker B; other site 340100009095 D-loop; other site 340100009096 H-loop/switch region; other site 340100009097 SlyX; Region: SlyX; cl01090 340100009098 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 340100009099 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 340100009100 galactarate dehydratase; Region: galactar-dH20; TIGR03248 340100009101 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 340100009102 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 340100009103 enterobactin exporter EntS; Provisional; Region: PRK10489 340100009104 Uncharacterized conserved protein [Function unknown]; Region: COG3791 340100009105 allantoate amidohydrolase; Reviewed; Region: PRK09290 340100009106 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 340100009107 active site 340100009108 metal binding site [ion binding]; metal-binding site 340100009109 dimer interface [polypeptide binding]; other site 340100009110 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009111 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009112 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 340100009113 putative effector binding pocket; other site 340100009114 dimerization interface [polypeptide binding]; other site 340100009115 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 340100009116 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 340100009117 substrate binding site [chemical binding]; other site 340100009118 oxyanion hole (OAH) forming residues; other site 340100009119 trimer interface [polypeptide binding]; other site 340100009120 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100009121 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100009122 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100009123 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 340100009124 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 340100009125 dimer interface [polypeptide binding]; other site 340100009126 active site 340100009127 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100009128 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100009129 active site 340100009130 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 340100009131 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 340100009132 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 340100009133 active site 340100009134 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100009135 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100009136 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100009137 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009138 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009139 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100009140 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009141 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100009142 EamA-like transporter family; Region: EamA; pfam00892 340100009143 EamA-like transporter family; Region: EamA; pfam00892 340100009144 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 340100009145 putative substrate translocation pore; other site 340100009146 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100009147 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 340100009148 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 340100009149 Fe-S cluster binding site [ion binding]; other site 340100009150 active site 340100009151 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100009152 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 340100009153 C-terminal domain interface [polypeptide binding]; other site 340100009154 GSH binding site (G-site) [chemical binding]; other site 340100009155 dimer interface [polypeptide binding]; other site 340100009156 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 340100009157 dimer interface [polypeptide binding]; other site 340100009158 N-terminal domain interface [polypeptide binding]; other site 340100009159 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100009160 MarR family; Region: MarR_2; pfam12802 340100009161 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 340100009162 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100009163 C-terminal domain interface [polypeptide binding]; other site 340100009164 GSH binding site (G-site) [chemical binding]; other site 340100009165 dimer interface [polypeptide binding]; other site 340100009166 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100009167 N-terminal domain interface [polypeptide binding]; other site 340100009168 dimer interface [polypeptide binding]; other site 340100009169 substrate binding pocket (H-site) [chemical binding]; other site 340100009170 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 340100009171 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 340100009172 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 340100009173 dimerization interface [polypeptide binding]; other site 340100009174 putative DNA binding site [nucleotide binding]; other site 340100009175 putative Zn2+ binding site [ion binding]; other site 340100009176 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 340100009177 putative hydrophobic ligand binding site [chemical binding]; other site 340100009178 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 340100009179 putative C-terminal domain interface [polypeptide binding]; other site 340100009180 putative GSH binding site (G-site) [chemical binding]; other site 340100009181 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100009182 putative dimer interface [polypeptide binding]; other site 340100009183 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 340100009184 dimer interface [polypeptide binding]; other site 340100009185 N-terminal domain interface [polypeptide binding]; other site 340100009186 putative substrate binding pocket (H-site) [chemical binding]; other site 340100009187 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 340100009188 Transcriptional regulator; Region: Rrf2; pfam02082 340100009189 Rrf2 family protein; Region: rrf2_super; TIGR00738 340100009190 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100009191 CoA binding domain; Region: CoA_binding_2; pfam13380 340100009192 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100009193 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100009194 Uncharacterized conserved protein [Function unknown]; Region: COG5361 340100009195 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 340100009196 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 340100009197 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009198 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009199 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 340100009200 putative dimerization interface [polypeptide binding]; other site 340100009201 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009202 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100009203 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 340100009204 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100009205 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100009206 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 340100009207 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 340100009208 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009209 MarR family; Region: MarR; pfam01047 340100009210 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 340100009211 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 340100009212 DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: CbpA; COG2214 340100009213 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 340100009214 HSP70 interaction site [polypeptide binding]; other site 340100009215 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 340100009216 substrate binding site [polypeptide binding]; other site 340100009217 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 340100009218 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100009219 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100009220 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 340100009221 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009222 DNA-binding site [nucleotide binding]; DNA binding site 340100009223 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 340100009224 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009225 homodimer interface [polypeptide binding]; other site 340100009226 catalytic residue [active] 340100009227 Cupin domain; Region: Cupin_2; pfam07883 340100009228 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 340100009229 Uncharacterized conserved protein [Function unknown]; Region: COG2128 340100009230 HD domain protein, cyanamide hydratase family; Region: cyanamide_fam; TIGR03401 340100009231 Predicted transcriptional regulators [Transcription]; Region: COG1733 340100009232 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 340100009233 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 340100009234 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 340100009235 CoenzymeA binding site [chemical binding]; other site 340100009236 subunit interaction site [polypeptide binding]; other site 340100009237 PHB binding site; other site 340100009238 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009239 The 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 340100009240 dimerization interface [polypeptide binding]; other site 340100009241 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 340100009242 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 340100009243 active site 1 [active] 340100009244 dimer interface [polypeptide binding]; other site 340100009245 hexamer interface [polypeptide binding]; other site 340100009246 active site 2 [active] 340100009247 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 340100009248 active site 1 [active] 340100009249 dimer interface [polypeptide binding]; other site 340100009250 hexamer interface [polypeptide binding]; other site 340100009251 active site 2 [active] 340100009252 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100009253 classical (c) SDRs; Region: SDR_c; cd05233 340100009254 NAD(P) binding site [chemical binding]; other site 340100009255 active site 340100009256 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100009257 Transposase; Region: HTH_Tnp_1; pfam01527 340100009258 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100009259 Transposase; Region: HTH_Tnp_1; pfam01527 340100009260 putative transposase OrfB; Reviewed; Region: PHA02517 340100009261 HTH-like domain; Region: HTH_21; pfam13276 340100009262 Integrase core domain; Region: rve; pfam00665 340100009263 Integrase core domain; Region: rve_3; pfam13683 340100009264 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 340100009265 binding surface 340100009266 TPR motif; other site 340100009267 TPR repeat; Region: TPR_11; pfam13414 340100009268 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 340100009269 binding surface 340100009270 TPR motif; other site 340100009271 TPR repeat; Region: TPR_11; pfam13414 340100009272 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 340100009273 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 340100009274 E3 interaction surface; other site 340100009275 lipoyl attachment site [posttranslational modification]; other site 340100009276 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 340100009277 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100009278 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100009279 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100009280 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 340100009281 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 340100009282 E3 interaction surface; other site 340100009283 lipoyl attachment site [posttranslational modification]; other site 340100009284 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 340100009285 E3 interaction surface; other site 340100009286 lipoyl attachment site [posttranslational modification]; other site 340100009287 e3 binding domain; Region: E3_binding; pfam02817 340100009288 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 340100009289 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 340100009290 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 340100009291 dimer interface [polypeptide binding]; other site 340100009292 TPP-binding site [chemical binding]; other site 340100009293 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 340100009294 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 340100009295 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 340100009296 putative active site [active] 340100009297 heme pocket [chemical binding]; other site 340100009298 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 340100009299 dimer interface [polypeptide binding]; other site 340100009300 phosphorylation site [posttranslational modification] 340100009301 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 340100009302 ATP binding site [chemical binding]; other site 340100009303 Mg2+ binding site [ion binding]; other site 340100009304 G-X-G motif; other site 340100009305 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100009306 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100009307 active site 340100009308 phosphorylation site [posttranslational modification] 340100009309 intermolecular recognition site; other site 340100009310 dimerization interface [polypeptide binding]; other site 340100009311 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 340100009312 DNA binding residues [nucleotide binding] 340100009313 dimerization interface [polypeptide binding]; other site 340100009314 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 340100009315 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 340100009316 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 340100009317 homodimer interface [polypeptide binding]; other site 340100009318 NADP binding site [chemical binding]; other site 340100009319 substrate binding site [chemical binding]; other site 340100009320 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 340100009321 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 340100009322 active site 340100009323 Zn binding site [ion binding]; other site 340100009324 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 340100009325 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 340100009326 Cu(I) binding site [ion binding]; other site 340100009327 Predicted membrane protein [Function unknown]; Region: COG2261 340100009328 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100009329 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100009330 Protein export membrane protein; Region: SecD_SecF; cl14618 340100009331 Protein export membrane protein; Region: SecD_SecF; cl14618 340100009332 multidrug efflux system protein MdtE; Provisional; Region: PRK09859 340100009333 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100009334 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100009335 transcriptional regulator; Provisional; Region: PRK10632 340100009336 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009337 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 340100009338 putative effector binding pocket; other site 340100009339 dimerization interface [polypeptide binding]; other site 340100009340 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 340100009341 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 340100009342 RNA binding surface [nucleotide binding]; other site 340100009343 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 340100009344 active site 340100009345 Chorismate lyase; Region: Chor_lyase; cl01230 340100009346 YaeQ protein; Region: YaeQ; pfam07152 340100009347 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100009348 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 340100009349 tartrate dehydrogenase; Region: TTC; TIGR02089 340100009350 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 340100009351 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 340100009352 substrate binding site [chemical binding]; other site 340100009353 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 340100009354 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 340100009355 substrate binding site [chemical binding]; other site 340100009356 ligand binding site [chemical binding]; other site 340100009357 Peptidase family M48; Region: Peptidase_M48; pfam01435 340100009358 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 340100009359 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 340100009360 Tetramer interface [polypeptide binding]; other site 340100009361 active site 340100009362 FMN-binding site [chemical binding]; other site 340100009363 hypothetical protein; Validated; Region: PRK00029 340100009364 Uncharacterized conserved protein [Function unknown]; Region: COG0397 340100009365 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 340100009366 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 340100009367 FOG: CBS domain [General function prediction only]; Region: COG0517 340100009368 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 340100009369 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 340100009370 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 340100009371 FMN binding site [chemical binding]; other site 340100009372 active site 340100009373 catalytic residues [active] 340100009374 substrate binding site [chemical binding]; other site 340100009375 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 340100009376 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 340100009377 putative active site [active] 340100009378 putative substrate binding site [chemical binding]; other site 340100009379 ATP binding site [chemical binding]; other site 340100009380 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009381 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009382 LysR substrate binding domain; Region: LysR_substrate; pfam03466 340100009383 dimerization interface [polypeptide binding]; other site 340100009384 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 340100009385 Flavodoxin; Region: Flavodoxin_1; pfam00258 340100009386 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 340100009387 FAD binding pocket [chemical binding]; other site 340100009388 FAD binding motif [chemical binding]; other site 340100009389 catalytic residues [active] 340100009390 NAD binding pocket [chemical binding]; other site 340100009391 phosphate binding motif [ion binding]; other site 340100009392 beta-alpha-beta structure motif; other site 340100009393 sulfite reductase subunit beta; Provisional; Region: PRK13504 340100009394 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100009395 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100009396 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 340100009397 dimer interface [polypeptide binding]; other site 340100009398 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 340100009399 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340100009400 catalytic triad [active] 340100009401 replicative DNA helicase; Provisional; Region: PRK07004 340100009402 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 340100009403 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 340100009404 Walker A motif; other site 340100009405 ATP binding site [chemical binding]; other site 340100009406 Walker B motif; other site 340100009407 DNA binding loops [nucleotide binding] 340100009408 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 340100009409 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 340100009410 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 340100009411 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 340100009412 primosomal replication protein N; Reviewed; Region: PRK00036 340100009413 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 340100009414 Protein of unknown function (DUF817); Region: DUF817; cl01520 340100009415 putative GTP cyclohydrolase; Provisional; Region: PRK13674 340100009416 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 340100009417 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 340100009418 TPP-binding site; other site 340100009419 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 340100009420 PYR/PP interface [polypeptide binding]; other site 340100009421 dimer interface [polypeptide binding]; other site 340100009422 TPP binding site [chemical binding]; other site 340100009423 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100009424 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 340100009425 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340100009426 substrate binding pocket [chemical binding]; other site 340100009427 chain length determination region; other site 340100009428 substrate-Mg2+ binding site; other site 340100009429 catalytic residues [active] 340100009430 aspartate-rich region 1; other site 340100009431 active site lid residues [active] 340100009432 aspartate-rich region 2; other site 340100009433 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 340100009434 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100009435 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 340100009436 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100009437 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009438 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 340100009439 Acyltransferase family; Region: Acyl_transf_3; pfam01757 340100009440 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100009441 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 340100009442 [2Fe-2S] cluster binding site [ion binding]; other site 340100009443 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 340100009444 alpha subunit interface [polypeptide binding]; other site 340100009445 active site 340100009446 substrate binding site [chemical binding]; other site 340100009447 Fe binding site [ion binding]; other site 340100009448 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 340100009449 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 340100009450 active site residue [active] 340100009451 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 340100009452 active site residue [active] 340100009453 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100009454 heat shock protein HtpX; Provisional; Region: PRK05457 340100009455 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 340100009456 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 340100009457 NADP binding site [chemical binding]; other site 340100009458 dimer interface [polypeptide binding]; other site 340100009459 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100009460 EamA-like transporter family; Region: EamA; pfam00892 340100009461 EamA-like transporter family; Region: EamA; pfam00892 340100009462 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100009463 MarR family; Region: MarR_2; cl17246 340100009464 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100009465 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100009466 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 340100009467 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100009468 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100009469 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100009470 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 340100009471 putative substrate translocation pore; other site 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 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 340100009474 tartrate dehydrogenase; Region: TTC; TIGR02089 340100009475 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 340100009476 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009477 DNA-binding site [nucleotide binding]; DNA binding site 340100009478 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 340100009479 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009480 homodimer interface [polypeptide binding]; other site 340100009481 catalytic residue [active] 340100009482 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100009483 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 340100009484 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100009485 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 340100009486 dimer interface [polypeptide binding]; other site 340100009487 conserved gate region; other site 340100009488 putative PBP binding loops; other site 340100009489 ABC-ATPase subunit interface; other site 340100009490 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 340100009491 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 340100009492 dimer interface [polypeptide binding]; other site 340100009493 conserved gate region; other site 340100009494 putative PBP binding loops; other site 340100009495 ABC-ATPase subunit interface; other site 340100009496 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100009497 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100009498 Walker A/P-loop; other site 340100009499 ATP binding site [chemical binding]; other site 340100009500 Q-loop/lid; other site 340100009501 ABC transporter signature motif; other site 340100009502 Walker B; other site 340100009503 D-loop; other site 340100009504 H-loop/switch region; other site 340100009505 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 340100009506 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100009507 Walker A/P-loop; other site 340100009508 ATP binding site [chemical binding]; other site 340100009509 Q-loop/lid; other site 340100009510 ABC transporter signature motif; other site 340100009511 Walker B; other site 340100009512 D-loop; other site 340100009513 H-loop/switch region; other site 340100009514 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 340100009515 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 340100009516 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 340100009517 inhibitor-cofactor binding pocket; inhibition site 340100009518 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009519 catalytic residue [active] 340100009520 Cupin domain; Region: Cupin_2; cl17218 340100009521 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 340100009522 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 340100009523 active site 340100009524 Zn binding site [ion binding]; other site 340100009525 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100009526 EamA-like transporter family; Region: EamA; pfam00892 340100009527 EamA-like transporter family; Region: EamA; pfam00892 340100009528 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 340100009529 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 340100009530 FeS/SAM binding site; other site 340100009531 HemN C-terminal domain; Region: HemN_C; pfam06969 340100009532 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 340100009533 ATP cone domain; Region: ATP-cone; pfam03477 340100009534 Class III ribonucleotide reductase; Region: RNR_III; cd01675 340100009535 effector binding site; other site 340100009536 active site 340100009537 Zn binding site [ion binding]; other site 340100009538 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 340100009539 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 340100009540 FeS/SAM binding site; other site 340100009541 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100009542 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 340100009543 FMN binding site [chemical binding]; other site 340100009544 substrate binding site [chemical binding]; other site 340100009545 putative catalytic residue [active] 340100009546 DGC domain; Region: DGC; pfam08859 340100009547 SCP-2 sterol transfer family; Region: SCP2; cl01225 340100009548 putative protease; Provisional; Region: PRK15447 340100009549 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 340100009550 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 340100009551 Peptidase family U32; Region: Peptidase_U32; pfam01136 340100009552 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 340100009553 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 340100009554 putative ligand binding site [chemical binding]; other site 340100009555 NAD binding site [chemical binding]; other site 340100009556 dimerization interface [polypeptide binding]; other site 340100009557 catalytic site [active] 340100009558 aminotransferase; Provisional; Region: PRK06105 340100009559 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 340100009560 inhibitor-cofactor binding pocket; inhibition site 340100009561 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100009562 catalytic residue [active] 340100009563 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 340100009564 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 340100009565 hypothetical protein; Validated; Region: PRK00110 340100009566 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 340100009567 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 340100009568 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 340100009569 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 340100009570 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 340100009571 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 340100009572 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 340100009573 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 340100009574 active site 340100009575 (T/H)XGH motif; other site 340100009576 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 340100009577 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 340100009578 Maf-like protein; Region: Maf; pfam02545 340100009579 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 340100009580 active site 340100009581 dimer interface [polypeptide binding]; other site 340100009582 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340100009583 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 340100009584 ribonuclease G; Provisional; Region: PRK11712 340100009585 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 340100009586 homodimer interface [polypeptide binding]; other site 340100009587 oligonucleotide binding site [chemical binding]; other site 340100009588 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 340100009589 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 340100009590 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100009591 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 340100009592 Walker A/P-loop; other site 340100009593 ATP binding site [chemical binding]; other site 340100009594 Q-loop/lid; other site 340100009595 ABC transporter signature motif; other site 340100009596 Walker B; other site 340100009597 D-loop; other site 340100009598 H-loop/switch region; other site 340100009599 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 340100009600 Uncharacterized conserved protein [Function unknown]; Region: COG1434 340100009601 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 340100009602 putative active site [active] 340100009603 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100009604 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 340100009605 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 340100009606 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 340100009607 putative metal binding site; other site 340100009608 Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins; Region: CE4_Ecf1_like_5s; cd10969 340100009609 putative active site [active] 340100009610 putative metal binding site [ion binding]; other site 340100009611 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100009612 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 340100009613 putative ADP-binding pocket [chemical binding]; other site 340100009614 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 340100009615 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 340100009616 putative active site [active] 340100009617 putative PHP Thumb interface [polypeptide binding]; other site 340100009618 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 340100009619 generic binding surface I; other site 340100009620 generic binding surface II; other site 340100009621 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 340100009622 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 340100009623 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 340100009624 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 340100009625 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 340100009626 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 340100009627 PhoU domain; Region: PhoU; pfam01895 340100009628 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009629 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009630 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 340100009631 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 340100009632 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 340100009633 DNA polymerase I; Provisional; Region: PRK05755 340100009634 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 340100009635 active site 340100009636 metal binding site 1 [ion binding]; metal-binding site 340100009637 putative 5' ssDNA interaction site; other site 340100009638 metal binding site 3; metal-binding site 340100009639 metal binding site 2 [ion binding]; metal-binding site 340100009640 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 340100009641 putative DNA binding site [nucleotide binding]; other site 340100009642 putative metal binding site [ion binding]; other site 340100009643 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 340100009644 active site 340100009645 catalytic site [active] 340100009646 substrate binding site [chemical binding]; other site 340100009647 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 340100009648 active site 340100009649 DNA binding site [nucleotide binding] 340100009650 catalytic site [active] 340100009651 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 340100009652 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009653 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009654 LysR substrate binding domain; Region: LysR_substrate; pfam03466 340100009655 dimerization interface [polypeptide binding]; other site 340100009656 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 340100009657 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 340100009658 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 340100009659 G1 box; other site 340100009660 putative GEF interaction site [polypeptide binding]; other site 340100009661 GTP/Mg2+ binding site [chemical binding]; other site 340100009662 Switch I region; other site 340100009663 G2 box; other site 340100009664 G3 box; other site 340100009665 Switch II region; other site 340100009666 G4 box; other site 340100009667 G5 box; other site 340100009668 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 340100009669 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 340100009670 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00020 340100009671 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 340100009672 RNA binding site [nucleotide binding]; other site 340100009673 active site 340100009674 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 340100009675 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 340100009676 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 340100009677 translation initiation factor IF-2; Region: IF-2; TIGR00487 340100009678 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 340100009679 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 340100009680 G1 box; other site 340100009681 putative GEF interaction site [polypeptide binding]; other site 340100009682 GTP/Mg2+ binding site [chemical binding]; other site 340100009683 Switch I region; other site 340100009684 G2 box; other site 340100009685 G3 box; other site 340100009686 Switch II region; other site 340100009687 G4 box; other site 340100009688 G5 box; other site 340100009689 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 340100009690 Translation-initiation factor 2; Region: IF-2; pfam11987 340100009691 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 340100009692 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 340100009693 NusA N-terminal domain; Region: NusA_N; pfam08529 340100009694 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 340100009695 RNA binding site [nucleotide binding]; other site 340100009696 homodimer interface [polypeptide binding]; other site 340100009697 NusA-like KH domain; Region: KH_5; pfam13184 340100009698 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 340100009699 G-X-X-G motif; other site 340100009700 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 340100009701 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 340100009702 ribosome maturation protein RimP; Reviewed; Region: PRK00092 340100009703 Sm and related proteins; Region: Sm_like; cl00259 340100009704 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 340100009705 putative oligomer interface [polypeptide binding]; other site 340100009706 putative RNA binding site [nucleotide binding]; other site 340100009707 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 340100009708 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 340100009709 RNA binding surface [nucleotide binding]; other site 340100009710 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 340100009711 probable active site [active] 340100009712 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 340100009713 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009714 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009715 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 340100009716 putative effector binding pocket; other site 340100009717 dimerization interface [polypeptide binding]; other site 340100009718 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 340100009719 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 340100009720 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 340100009721 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 340100009722 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100009723 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 340100009724 putative substrate translocation pore; other site 340100009725 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 340100009726 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009727 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009728 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 340100009729 putative substrate binding pocket [chemical binding]; other site 340100009730 putative dimerization interface [polypeptide binding]; other site 340100009731 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100009732 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009733 The 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 340100009734 dimerization interface [polypeptide binding]; other site 340100009735 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 340100009736 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 340100009737 maleylacetoacetate isomerase; Region: maiA; TIGR01262 340100009738 C-terminal domain interface [polypeptide binding]; other site 340100009739 GSH binding site (G-site) [chemical binding]; other site 340100009740 putative dimer interface [polypeptide binding]; other site 340100009741 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 340100009742 dimer interface [polypeptide binding]; other site 340100009743 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 340100009744 N-terminal domain interface [polypeptide binding]; other site 340100009745 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 340100009746 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 340100009747 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 340100009748 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 340100009749 hypothetical protein; Reviewed; Region: PRK00024 340100009750 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100009751 MPN+ (JAMM) motif; other site 340100009752 Zinc-binding site [ion binding]; other site 340100009753 Putative cyclase; Region: Cyclase; cl00814 340100009754 tryptophan 2,3-dioxygenase; Region: trp_2_3_diox; TIGR03036 340100009755 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 340100009756 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 340100009757 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 340100009758 cation binding site [ion binding]; other site 340100009759 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100009760 DNA repair protein RadA; Provisional; Region: PRK11823 340100009761 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 340100009762 Walker A motif/ATP binding site; other site 340100009763 ATP binding site [chemical binding]; other site 340100009764 Walker B motif; other site 340100009765 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 340100009766 von Willebrand factor; Region: vWF_A; pfam12450 340100009767 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 340100009768 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 340100009769 metal ion-dependent adhesion site (MIDAS); other site 340100009770 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 340100009771 RNA polymerase sigma factor; Provisional; Region: PRK12513 340100009772 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100009773 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 340100009774 DNA binding residues [nucleotide binding] 340100009775 short chain dehydrogenase; Provisional; Region: PRK07577 340100009776 classical (c) SDRs; Region: SDR_c; cd05233 340100009777 NAD(P) binding site [chemical binding]; other site 340100009778 active site 340100009779 alanine racemase; Reviewed; Region: dadX; PRK03646 340100009780 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 340100009781 active site 340100009782 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100009783 substrate binding site [chemical binding]; other site 340100009784 catalytic residues [active] 340100009785 dimer interface [polypeptide binding]; other site 340100009786 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 340100009787 active site lid residues [active] 340100009788 substrate binding pocket [chemical binding]; other site 340100009789 catalytic residues [active] 340100009790 substrate-Mg2+ binding site; other site 340100009791 aspartate-rich region 1; other site 340100009792 aspartate-rich region 2; other site 340100009793 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 340100009794 active site lid residues [active] 340100009795 substrate binding pocket [chemical binding]; other site 340100009796 catalytic residues [active] 340100009797 substrate-Mg2+ binding site; other site 340100009798 aspartate-rich region 1; other site 340100009799 aspartate-rich region 2; other site 340100009800 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 340100009801 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 340100009802 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100009803 Transposase; Region: HTH_Tnp_1; pfam01527 340100009804 putative transposase OrfB; Reviewed; Region: PHA02517 340100009805 HTH-like domain; Region: HTH_21; pfam13276 340100009806 Integrase core domain; Region: rve; pfam00665 340100009807 Integrase core domain; Region: rve_3; pfam13683 340100009808 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 340100009809 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 340100009810 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 340100009811 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 340100009812 ApbE family; Region: ApbE; pfam02424 340100009813 Flavodoxin; Region: Flavodoxin_1; pfam00258 340100009814 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 340100009815 FAD binding pocket [chemical binding]; other site 340100009816 FAD binding motif [chemical binding]; other site 340100009817 catalytic residues [active] 340100009818 NAD binding pocket [chemical binding]; other site 340100009819 phosphate binding motif [ion binding]; other site 340100009820 beta-alpha-beta structure motif; other site 340100009821 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 340100009822 Clp amino terminal domain; Region: Clp_N; pfam02861 340100009823 Clp amino terminal domain; Region: Clp_N; pfam02861 340100009824 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 340100009825 Walker A motif; other site 340100009826 ATP binding site [chemical binding]; other site 340100009827 Walker B motif; other site 340100009828 arginine finger; other site 340100009829 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 340100009830 Walker A motif; other site 340100009831 ATP binding site [chemical binding]; other site 340100009832 Walker B motif; other site 340100009833 arginine finger; other site 340100009834 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 340100009835 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 340100009836 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 340100009837 ligand binding site [chemical binding]; other site 340100009838 flexible hinge region; other site 340100009839 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 340100009840 putative switch regulator; other site 340100009841 non-specific DNA interactions [nucleotide binding]; other site 340100009842 DNA binding site [nucleotide binding] 340100009843 sequence specific DNA binding site [nucleotide binding]; other site 340100009844 putative cAMP binding site [chemical binding]; other site 340100009845 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 340100009846 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 340100009847 dimer interface [polypeptide binding]; other site 340100009848 ADP-ribose binding site [chemical binding]; other site 340100009849 active site 340100009850 nudix motif; other site 340100009851 metal binding site [ion binding]; metal-binding site 340100009852 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 340100009853 active site 340100009854 Zn binding site [ion binding]; other site 340100009855 NlpE N-terminal domain; Region: NlpE; pfam04170 340100009856 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 340100009857 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100009858 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009859 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100009860 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009861 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100009862 Protein of unknown function (DUF342); Region: DUF342; pfam03961 340100009863 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 340100009864 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 340100009865 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 340100009866 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100009867 MarR family; Region: MarR; pfam01047 340100009868 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100009869 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 340100009870 Coenzyme A binding pocket [chemical binding]; other site 340100009871 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 340100009872 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100009873 conserved cys residue [active] 340100009874 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009875 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 340100009876 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100009877 putative substrate translocation pore; other site 340100009878 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100009879 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 340100009880 N-terminal plug; other site 340100009881 ligand-binding site [chemical binding]; other site 340100009882 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 340100009883 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 340100009884 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 340100009885 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 340100009886 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 340100009887 trimer interface [polypeptide binding]; other site 340100009888 eyelet of channel; other site 340100009889 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 340100009890 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 340100009891 N-terminal plug; other site 340100009892 ligand-binding site [chemical binding]; other site 340100009893 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100009894 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 340100009895 active site 340100009896 benzoate transport; Region: 2A0115; TIGR00895 340100009897 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 340100009898 putative substrate translocation pore; other site 340100009899 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100009900 FCD domain; Region: FCD; pfam07729 340100009901 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100009902 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 340100009903 putative substrate translocation pore; other site 340100009904 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100009905 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100009906 The 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 340100009907 dimerization interface [polypeptide binding]; other site 340100009908 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 340100009909 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100009910 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100009911 (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 340100009912 active site 340100009913 catalytic site [active] 340100009914 (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 340100009915 active site 340100009916 catalytic site [active] 340100009917 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009918 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100009919 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100009920 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 340100009921 S-adenosylmethionine binding site [chemical binding]; other site 340100009922 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 340100009923 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 340100009924 active site 340100009925 substrate binding site [chemical binding]; other site 340100009926 Mg2+ binding site [ion binding]; other site 340100009927 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 340100009928 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100009929 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 340100009930 Cytochrome c; Region: Cytochrom_C; cl11414 340100009931 Cytochrome c; Region: Cytochrom_C; cl11414 340100009932 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 340100009933 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 340100009934 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 340100009935 Cytochrome c; Region: Cytochrom_C; pfam00034 340100009936 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100009937 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 340100009938 D-pathway; other site 340100009939 Low-spin heme binding site [chemical binding]; other site 340100009940 Putative water exit pathway; other site 340100009941 Binuclear center (active site) [active] 340100009942 K-pathway; other site 340100009943 Putative proton exit pathway; other site 340100009944 MASE1; Region: MASE1; cl17823 340100009945 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100009946 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 340100009947 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 340100009948 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 340100009949 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 340100009950 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100009951 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100009952 DNA-binding site [nucleotide binding]; DNA binding site 340100009953 FCD domain; Region: FCD; pfam07729 340100009954 dihydroxy-acid dehydratase; Provisional; Region: PRK13016 340100009955 hypothetical protein; Validated; Region: PRK08245 340100009956 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100009957 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 340100009958 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 340100009959 conserved cys residue [active] 340100009960 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009961 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100009962 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 340100009963 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 340100009964 putative dimer interface [polypeptide binding]; other site 340100009965 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100009966 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100009967 Coenzyme A binding pocket [chemical binding]; other site 340100009968 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 340100009969 Haemolysin-III related; Region: HlyIII; cl03831 340100009970 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 340100009971 ergothioneine biosynthesis protein EgtC; Region: TIGR03442 340100009972 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 340100009973 putative active site [active] 340100009974 putative dimer interface [polypeptide binding]; other site 340100009975 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 340100009976 Moco binding site; other site 340100009977 metal coordination site [ion binding]; other site 340100009978 dimerization interface [polypeptide binding]; other site 340100009979 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100009980 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 340100009981 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100009982 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 340100009983 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 340100009984 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100009985 active site 340100009986 catalytic tetrad [active] 340100009987 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 340100009988 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 340100009989 motif II; other site 340100009990 ABC-2 type transporter; Region: ABC2_membrane; cl17235 340100009991 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 340100009992 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340100009993 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 340100009994 Walker A/P-loop; other site 340100009995 ATP binding site [chemical binding]; other site 340100009996 Q-loop/lid; other site 340100009997 ABC transporter signature motif; other site 340100009998 Walker B; other site 340100009999 D-loop; other site 340100010000 H-loop/switch region; other site 340100010001 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 340100010002 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 340100010003 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 340100010004 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100010005 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 340100010006 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 340100010007 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 340100010008 Cytochrome c; Region: Cytochrom_C; pfam00034 340100010009 Cytochrome c; Region: Cytochrom_C; pfam00034 340100010010 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 340100010011 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 340100010012 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 340100010013 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 340100010014 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 340100010015 Low-spin heme binding site [chemical binding]; other site 340100010016 Putative water exit pathway; other site 340100010017 Binuclear center (active site) [active] 340100010018 Putative proton exit pathway; other site 340100010019 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 340100010020 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 340100010021 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 340100010022 dimerization interface [polypeptide binding]; other site 340100010023 putative DNA binding site [nucleotide binding]; other site 340100010024 putative Zn2+ binding site [ion binding]; other site 340100010025 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 340100010026 active site residue [active] 340100010027 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 340100010028 isocitrate lyase; Provisional; Region: PRK15063 340100010029 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 340100010030 tetramer interface [polypeptide binding]; other site 340100010031 active site 340100010032 Mg2+/Mn2+ binding site [ion binding]; other site 340100010033 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 340100010034 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 340100010035 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 340100010036 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 340100010037 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 340100010038 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100010039 putative substrate translocation pore; other site 340100010040 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 340100010041 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 340100010042 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 340100010043 active site 340100010044 catalytic site [active] 340100010045 putative DNA binding site [nucleotide binding]; other site 340100010046 GIY-YIG motif/motif A; other site 340100010047 metal binding site [ion binding]; metal-binding site 340100010048 UvrB/uvrC motif; Region: UVR; pfam02151 340100010049 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 340100010050 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 340100010051 beta-hexosaminidase; Provisional; Region: PRK05337 340100010052 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 340100010053 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 340100010054 active site 340100010055 hydrophilic channel; other site 340100010056 dimerization interface [polypeptide binding]; other site 340100010057 catalytic residues [active] 340100010058 active site lid [active] 340100010059 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100010060 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100010061 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100010062 Protein export membrane protein; Region: SecD_SecF; cl14618 340100010063 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 340100010064 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100010065 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100010066 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 340100010067 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100010068 DNA binding site [nucleotide binding] 340100010069 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 340100010070 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 340100010071 nucleophile elbow; other site 340100010072 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 340100010073 Patatin phospholipase; Region: DUF3734; pfam12536 340100010074 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 340100010075 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 340100010076 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 340100010077 molybdenum-pterin binding domain; Region: Mop; TIGR00638 340100010078 TOBE domain; Region: TOBE; cl01440 340100010079 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 340100010080 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100010081 Walker A/P-loop; other site 340100010082 ATP binding site [chemical binding]; other site 340100010083 Q-loop/lid; other site 340100010084 ABC transporter signature motif; other site 340100010085 Walker B; other site 340100010086 D-loop; other site 340100010087 H-loop/switch region; other site 340100010088 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100010089 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 340100010090 TM-ABC transporter signature motif; other site 340100010091 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 340100010092 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 340100010093 zinc binding site [ion binding]; other site 340100010094 putative ligand binding site [chemical binding]; other site 340100010095 DctM-like transporters; Region: DctM; pfam06808 340100010096 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100010097 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100010098 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100010099 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100010100 malonyl-CoA synthase; Validated; Region: PRK07514 340100010101 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 340100010102 acyl-activating enzyme (AAE) consensus motif; other site 340100010103 active site 340100010104 AMP binding site [chemical binding]; other site 340100010105 CoA binding site [chemical binding]; other site 340100010106 enoyl-CoA hydratase; Provisional; Region: PRK06127 340100010107 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 340100010108 substrate binding site [chemical binding]; other site 340100010109 oxyanion hole (OAH) forming residues; other site 340100010110 trimer interface [polypeptide binding]; other site 340100010111 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 340100010112 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 340100010113 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100010114 DNA-binding site [nucleotide binding]; DNA binding site 340100010115 FCD domain; Region: FCD; pfam07729 340100010116 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100010117 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 340100010118 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 340100010119 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100010120 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100010121 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100010122 active site 340100010123 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010124 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 340100010125 CoA binding domain; Region: CoA_binding_2; pfam13380 340100010126 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100010127 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100010128 enoyl-CoA hydratase; Provisional; Region: PRK08290 340100010129 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 340100010130 substrate binding site [chemical binding]; other site 340100010131 oxyanion hole (OAH) forming residues; other site 340100010132 trimer interface [polypeptide binding]; other site 340100010133 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100010134 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100010135 beta-ketothiolase; Provisional; Region: PRK09051 340100010136 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 340100010137 dimer interface [polypeptide binding]; other site 340100010138 active site 340100010139 enoyl-CoA hydratase; Provisional; Region: PRK09245 340100010140 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 340100010141 substrate binding site [chemical binding]; other site 340100010142 oxyanion hole (OAH) forming residues; other site 340100010143 trimer interface [polypeptide binding]; other site 340100010144 putative transposase OrfB; Reviewed; Region: PHA02517 340100010145 HTH-like domain; Region: HTH_21; pfam13276 340100010146 Integrase core domain; Region: rve; pfam00665 340100010147 Integrase core domain; Region: rve_3; pfam13683 340100010148 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100010149 Transposase; Region: HTH_Tnp_1; pfam01527 340100010150 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100010151 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100010152 active site 340100010153 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100010154 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010155 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010156 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 340100010157 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 340100010158 NADP binding site [chemical binding]; other site 340100010159 dimer interface [polypeptide binding]; other site 340100010160 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100010161 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 340100010162 active site pocket [active] 340100010163 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100010164 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 340100010165 ligand binding site [chemical binding]; other site 340100010166 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 340100010167 TM-ABC transporter signature motif; other site 340100010168 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100010169 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 340100010170 TM-ABC transporter signature motif; other site 340100010171 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100010172 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100010173 Walker A/P-loop; other site 340100010174 ATP binding site [chemical binding]; other site 340100010175 Q-loop/lid; other site 340100010176 ABC transporter signature motif; other site 340100010177 Walker B; other site 340100010178 D-loop; other site 340100010179 H-loop/switch region; other site 340100010180 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100010181 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100010182 Walker A/P-loop; other site 340100010183 ATP binding site [chemical binding]; other site 340100010184 Q-loop/lid; other site 340100010185 ABC transporter signature motif; other site 340100010186 Walker B; other site 340100010187 D-loop; other site 340100010188 H-loop/switch region; other site 340100010189 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100010190 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 340100010191 active site pocket [active] 340100010192 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 340100010193 active site 1 [active] 340100010194 dimer interface [polypeptide binding]; other site 340100010195 hexamer interface [polypeptide binding]; other site 340100010196 active site 2 [active] 340100010197 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 340100010198 hexamer interface [polypeptide binding]; other site 340100010199 active site 2 [active] 340100010200 dimer interface [polypeptide binding]; other site 340100010201 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010202 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010203 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 340100010204 dimerization interface [polypeptide binding]; other site 340100010205 substrate binding pocket [chemical binding]; other site 340100010206 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100010207 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100010208 PYR/PP interface [polypeptide binding]; other site 340100010209 dimer interface [polypeptide binding]; other site 340100010210 TPP binding site [chemical binding]; other site 340100010211 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100010212 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 340100010213 TPP-binding site [chemical binding]; other site 340100010214 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010215 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 340100010216 dimerization interface [polypeptide binding]; other site 340100010217 substrate binding pocket [chemical binding]; other site 340100010218 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010219 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010220 (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 340100010221 active site 340100010222 catalytic site [active] 340100010223 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010224 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 340100010225 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 340100010226 Walker A/P-loop; other site 340100010227 ATP binding site [chemical binding]; other site 340100010228 Q-loop/lid; other site 340100010229 ABC transporter signature motif; other site 340100010230 Walker B; other site 340100010231 D-loop; other site 340100010232 H-loop/switch region; other site 340100010233 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 340100010234 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 340100010235 dimer interface [polypeptide binding]; other site 340100010236 conserved gate region; other site 340100010237 putative PBP binding loops; other site 340100010238 ABC-ATPase subunit interface; other site 340100010239 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 340100010240 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 340100010241 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 340100010242 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100010243 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 340100010244 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 340100010245 putative substrate translocation pore; other site 340100010246 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 340100010247 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 340100010248 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 340100010249 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100010250 putative ligand binding site [chemical binding]; other site 340100010251 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 340100010252 TM-ABC transporter signature motif; other site 340100010253 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100010254 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 340100010255 TM-ABC transporter signature motif; other site 340100010256 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100010257 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100010258 Walker A/P-loop; other site 340100010259 ATP binding site [chemical binding]; other site 340100010260 Q-loop/lid; other site 340100010261 ABC transporter signature motif; other site 340100010262 Walker B; other site 340100010263 D-loop; other site 340100010264 H-loop/switch region; other site 340100010265 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 340100010266 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 340100010267 Sulfate transporter family; Region: Sulfate_transp; pfam00916 340100010268 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 340100010269 Hemerythrin-like domain; Region: Hr-like; cd12108 340100010270 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 340100010271 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 340100010272 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 340100010273 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 340100010274 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 340100010275 Cl- selectivity filter; other site 340100010276 Cl- binding residues [ion binding]; other site 340100010277 pore gating glutamate residue; other site 340100010278 dimer interface [polypeptide binding]; other site 340100010279 FOG: CBS domain [General function prediction only]; Region: COG0517 340100010280 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 340100010281 Bacterial DNA-binding protein; Region: Bac_DNA_binding; pfam00216 340100010282 IHF dimer interface [polypeptide binding]; other site 340100010283 IHF - DNA interface [nucleotide binding]; other site 340100010284 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100010285 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 340100010286 putative substrate translocation pore; other site 340100010287 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 340100010288 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 340100010289 HIGH motif; other site 340100010290 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340100010291 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340100010292 active site 340100010293 KMSKS motif; other site 340100010294 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 340100010295 tRNA binding surface [nucleotide binding]; other site 340100010296 Lipopolysaccharide-assembly; Region: LptE; pfam04390 340100010297 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 340100010298 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 340100010299 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 340100010300 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 340100010301 putative catalytic cysteine [active] 340100010302 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010303 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010304 The 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 340100010305 dimerization interface [polypeptide binding]; other site 340100010306 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100010307 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 340100010308 putative substrate translocation pore; other site 340100010309 Predicted acetyltransferase [General function prediction only]; Region: COG2388 340100010310 hypothetical protein; Provisional; Region: PRK01842 340100010311 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100010312 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010313 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 340100010314 dimerization interface [polypeptide binding]; other site 340100010315 substrate binding pocket [chemical binding]; other site 340100010316 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 340100010317 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 340100010318 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100010319 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 340100010320 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100010321 DNA-binding site [nucleotide binding]; DNA binding site 340100010322 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 340100010323 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100010324 homodimer interface [polypeptide binding]; other site 340100010325 catalytic residue [active] 340100010326 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100010327 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 340100010328 DctM-like transporters; Region: DctM; pfam06808 340100010329 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100010330 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 340100010331 homodimer interface [polypeptide binding]; other site 340100010332 catalytic residues [active] 340100010333 NAD binding site [chemical binding]; other site 340100010334 substrate binding pocket [chemical binding]; other site 340100010335 flexible flap; other site 340100010336 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 340100010337 EamA-like transporter family; Region: EamA; pfam00892 340100010338 YciI-like protein; Reviewed; Region: PRK12866 340100010339 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 340100010340 LysE type translocator; Region: LysE; cl00565 340100010341 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100010342 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010343 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 340100010344 dimerizarion interface [polypeptide binding]; other site 340100010345 CrgA pocket; other site 340100010346 substrate binding pocket [chemical binding]; other site 340100010347 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100010348 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 340100010349 octamer interface [polypeptide binding]; other site 340100010350 active site 340100010351 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010352 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 340100010353 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 340100010354 glutathione s-transferase; Provisional; Region: PTZ00057 340100010355 GSH binding site (G-site) [chemical binding]; other site 340100010356 C-terminal domain interface [polypeptide binding]; other site 340100010357 dimer interface [polypeptide binding]; other site 340100010358 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 340100010359 dimer interface [polypeptide binding]; other site 340100010360 N-terminal domain interface [polypeptide binding]; other site 340100010361 substrate binding pocket (H-site) [chemical binding]; other site 340100010362 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 340100010363 active site 340100010364 catalytic site [active] 340100010365 substrate binding site [chemical binding]; other site 340100010366 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 340100010367 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 340100010368 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 340100010369 substrate binding site [chemical binding]; other site 340100010370 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 340100010371 substrate binding site [chemical binding]; other site 340100010372 ligand binding site [chemical binding]; other site 340100010373 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010374 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010375 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 340100010376 putative dimerization interface [polypeptide binding]; other site 340100010377 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 340100010378 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 340100010379 ligand binding site [chemical binding]; other site 340100010380 NAD binding site [chemical binding]; other site 340100010381 dimerization interface [polypeptide binding]; other site 340100010382 catalytic site [active] 340100010383 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010384 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100010385 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 340100010386 N-terminal plug; other site 340100010387 ligand-binding site [chemical binding]; other site 340100010388 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100010389 3-hydroxyacyl-CoA dehydrogenase; Validated; Region: PRK06129 340100010390 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100010391 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100010392 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100010393 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100010394 catalytic residue [active] 340100010395 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 340100010396 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100010397 Walker A/P-loop; other site 340100010398 ATP binding site [chemical binding]; other site 340100010399 Q-loop/lid; other site 340100010400 ABC transporter signature motif; other site 340100010401 Walker B; other site 340100010402 D-loop; other site 340100010403 H-loop/switch region; other site 340100010404 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 340100010405 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100010406 Walker A/P-loop; other site 340100010407 ATP binding site [chemical binding]; other site 340100010408 Q-loop/lid; other site 340100010409 ABC transporter signature motif; other site 340100010410 Walker B; other site 340100010411 D-loop; other site 340100010412 H-loop/switch region; other site 340100010413 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 340100010414 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100010415 active site 340100010416 catalytic tetrad [active] 340100010417 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010418 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010419 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 340100010420 putative effector binding pocket; other site 340100010421 putative dimerization interface [polypeptide binding]; other site 340100010422 aconitate hydratase; Provisional; Region: acnA; PRK12881 340100010423 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 340100010424 substrate binding site [chemical binding]; other site 340100010425 ligand binding site [chemical binding]; other site 340100010426 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 340100010427 substrate binding site [chemical binding]; other site 340100010428 Protein of unknown function (DUF2863); Region: DUF2863; pfam11062 340100010429 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 340100010430 elongation factor P; Validated; Region: PRK00529 340100010431 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 340100010432 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 340100010433 RNA binding site [nucleotide binding]; other site 340100010434 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 340100010435 RNA binding site [nucleotide binding]; other site 340100010436 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 340100010437 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 340100010438 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 340100010439 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 340100010440 Walker A motif; other site 340100010441 ATP binding site [chemical binding]; other site 340100010442 Walker B motif; other site 340100010443 arginine finger; other site 340100010444 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100010445 Predicted membrane protein [Function unknown]; Region: COG4655 340100010446 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 340100010447 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 340100010448 TPR repeat; Region: TPR_11; pfam13414 340100010449 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 340100010450 binding surface 340100010451 TPR motif; other site 340100010452 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 340100010453 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 340100010454 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 340100010455 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 340100010456 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 340100010457 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 340100010458 ATP binding site [chemical binding]; other site 340100010459 Walker A motif; other site 340100010460 hexamer interface [polypeptide binding]; other site 340100010461 Walker B motif; other site 340100010462 Response regulator receiver domain; Region: Response_reg; pfam00072 340100010463 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100010464 active site 340100010465 phosphorylation site [posttranslational modification] 340100010466 intermolecular recognition site; other site 340100010467 dimerization interface [polypeptide binding]; other site 340100010468 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 340100010469 AAA domain; Region: AAA_31; pfam13614 340100010470 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 340100010471 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 340100010472 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340100010473 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 340100010474 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 340100010475 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 340100010476 TadE-like protein; Region: TadE; pfam07811 340100010477 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 340100010478 Flp/Fap pilin component; Region: Flp_Fap; cl01585 340100010479 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 340100010480 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 340100010481 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 340100010482 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 340100010483 MarR family; Region: MarR; pfam01047 340100010484 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100010485 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100010486 Walker A/P-loop; other site 340100010487 ATP binding site [chemical binding]; other site 340100010488 Q-loop/lid; other site 340100010489 ABC transporter signature motif; other site 340100010490 Walker B; other site 340100010491 D-loop; other site 340100010492 H-loop/switch region; other site 340100010493 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100010494 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100010495 Walker A/P-loop; other site 340100010496 ATP binding site [chemical binding]; other site 340100010497 Q-loop/lid; other site 340100010498 ABC transporter signature motif; other site 340100010499 Walker B; other site 340100010500 D-loop; other site 340100010501 H-loop/switch region; other site 340100010502 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100010503 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 340100010504 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 340100010505 dimer interface [polypeptide binding]; other site 340100010506 conserved gate region; other site 340100010507 putative PBP binding loops; other site 340100010508 ABC-ATPase subunit interface; other site 340100010509 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100010510 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 340100010511 dimer interface [polypeptide binding]; other site 340100010512 putative PBP binding loops; other site 340100010513 ABC-ATPase subunit interface; other site 340100010514 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 340100010515 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100010516 Staphylococcal nuclease homologues; Region: SNc; smart00318 340100010517 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 340100010518 Catalytic site; other site 340100010519 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 340100010520 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 340100010521 oligomer interface [polypeptide binding]; other site 340100010522 metal binding site [ion binding]; metal-binding site 340100010523 metal binding site [ion binding]; metal-binding site 340100010524 putative Cl binding site [ion binding]; other site 340100010525 basic sphincter; other site 340100010526 hydrophobic gate; other site 340100010527 periplasmic entrance; other site 340100010528 metabolite-proton symporter; Region: 2A0106; TIGR00883 340100010529 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 340100010530 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 340100010531 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 340100010532 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340100010533 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 340100010534 D-pathway; other site 340100010535 Putative ubiquinol binding site [chemical binding]; other site 340100010536 Low-spin heme (heme b) binding site [chemical binding]; other site 340100010537 Putative water exit pathway; other site 340100010538 Binuclear center (heme o3/CuB) [ion binding]; other site 340100010539 K-pathway; other site 340100010540 Putative proton exit pathway; other site 340100010541 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 340100010542 Subunit I/III interface [polypeptide binding]; other site 340100010543 Subunit III/IV interface [polypeptide binding]; other site 340100010544 Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion]; Region: CyoD; COG3125 340100010545 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 340100010546 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 340100010547 Part of AAA domain; Region: AAA_19; pfam13245 340100010548 Family description; Region: UvrD_C_2; pfam13538 340100010549 Protein of unknown function DUF72; Region: DUF72; pfam01904 340100010550 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 340100010551 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100010552 DNA-binding site [nucleotide binding]; DNA binding site 340100010553 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 340100010554 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100010555 homodimer interface [polypeptide binding]; other site 340100010556 catalytic residue [active] 340100010557 4-aminobutyrate aminotransferase; Provisional; Region: PRK06777 340100010558 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 340100010559 inhibitor-cofactor binding pocket; inhibition site 340100010560 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100010561 catalytic residue [active] 340100010562 succinic semialdehyde dehydrogenase; Region: PLN02278 340100010563 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100010564 tetramerization interface [polypeptide binding]; other site 340100010565 NAD(P) binding site [chemical binding]; other site 340100010566 catalytic residues [active] 340100010567 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 340100010568 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 340100010569 active site 340100010570 putative lithium-binding site [ion binding]; other site 340100010571 substrate binding site [chemical binding]; other site 340100010572 NAD-dependent deacetylase; Provisional; Region: PRK05333 340100010573 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 340100010574 serine O-acetyltransferase; Region: cysE; TIGR01172 340100010575 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 340100010576 trimer interface [polypeptide binding]; other site 340100010577 active site 340100010578 substrate binding site [chemical binding]; other site 340100010579 CoA binding site [chemical binding]; other site 340100010580 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100010581 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100010582 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 340100010583 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 340100010584 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100010585 active site 340100010586 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 340100010587 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 340100010588 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 340100010589 dimer interface [polypeptide binding]; other site 340100010590 active site 340100010591 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 340100010592 substrate binding site [chemical binding]; other site 340100010593 oxyanion hole (OAH) forming residues; other site 340100010594 trimer interface [polypeptide binding]; other site 340100010595 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 340100010596 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100010597 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100010598 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 340100010599 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 340100010600 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100010601 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100010602 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100010603 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 340100010604 substrate binding site [chemical binding]; other site 340100010605 oxyanion hole (OAH) forming residues; other site 340100010606 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 340100010607 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 340100010608 dimer interface [polypeptide binding]; other site 340100010609 active site 340100010610 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 340100010611 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 340100010612 acyl-activating enzyme (AAE) consensus motif; other site 340100010613 putative AMP binding site [chemical binding]; other site 340100010614 putative active site [active] 340100010615 putative CoA binding site [chemical binding]; other site 340100010616 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 340100010617 Sulfatase; Region: Sulfatase; cl17466 340100010618 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100010619 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100010620 MarR family; Region: MarR_2; pfam12802 340100010621 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 340100010622 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 340100010623 N-terminal plug; other site 340100010624 ligand-binding site [chemical binding]; other site 340100010625 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010626 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100010627 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 340100010628 active site 340100010629 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100010630 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100010631 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100010632 DNA-binding site [nucleotide binding]; DNA binding site 340100010633 FCD domain; Region: FCD; pfam07729 340100010634 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 340100010635 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100010636 putative substrate translocation pore; other site 340100010637 Cupin domain; Region: Cupin_2; pfam07883 340100010638 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 340100010639 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100010640 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 340100010641 dimerization interface [polypeptide binding]; other site 340100010642 putative DNA binding site [nucleotide binding]; other site 340100010643 putative Zn2+ binding site [ion binding]; other site 340100010644 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 340100010645 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 340100010646 FMN binding site [chemical binding]; other site 340100010647 active site 340100010648 substrate binding site [chemical binding]; other site 340100010649 catalytic residue [active] 340100010650 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 340100010651 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 340100010652 FMN binding site [chemical binding]; other site 340100010653 substrate binding site [chemical binding]; other site 340100010654 putative catalytic residue [active] 340100010655 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010656 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010657 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010658 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 340100010659 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 340100010660 substrate binding site [chemical binding]; other site 340100010661 oxyanion hole (OAH) forming residues; other site 340100010662 trimer interface [polypeptide binding]; other site 340100010663 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100010664 MarR family; Region: MarR_2; pfam12802 340100010665 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100010666 active site 340100010667 catalytic residues [active] 340100010668 metal binding site [ion binding]; metal-binding site 340100010669 AMP-binding domain protein; Validated; Region: PRK08315 340100010670 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100010671 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 340100010672 acyl-activating enzyme (AAE) consensus motif; other site 340100010673 acyl-activating enzyme (AAE) consensus motif; other site 340100010674 putative AMP binding site [chemical binding]; other site 340100010675 putative active site [active] 340100010676 putative CoA binding site [chemical binding]; other site 340100010677 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100010678 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 340100010679 substrate binding site [chemical binding]; other site 340100010680 oxyanion hole (OAH) forming residues; other site 340100010681 trimer interface [polypeptide binding]; other site 340100010682 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010683 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010684 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010685 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100010686 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100010687 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 340100010688 putative effector binding pocket; other site 340100010689 dimerization interface [polypeptide binding]; other site 340100010690 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 340100010691 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 340100010692 putative NAD(P) binding site [chemical binding]; other site 340100010693 dimer interface [polypeptide binding]; other site 340100010694 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 340100010695 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 340100010696 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 340100010697 active site 340100010698 DNA binding site [nucleotide binding] 340100010699 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 340100010700 DNA binding site [nucleotide binding] 340100010701 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 340100010702 nucleotide binding site [chemical binding]; other site 340100010703 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 340100010704 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 340100010705 putative DNA binding site [nucleotide binding]; other site 340100010706 putative homodimer interface [polypeptide binding]; other site 340100010707 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 340100010708 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 340100010709 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 340100010710 putative active site [active] 340100010711 heme pocket [chemical binding]; other site 340100010712 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 340100010713 dimer interface [polypeptide binding]; other site 340100010714 phosphorylation site [posttranslational modification] 340100010715 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 340100010716 ATP binding site [chemical binding]; other site 340100010717 Mg2+ binding site [ion binding]; other site 340100010718 G-X-G motif; other site 340100010719 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 340100010720 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100010721 active site 340100010722 phosphorylation site [posttranslational modification] 340100010723 intermolecular recognition site; other site 340100010724 dimerization interface [polypeptide binding]; other site 340100010725 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 340100010726 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 340100010727 putative acyl-acceptor binding pocket; other site 340100010728 aspartate kinase; Reviewed; Region: PRK06635 340100010729 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 340100010730 putative nucleotide binding site [chemical binding]; other site 340100010731 putative catalytic residues [active] 340100010732 putative Mg ion binding site [ion binding]; other site 340100010733 putative aspartate binding site [chemical binding]; other site 340100010734 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 340100010735 putative allosteric regulatory site; other site 340100010736 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 340100010737 putative allosteric regulatory residue; other site 340100010738 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 340100010739 Ligand Binding Site [chemical binding]; other site 340100010740 TilS substrate binding domain; Region: TilS; pfam09179 340100010741 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 340100010742 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 340100010743 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100010744 endonuclease III; Region: ENDO3c; smart00478 340100010745 minor groove reading motif; other site 340100010746 helix-hairpin-helix signature motif; other site 340100010747 substrate binding pocket [chemical binding]; other site 340100010748 active site 340100010749 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 340100010750 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 340100010751 active site 340100010752 HIGH motif; other site 340100010753 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 340100010754 KMSKS motif; other site 340100010755 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 340100010756 tRNA binding surface [nucleotide binding]; other site 340100010757 anticodon binding site; other site 340100010758 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 340100010759 binding surface 340100010760 Tetratricopeptide repeat; Region: TPR_16; pfam13432 340100010761 TPR motif; other site 340100010762 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 340100010763 substrate binding site [chemical binding]; other site 340100010764 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 340100010765 putative active site [active] 340100010766 putative metal binding site [ion binding]; other site 340100010767 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 340100010768 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 340100010769 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 340100010770 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 340100010771 Transporter associated domain; Region: CorC_HlyC; pfam03471 340100010772 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 340100010773 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 340100010774 active site 340100010775 dimerization interface [polypeptide binding]; other site 340100010776 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 340100010777 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 340100010778 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010779 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100010780 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; cl17393 340100010781 DNA-binding interface [nucleotide binding]; DNA binding site 340100010782 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100010783 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 340100010784 Conserved TM helix; Region: TM_helix; pfam05552 340100010785 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340100010786 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 340100010787 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 340100010788 Imelysin; Region: Peptidase_M75; cl09159 340100010789 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 340100010790 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 340100010791 Imelysin; Region: Peptidase_M75; cl09159 340100010792 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 340100010793 Predicted flavoprotein [General function prediction only]; Region: COG0431 340100010794 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100010795 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 340100010796 Dodecin; Region: Dodecin; pfam07311 340100010797 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 340100010798 MutS domain I; Region: MutS_I; pfam01624 340100010799 MutS domain II; Region: MutS_II; pfam05188 340100010800 MutS domain III; Region: MutS_III; pfam05192 340100010801 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 340100010802 Walker A/P-loop; other site 340100010803 ATP binding site [chemical binding]; other site 340100010804 Q-loop/lid; other site 340100010805 ABC transporter signature motif; other site 340100010806 Walker B; other site 340100010807 D-loop; other site 340100010808 H-loop/switch region; other site 340100010809 Cupin superfamily protein; Region: Cupin_4; pfam08007 340100010810 Cupin-like domain; Region: Cupin_8; pfam13621 340100010811 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 340100010812 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 340100010813 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340100010814 dihydrodipicolinate synthase; Region: dapA; TIGR00674 340100010815 dimer interface [polypeptide binding]; other site 340100010816 active site 340100010817 catalytic residue [active] 340100010818 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 340100010819 Peptidase family M50; Region: Peptidase_M50; pfam02163 340100010820 active site 340100010821 putative substrate binding region [chemical binding]; other site 340100010822 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 340100010823 Predicted metalloprotease [General function prediction only]; Region: COG2321 340100010824 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 340100010825 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340100010826 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 340100010827 active site 340100010828 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 340100010829 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 340100010830 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100010831 Helix-turn-helix domain; Region: HTH_18; pfam12833 340100010832 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 340100010833 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100010834 NAD(P) binding site [chemical binding]; other site 340100010835 active site 340100010836 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 340100010837 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 340100010838 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 340100010839 putative active site [active] 340100010840 catalytic site [active] 340100010841 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 340100010842 putative active site [active] 340100010843 catalytic site [active] 340100010844 3-carboxy-cis,cis-muconate cycloisomerase; Provisional; Region: PRK09053 340100010845 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 340100010846 tetramer interface [polypeptide binding]; other site 340100010847 active site 340100010848 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100010849 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 340100010850 sequence-specific DNA binding site [nucleotide binding]; other site 340100010851 salt bridge; other site 340100010852 Cupin domain; Region: Cupin_2; pfam07883 340100010853 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 340100010854 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 340100010855 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100010856 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 340100010857 dimer interface [polypeptide binding]; other site 340100010858 conserved gate region; other site 340100010859 putative PBP binding loops; other site 340100010860 ABC-ATPase subunit interface; other site 340100010861 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 340100010862 dimer interface [polypeptide binding]; other site 340100010863 conserved gate region; other site 340100010864 putative PBP binding loops; other site 340100010865 ABC-ATPase subunit interface; other site 340100010866 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100010867 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 340100010868 substrate binding pocket [chemical binding]; other site 340100010869 membrane-bound complex binding site; other site 340100010870 hinge residues; other site 340100010871 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100010872 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100010873 Walker A/P-loop; other site 340100010874 ATP binding site [chemical binding]; other site 340100010875 Q-loop/lid; other site 340100010876 ABC transporter signature motif; other site 340100010877 Walker B; other site 340100010878 D-loop; other site 340100010879 H-loop/switch region; other site 340100010880 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 340100010881 aldehyde dehydrogenase family 7 member; Region: PLN02315 340100010882 tetrameric interface [polypeptide binding]; other site 340100010883 NAD binding site [chemical binding]; other site 340100010884 catalytic residues [active] 340100010885 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 340100010886 substrate binding site [chemical binding]; other site 340100010887 dimerization interface [polypeptide binding]; other site 340100010888 active site 340100010889 calcium binding site [ion binding]; other site 340100010890 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 340100010891 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 340100010892 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 340100010893 2-methylcitrate dehydratase; Region: prpD; TIGR02330 340100010894 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 340100010895 dimerization interface [polypeptide binding]; other site 340100010896 putative DNA binding site [nucleotide binding]; other site 340100010897 putative Zn2+ binding site [ion binding]; other site 340100010898 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_6; cd08899 340100010899 putative hydrophobic ligand binding site [chemical binding]; other site 340100010900 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 340100010901 putative substrate translocation pore; other site 340100010902 Propionate catabolism activator; Region: PrpR_N; pfam06506 340100010903 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 340100010904 PAS domain; Region: PAS; smart00091 340100010905 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 340100010906 Walker A motif; other site 340100010907 ATP binding site [chemical binding]; other site 340100010908 Walker B motif; other site 340100010909 arginine finger; other site 340100010910 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 340100010911 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100010912 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100010913 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100010914 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 340100010915 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 340100010916 catalytic triad [active] 340100010917 conserved cis-peptide bond; other site 340100010918 dihydrolipoamide dehydrogenase; Validated; Region: PRK05976 340100010919 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100010920 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100010921 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 340100010922 E3 interaction surface; other site 340100010923 lipoyl attachment site [posttranslational modification]; other site 340100010924 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11857 340100010925 e3 binding domain; Region: E3_binding; pfam02817 340100010926 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 340100010927 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 340100010928 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 340100010929 alpha subunit interface [polypeptide binding]; other site 340100010930 TPP binding site [chemical binding]; other site 340100010931 heterodimer interface [polypeptide binding]; other site 340100010932 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100010933 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal; Region: OxoDH_E1alpha_N; pfam12573 340100010934 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 340100010935 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 340100010936 tetramer interface [polypeptide binding]; other site 340100010937 TPP-binding site [chemical binding]; other site 340100010938 heterodimer interface [polypeptide binding]; other site 340100010939 phosphorylation loop region [posttranslational modification] 340100010940 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100010941 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 340100010942 C-terminal domain interface [polypeptide binding]; other site 340100010943 GSH binding site (G-site) [chemical binding]; other site 340100010944 dimer interface [polypeptide binding]; other site 340100010945 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 340100010946 N-terminal domain interface [polypeptide binding]; other site 340100010947 dimer interface [polypeptide binding]; other site 340100010948 substrate binding pocket (H-site) [chemical binding]; other site 340100010949 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 340100010950 RNA binding surface [nucleotide binding]; other site 340100010951 MgtC family; Region: MgtC; pfam02308 340100010952 Fic/DOC family; Region: Fic; cl00960 340100010953 Predicted permease; Region: DUF318; cl17795 340100010954 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 340100010955 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100010956 putative active site [active] 340100010957 metal binding site [ion binding]; metal-binding site 340100010958 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 340100010959 dimer interface [polypeptide binding]; other site 340100010960 FMN binding site [chemical binding]; other site 340100010961 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100010962 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100010963 outer membrane receptor FepA; Provisional; Region: PRK13528 340100010964 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 340100010965 N-terminal plug; other site 340100010966 ligand-binding site [chemical binding]; other site 340100010967 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 340100010968 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 340100010969 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 340100010970 Walker A/P-loop; other site 340100010971 ATP binding site [chemical binding]; other site 340100010972 Q-loop/lid; other site 340100010973 ABC transporter signature motif; other site 340100010974 Walker B; other site 340100010975 D-loop; other site 340100010976 H-loop/switch region; other site 340100010977 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 340100010978 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 340100010979 dimer interface [polypeptide binding]; other site 340100010980 conserved gate region; other site 340100010981 putative PBP binding loops; other site 340100010982 ABC-ATPase subunit interface; other site 340100010983 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 340100010984 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 340100010985 dimer interface [polypeptide binding]; other site 340100010986 conserved gate region; other site 340100010987 putative PBP binding loops; other site 340100010988 ABC-ATPase subunit interface; other site 340100010989 PBP superfamily domain; Region: PBP_like_2; cl17296 340100010990 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 340100010991 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 340100010992 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 340100010993 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 340100010994 putative active site [active] 340100010995 catalytic site [active] 340100010996 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 340100010997 putative domain interface [polypeptide binding]; other site 340100010998 putative active site [active] 340100010999 catalytic site [active] 340100011000 exopolyphosphatase; Region: exo_poly_only; TIGR03706 340100011001 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 340100011002 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 340100011003 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 340100011004 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 340100011005 active site 340100011006 substrate binding site [chemical binding]; other site 340100011007 metal binding site [ion binding]; metal-binding site 340100011008 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 340100011009 dihydropteroate synthase; Region: DHPS; TIGR01496 340100011010 substrate binding pocket [chemical binding]; other site 340100011011 dimer interface [polypeptide binding]; other site 340100011012 inhibitor binding site; inhibition site 340100011013 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 340100011014 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 340100011015 Walker A motif; other site 340100011016 ATP binding site [chemical binding]; other site 340100011017 Walker B motif; other site 340100011018 arginine finger; other site 340100011019 Peptidase family M41; Region: Peptidase_M41; pfam01434 340100011020 FtsJ-like methyltransferase; Region: FtsJ; cl17430 340100011021 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 340100011022 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; pfam01985 340100011023 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 340100011024 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 340100011025 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 340100011026 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 340100011027 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 340100011028 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 340100011029 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 340100011030 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 340100011031 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 340100011032 dimer interface [polypeptide binding]; other site 340100011033 conserved gate region; other site 340100011034 putative PBP binding loops; other site 340100011035 ABC-ATPase subunit interface; other site 340100011036 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 340100011037 dimer interface [polypeptide binding]; other site 340100011038 conserved gate region; other site 340100011039 putative PBP binding loops; other site 340100011040 ABC-ATPase subunit interface; other site 340100011041 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 340100011042 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100011043 Walker A/P-loop; other site 340100011044 ATP binding site [chemical binding]; other site 340100011045 Q-loop/lid; other site 340100011046 ABC transporter signature motif; other site 340100011047 Walker B; other site 340100011048 D-loop; other site 340100011049 H-loop/switch region; other site 340100011050 TOBE domain; Region: TOBE_2; pfam08402 340100011051 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011052 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011053 The 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 340100011054 dimerization interface [polypeptide binding]; other site 340100011055 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 340100011056 catalytic core [active] 340100011057 short chain dehydrogenase; Provisional; Region: PRK07024 340100011058 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100011059 NAD(P) binding site [chemical binding]; other site 340100011060 active site 340100011061 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 340100011062 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100011063 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 340100011064 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 340100011065 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340100011066 ATP-grasp domain; Region: ATP-grasp_4; cl17255 340100011067 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 340100011068 IMP binding site; other site 340100011069 dimer interface [polypeptide binding]; other site 340100011070 interdomain contacts; other site 340100011071 partial ornithine binding site; other site 340100011072 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 340100011073 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 340100011074 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 340100011075 catalytic site [active] 340100011076 subunit interface [polypeptide binding]; other site 340100011077 transaldolase-like protein; Provisional; Region: PTZ00411 340100011078 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 340100011079 active site 340100011080 dimer interface [polypeptide binding]; other site 340100011081 catalytic residue [active] 340100011082 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 340100011083 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 340100011084 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 340100011085 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 340100011086 dimer interface [polypeptide binding]; other site 340100011087 conserved gate region; other site 340100011088 putative PBP binding loops; other site 340100011089 ABC-ATPase subunit interface; other site 340100011090 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 340100011091 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100011092 Walker A/P-loop; other site 340100011093 ATP binding site [chemical binding]; other site 340100011094 Q-loop/lid; other site 340100011095 ABC transporter signature motif; other site 340100011096 Walker B; other site 340100011097 D-loop; other site 340100011098 H-loop/switch region; other site 340100011099 NMT1-like family; Region: NMT1_2; pfam13379 340100011100 NMT1/THI5 like; Region: NMT1; pfam09084 340100011101 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100011102 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100011103 recombination protein RecR; Reviewed; Region: recR; PRK00076 340100011104 RecR protein; Region: RecR; pfam02132 340100011105 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 340100011106 putative active site [active] 340100011107 putative metal-binding site [ion binding]; other site 340100011108 tetramer interface [polypeptide binding]; other site 340100011109 hypothetical protein; Validated; Region: PRK00153 340100011110 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 340100011111 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 340100011112 Walker A motif; other site 340100011113 ATP binding site [chemical binding]; other site 340100011114 Walker B motif; other site 340100011115 arginine finger; other site 340100011116 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 340100011117 Part of AAA domain; Region: AAA_19; pfam13245 340100011118 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 340100011119 Family description; Region: UvrD_C_2; pfam13538 340100011120 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 340100011121 probable DNA repair protein; Region: TIGR03623 340100011122 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100011123 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 340100011124 putative substrate translocation pore; other site 340100011125 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 340100011126 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 340100011127 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 340100011128 intracellular protease, PfpI family; Region: PfpI; TIGR01382 340100011129 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 340100011130 conserved cys residue [active] 340100011131 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 340100011132 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 340100011133 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 340100011134 Hemerythrin-like domain; Region: Hr-like; cd12108 340100011135 Fe binding site [ion binding]; other site 340100011136 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 340100011137 putative deacylase active site [active] 340100011138 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 340100011139 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 340100011140 active site 340100011141 DNA binding site [nucleotide binding] 340100011142 Int/Topo IB signature motif; other site 340100011143 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 340100011144 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011145 The 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 340100011146 dimerization interface [polypeptide binding]; other site 340100011147 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100011148 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100011149 PYR/PP interface [polypeptide binding]; other site 340100011150 dimer interface [polypeptide binding]; other site 340100011151 TPP binding site [chemical binding]; other site 340100011152 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100011153 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 340100011154 TPP-binding site [chemical binding]; other site 340100011155 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 340100011156 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100011157 FAD binding site [chemical binding]; other site 340100011158 substrate binding pocket [chemical binding]; other site 340100011159 catalytic base [active] 340100011160 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 340100011161 putative active site [active] 340100011162 putative catalytic site [active] 340100011163 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 340100011164 4Fe-4S binding domain; Region: Fer4; pfam00037 340100011165 4Fe-4S binding domain; Region: Fer4; pfam00037 340100011166 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 340100011167 dimerization interface [polypeptide binding]; other site 340100011168 FAD binding pocket [chemical binding]; other site 340100011169 FAD binding motif [chemical binding]; other site 340100011170 catalytic residues [active] 340100011171 NAD binding pocket [chemical binding]; other site 340100011172 phosphate binding motif [ion binding]; other site 340100011173 beta-alpha-beta structure motif; other site 340100011174 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 340100011175 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 340100011176 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 340100011177 substrate binding site [chemical binding]; other site 340100011178 oxyanion hole (OAH) forming residues; other site 340100011179 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 340100011180 oxyanion hole (OAH) forming residues; other site 340100011181 trimer interface [polypeptide binding]; other site 340100011182 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 340100011183 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 340100011184 non-specific DNA binding site [nucleotide binding]; other site 340100011185 salt bridge; other site 340100011186 sequence-specific DNA binding site [nucleotide binding]; other site 340100011187 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 340100011188 ADP binding site [chemical binding]; other site 340100011189 magnesium binding site [ion binding]; other site 340100011190 putative shikimate binding site; other site 340100011191 aldehyde dehydrogenase; Provisional; Region: PRK11903 340100011192 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 340100011193 NAD(P) binding site [chemical binding]; other site 340100011194 catalytic residues [active] 340100011195 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 340100011196 Benzoate CoA ligase (BCL) and 4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase); Region: BCL_4HBCL; cd05959 340100011197 dimer interface [polypeptide binding]; other site 340100011198 acyl-activating enzyme (AAE) consensus motif; other site 340100011199 putative active site [active] 340100011200 putative AMP binding site [chemical binding]; other site 340100011201 putative CoA binding site [chemical binding]; other site 340100011202 chemical substrate binding site [chemical binding]; other site 340100011203 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100011204 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100011205 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 340100011206 putative ligand binding site [chemical binding]; other site 340100011207 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 340100011208 TM-ABC transporter signature motif; other site 340100011209 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100011210 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 340100011211 TM-ABC transporter signature motif; other site 340100011212 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100011213 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100011214 Walker A/P-loop; other site 340100011215 ATP binding site [chemical binding]; other site 340100011216 Q-loop/lid; other site 340100011217 ABC transporter signature motif; other site 340100011218 Walker B; other site 340100011219 D-loop; other site 340100011220 H-loop/switch region; other site 340100011221 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100011222 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100011223 Walker A/P-loop; other site 340100011224 ATP binding site [chemical binding]; other site 340100011225 Q-loop/lid; other site 340100011226 ABC transporter signature motif; other site 340100011227 Walker B; other site 340100011228 D-loop; other site 340100011229 H-loop/switch region; other site 340100011230 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011231 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100011232 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 340100011233 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100011234 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 340100011235 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 340100011236 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 340100011237 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100011238 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100011239 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011240 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011241 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 340100011242 putative effector binding pocket; other site 340100011243 dimerization interface [polypeptide binding]; other site 340100011244 hypothetical protein; Validated; Region: PRK07586 340100011245 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100011246 PYR/PP interface [polypeptide binding]; other site 340100011247 dimer interface [polypeptide binding]; other site 340100011248 TPP binding site [chemical binding]; other site 340100011249 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 340100011250 TPP-binding site [chemical binding]; other site 340100011251 dimer interface [polypeptide binding]; other site 340100011252 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100011253 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 340100011254 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011255 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011256 The 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 340100011257 dimerization interface [polypeptide binding]; other site 340100011258 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011259 Coenzyme A transferase; Region: CoA_trans; cl17247 340100011260 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100011261 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 340100011262 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100011263 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100011264 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 340100011265 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 340100011266 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 340100011267 ATP-grasp domain; Region: ATP-grasp; pfam02222 340100011268 AIR carboxylase; Region: AIRC; pfam00731 340100011269 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 340100011270 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 340100011271 ATP binding site [chemical binding]; other site 340100011272 active site 340100011273 substrate binding site [chemical binding]; other site 340100011274 Uncharacterized conserved protein [Function unknown]; Region: COG3791 340100011275 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 340100011276 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 340100011277 intersubunit interface [polypeptide binding]; other site 340100011278 active site 340100011279 zinc binding site [ion binding]; other site 340100011280 Na+ binding site [ion binding]; other site 340100011281 Uncharacterized conserved protein [Function unknown]; Region: COG3791 340100011282 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 340100011283 rRNA binding site [nucleotide binding]; other site 340100011284 predicted 30S ribosome binding site; other site 340100011285 hypothetical protein; Provisional; Region: PRK09262 340100011286 Uncharacterized proteins, LmbE homologs [Function unknown]; Region: COG2120 340100011287 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011288 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100011289 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011290 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 340100011291 dimerization interface [polypeptide binding]; other site 340100011292 substrate binding pocket [chemical binding]; other site 340100011293 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 340100011294 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100011295 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 340100011296 MPT binding site; other site 340100011297 trimer interface [polypeptide binding]; other site 340100011298 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 340100011299 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 340100011300 AzlC protein; Region: AzlC; pfam03591 340100011301 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100011302 Coenzyme A binding pocket [chemical binding]; other site 340100011303 DinB family; Region: DinB; cl17821 340100011304 DinB superfamily; Region: DinB_2; pfam12867 340100011305 glutathione S-transferase; Provisional; Region: PRK15113 340100011306 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 340100011307 C-terminal domain interface [polypeptide binding]; other site 340100011308 GSH binding site (G-site) [chemical binding]; other site 340100011309 dimer interface [polypeptide binding]; other site 340100011310 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100011311 dimer interface [polypeptide binding]; other site 340100011312 N-terminal domain interface [polypeptide binding]; other site 340100011313 substrate binding pocket (H-site) [chemical binding]; other site 340100011314 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 340100011315 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100011316 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 340100011317 cyanate hydratase; Validated; Region: PRK02866 340100011318 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 340100011319 oligomer interface [polypeptide binding]; other site 340100011320 active site 340100011321 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 340100011322 Phosphoglycerate kinase; Region: PGK; pfam00162 340100011323 substrate binding site [chemical binding]; other site 340100011324 hinge regions; other site 340100011325 ADP binding site [chemical binding]; other site 340100011326 catalytic site [active] 340100011327 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 340100011328 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 340100011329 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 340100011330 transketolase; Reviewed; Region: PRK12753 340100011331 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 340100011332 TPP-binding site [chemical binding]; other site 340100011333 dimer interface [polypeptide binding]; other site 340100011334 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 340100011335 PYR/PP interface [polypeptide binding]; other site 340100011336 dimer interface [polypeptide binding]; other site 340100011337 TPP binding site [chemical binding]; other site 340100011338 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340100011339 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 340100011340 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 340100011341 putative RNAase interaction site [polypeptide binding]; other site 340100011342 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 340100011343 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 340100011344 active site 340100011345 nucleophile elbow; other site 340100011346 malic enzyme; Reviewed; Region: PRK12862 340100011347 Malic enzyme, N-terminal domain; Region: malic; pfam00390 340100011348 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 340100011349 putative NAD(P) binding site [chemical binding]; other site 340100011350 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 340100011351 aminotransferase; Validated; Region: PRK07337 340100011352 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 340100011353 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100011354 homodimer interface [polypeptide binding]; other site 340100011355 catalytic residue [active] 340100011356 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 340100011357 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100011358 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100011359 catalytic residue [active] 340100011360 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 340100011361 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 340100011362 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 340100011363 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 340100011364 [4Fe-4S] binding site [ion binding]; other site 340100011365 molybdopterin cofactor binding site; other site 340100011366 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 340100011367 molybdopterin cofactor binding site; other site 340100011368 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 340100011369 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 340100011370 [2Fe-2S] cluster binding site [ion binding]; other site 340100011371 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 340100011372 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100011373 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100011374 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 340100011375 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 340100011376 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100011377 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 340100011378 ANTAR domain; Region: ANTAR; pfam03861 340100011379 siroheme synthase; Provisional; Region: cysG; PRK10637 340100011380 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 340100011381 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 340100011382 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 340100011383 active site 340100011384 SAM binding site [chemical binding]; other site 340100011385 homodimer interface [polypeptide binding]; other site 340100011386 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100011387 active site 340100011388 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 340100011389 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 340100011390 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 340100011391 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 340100011392 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 340100011393 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 340100011394 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 340100011395 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 340100011396 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 340100011397 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 340100011398 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 340100011399 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 340100011400 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 340100011401 Protein export membrane protein; Region: SecD_SecF; pfam02355 340100011402 Malate/L-lactate dehydrogenases [Energy production and conversion]; Region: COG2055 340100011403 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 340100011404 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 340100011405 substrate binding pocket [chemical binding]; other site 340100011406 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 340100011407 active site 340100011408 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 340100011409 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 340100011410 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 340100011411 FeS/SAM binding site; other site 340100011412 TRAM domain; Region: TRAM; pfam01938 340100011413 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 340100011414 PhoH-like protein; Region: PhoH; pfam02562 340100011415 metal-binding heat shock protein; Provisional; Region: PRK00016 340100011416 FOG: CBS domain [General function prediction only]; Region: COG0517 340100011417 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 340100011418 Transporter associated domain; Region: CorC_HlyC; smart01091 340100011419 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 340100011420 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 340100011421 putative active site [active] 340100011422 catalytic triad [active] 340100011423 putative dimer interface [polypeptide binding]; other site 340100011424 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011425 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011426 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 340100011427 putative effector binding pocket; other site 340100011428 putative dimerization interface [polypeptide binding]; other site 340100011429 Predicted membrane protein [Function unknown]; Region: COG2259 340100011430 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 340100011431 short chain dehydrogenase; Provisional; Region: PRK12937 340100011432 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 340100011433 NADP binding site [chemical binding]; other site 340100011434 homodimer interface [polypeptide binding]; other site 340100011435 active site 340100011436 substrate binding site [chemical binding]; other site 340100011437 biotin synthase; Region: bioB; TIGR00433 340100011438 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 340100011439 FeS/SAM binding site; other site 340100011440 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 340100011441 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 340100011442 putative MFS family transporter protein; Provisional; Region: PRK03633 340100011443 putative substrate translocation pore; other site 340100011444 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 340100011445 catalytic triad [active] 340100011446 dimer interface [polypeptide binding]; other site 340100011447 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100011448 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100011449 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100011450 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 340100011451 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 340100011452 trimer interface [polypeptide binding]; other site 340100011453 dimer interface [polypeptide binding]; other site 340100011454 putative active site [active] 340100011455 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 340100011456 MoaE interaction surface [polypeptide binding]; other site 340100011457 MoeB interaction surface [polypeptide binding]; other site 340100011458 thiocarboxylated glycine; other site 340100011459 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 340100011460 MoaE homodimer interface [polypeptide binding]; other site 340100011461 MoaD interaction [polypeptide binding]; other site 340100011462 active site residues [active] 340100011463 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 340100011464 MPT binding site; other site 340100011465 trimer interface [polypeptide binding]; other site 340100011466 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 340100011467 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 340100011468 dimer interface [polypeptide binding]; other site 340100011469 putative functional site; other site 340100011470 putative MPT binding site; other site 340100011471 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100011472 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100011473 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100011474 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011475 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100011476 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100011477 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100011478 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 340100011479 substrate binding site [chemical binding]; other site 340100011480 oxyanion hole (OAH) forming residues; other site 340100011481 trimer interface [polypeptide binding]; other site 340100011482 Coenzyme A transferase; Region: CoA_trans; smart00882 340100011483 Coenzyme A transferase; Region: CoA_trans; cl17247 340100011484 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 340100011485 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100011486 acyl-activating enzyme (AAE) consensus motif; other site 340100011487 AMP binding site [chemical binding]; other site 340100011488 active site 340100011489 CoA binding site [chemical binding]; other site 340100011490 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 340100011491 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 340100011492 FeS/SAM binding site; other site 340100011493 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 340100011494 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 340100011495 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100011496 PBP superfamily domain; Region: PBP_like; pfam12727 340100011497 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 340100011498 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 340100011499 putative dimer interface [polypeptide binding]; other site 340100011500 [2Fe-2S] cluster binding site [ion binding]; other site 340100011501 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 340100011502 putative dimer interface [polypeptide binding]; other site 340100011503 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 340100011504 SLBB domain; Region: SLBB; pfam10531 340100011505 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 340100011506 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 340100011507 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 340100011508 catalytic loop [active] 340100011509 iron binding site [ion binding]; other site 340100011510 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; smart00929 340100011511 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 340100011512 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 340100011513 [4Fe-4S] binding site [ion binding]; other site 340100011514 molybdopterin cofactor binding site; other site 340100011515 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 340100011516 molybdopterin cofactor binding site; other site 340100011517 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 340100011518 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 340100011519 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 340100011520 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 340100011521 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 340100011522 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 340100011523 S-adenosylmethionine binding site [chemical binding]; other site 340100011524 Chromate transporter; Region: Chromate_transp; pfam02417 340100011525 Chromate transporter; Region: Chromate_transp; pfam02417 340100011526 threonine and homoserine efflux system; Provisional; Region: PRK10532 340100011527 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340100011528 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 340100011529 putative NAD(P) binding site [chemical binding]; other site 340100011530 putative active site [active] 340100011531 N-formylglutamate amidohydrolase; Region: FGase; cl01522 340100011532 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 340100011533 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 340100011534 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100011535 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 340100011536 DNA binding residues [nucleotide binding] 340100011537 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 340100011538 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 340100011539 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 340100011540 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 340100011541 Predicted integral membrane protein [Function unknown]; Region: COG5615 340100011542 integrase; Provisional; Region: PRK09692 340100011543 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 340100011544 active site 340100011545 Int/Topo IB signature motif; other site 340100011546 conjugal transfer protein TrbM; Provisional; Region: PRK13893 340100011547 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100011548 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100011549 catalytic residue [active] 340100011550 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 340100011551 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 340100011552 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 340100011553 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 340100011554 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 340100011555 Type IV secretion system proteins; Region: T4SS; pfam07996 340100011556 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 340100011557 VirB8 protein; Region: VirB8; pfam04335 340100011558 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100011559 VirB7 interaction site; other site 340100011560 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 340100011561 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 340100011562 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 340100011563 Walker A motif; other site 340100011564 hexamer interface [polypeptide binding]; other site 340100011565 ATP binding site [chemical binding]; other site 340100011566 Walker B motif; other site 340100011567 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100011568 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 340100011569 Walker A motif; other site 340100011570 ATP binding site [chemical binding]; other site 340100011571 Walker B motif; other site 340100011572 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100011573 Transposase; Region: HTH_Tnp_1; pfam01527 340100011574 putative transposase OrfB; Reviewed; Region: PHA02517 340100011575 HTH-like domain; Region: HTH_21; pfam13276 340100011576 Integrase core domain; Region: rve; pfam00665 340100011577 Integrase core domain; Region: rve_3; pfam13683 340100011578 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 340100011579 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100011580 FCD domain; Region: FCD; pfam07729 340100011581 glutathione reductase; Validated; Region: PRK06116 340100011582 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100011583 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340100011584 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 340100011585 glutathionine S-transferase; Provisional; Region: PRK10542 340100011586 C-terminal domain interface [polypeptide binding]; other site 340100011587 GSH binding site (G-site) [chemical binding]; other site 340100011588 dimer interface [polypeptide binding]; other site 340100011589 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 340100011590 dimer interface [polypeptide binding]; other site 340100011591 N-terminal domain interface [polypeptide binding]; other site 340100011592 substrate binding pocket (H-site) [chemical binding]; other site 340100011593 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100011594 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 340100011595 putative C-terminal domain interface [polypeptide binding]; other site 340100011596 putative GSH binding site (G-site) [chemical binding]; other site 340100011597 putative dimer interface [polypeptide binding]; other site 340100011598 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100011599 putative N-terminal domain interface [polypeptide binding]; other site 340100011600 putative dimer interface [polypeptide binding]; other site 340100011601 putative substrate binding pocket (H-site) [chemical binding]; other site 340100011602 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 340100011603 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 340100011604 C-terminal domain interface [polypeptide binding]; other site 340100011605 GSH binding site (G-site) [chemical binding]; other site 340100011606 dimer interface [polypeptide binding]; other site 340100011607 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100011608 N-terminal domain interface [polypeptide binding]; other site 340100011609 dimer interface [polypeptide binding]; other site 340100011610 substrate binding pocket (H-site) [chemical binding]; other site 340100011611 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 340100011612 YciI-like protein; Reviewed; Region: PRK12863 340100011613 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100011614 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 340100011615 active site 340100011616 dimer interface [polypeptide binding]; other site 340100011617 metal binding site [ion binding]; metal-binding site 340100011618 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 340100011619 Homeodomain-like domain; Region: HTH_32; pfam13565 340100011620 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100011621 Integrase core domain; Region: rve; pfam00665 340100011622 Integrase core domain; Region: rve_3; pfam13683 340100011623 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 340100011624 metal binding site [ion binding]; metal-binding site 340100011625 substrate binding pocket [chemical binding]; other site 340100011626 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 340100011627 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100011628 Winged helix-turn helix; Region: HTH_29; pfam13551 340100011629 Homeodomain-like domain; Region: HTH_32; pfam13565 340100011630 DDE superfamily endonuclease; Region: DDE_3; pfam13358 340100011631 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 340100011632 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100011633 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 340100011634 beta subunit interaction site [polypeptide binding]; other site 340100011635 alpha subunit interaction site [polypeptide binding]; other site 340100011636 iron-sulfur cluster [ion binding]; other site 340100011637 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 340100011638 beta subunit interface [polypeptide binding]; other site 340100011639 alpha subunit interface [polypeptide binding]; other site 340100011640 active site 340100011641 substrate binding site [chemical binding]; other site 340100011642 Fe binding site [ion binding]; other site 340100011643 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 340100011644 inter-subunit interface; other site 340100011645 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 340100011646 [2Fe-2S] cluster binding site [ion binding]; other site 340100011647 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 340100011648 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100011649 cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase; Region: BphB_TodD; TIGR03325 340100011650 cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)-like, classical (c) SDRs; Region: BphB-like_SDR_c; cd05348 340100011651 NAD binding site [chemical binding]; other site 340100011652 active site 340100011653 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 340100011654 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 340100011655 iron-sulfur cluster [ion binding]; other site 340100011656 [2Fe-2S] cluster binding site [ion binding]; other site 340100011657 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 340100011658 hydrophobic ligand binding site; other site 340100011659 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 340100011660 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 340100011661 putative substrate translocation pore; other site 340100011662 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100011663 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100011664 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100011665 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 340100011666 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 340100011667 dimerization interface [polypeptide binding]; other site 340100011668 putative substrate binding pocket [chemical binding]; other site 340100011669 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 340100011670 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 340100011671 dimer interface [polypeptide binding]; other site 340100011672 active site 340100011673 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 340100011674 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 340100011675 octamer interface [polypeptide binding]; other site 340100011676 active site 340100011677 Tripartite tricarboxylate transporter family receptor; Region: TctC; pfam03401 340100011678 Dienelactone hydrolase family; Region: DLH; pfam01738 340100011679 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 340100011680 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 340100011681 active site 340100011682 dimer interface [polypeptide binding]; other site 340100011683 metal binding site [ion binding]; metal-binding site 340100011684 Helix-turn-helix domain; Region: HTH_18; pfam12833 340100011685 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100011686 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100011687 Walker A/P-loop; other site 340100011688 ATP binding site [chemical binding]; other site 340100011689 Q-loop/lid; other site 340100011690 ABC transporter signature motif; other site 340100011691 Walker B; other site 340100011692 D-loop; other site 340100011693 H-loop/switch region; other site 340100011694 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100011695 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100011696 Walker A/P-loop; other site 340100011697 ATP binding site [chemical binding]; other site 340100011698 Q-loop/lid; other site 340100011699 ABC transporter signature motif; other site 340100011700 Walker B; other site 340100011701 D-loop; other site 340100011702 H-loop/switch region; other site 340100011703 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100011704 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 340100011705 TM-ABC transporter signature motif; other site 340100011706 Winged helix-turn helix; Region: HTH_29; pfam13551 340100011707 Integrase core domain; Region: rve; pfam00665 340100011708 AAA domain; Region: AAA_22; pfam13401 340100011709 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 340100011710 Walker A motif; other site 340100011711 ATP binding site [chemical binding]; other site 340100011712 Walker B motif; other site 340100011713 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100011714 Transposase; Region: HTH_Tnp_1; pfam01527 340100011715 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 340100011716 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 340100011717 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 340100011718 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 340100011719 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 340100011720 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 340100011721 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 340100011722 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 340100011723 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 340100011724 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 340100011725 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100011726 Transposase; Region: HTH_Tnp_1; pfam01527 340100011727 putative transposase OrfB; Reviewed; Region: PHA02517 340100011728 HTH-like domain; Region: HTH_21; pfam13276 340100011729 Integrase core domain; Region: rve; pfam00665 340100011730 Integrase core domain; Region: rve_3; pfam13683 340100011731 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 340100011732 AAA domain; Region: AAA_30; pfam13604 340100011733 Family description; Region: UvrD_C_2; pfam13538 340100011734 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 340100011735 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100011736 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 340100011737 dimer interface [polypeptide binding]; other site 340100011738 ssDNA binding site [nucleotide binding]; other site 340100011739 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100011740 Domain of unknown function (DUF3560); Region: DUF3560; pfam12083 340100011741 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100011742 MPN+ (JAMM) motif; other site 340100011743 Zinc-binding site [ion binding]; other site 340100011744 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 340100011745 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 340100011746 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 340100011747 catalytic residues [active] 340100011748 central insert; other site 340100011749 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 340100011750 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 340100011751 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 340100011752 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 340100011753 binding surface 340100011754 TPR motif; other site 340100011755 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3685 340100011756 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 340100011757 putative transposase OrfB; Reviewed; Region: PHA02517 340100011758 HTH-like domain; Region: HTH_21; pfam13276 340100011759 Integrase core domain; Region: rve; pfam00665 340100011760 Integrase core domain; Region: rve_3; pfam13683 340100011761 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100011762 Transposase; Region: HTH_Tnp_1; pfam01527 340100011763 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 340100011764 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011765 active site 340100011766 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 340100011767 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100011768 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 340100011769 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100011770 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 340100011771 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 340100011772 active site 340100011773 oxalacetate binding site [chemical binding]; other site 340100011774 citrylCoA binding site [chemical binding]; other site 340100011775 coenzyme A binding site [chemical binding]; other site 340100011776 catalytic triad [active] 340100011777 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 340100011778 active site 2 [active] 340100011779 active site 1 [active] 340100011780 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100011781 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011782 active site 340100011783 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100011784 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340100011785 NAD(P) binding site [chemical binding]; other site 340100011786 homotetramer interface [polypeptide binding]; other site 340100011787 homodimer interface [polypeptide binding]; other site 340100011788 active site 340100011789 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100011790 CoA binding domain; Region: CoA_binding_2; pfam13380 340100011791 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100011792 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100011793 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011794 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100011795 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100011796 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 340100011797 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 340100011798 Ligand binding site [chemical binding]; other site 340100011799 Electron transfer flavoprotein domain; Region: ETF; pfam01012 340100011800 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 340100011801 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 340100011802 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 340100011803 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100011804 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 340100011805 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 340100011806 active site 340100011807 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 340100011808 non-specific DNA binding site [nucleotide binding]; other site 340100011809 salt bridge; other site 340100011810 sequence-specific DNA binding site [nucleotide binding]; other site 340100011811 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 340100011812 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 340100011813 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 340100011814 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011815 aspartate aminotransferase; Provisional; Region: PRK05764 340100011816 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 340100011817 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100011818 homodimer interface [polypeptide binding]; other site 340100011819 catalytic residue [active] 340100011820 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 340100011821 homotrimer interaction site [polypeptide binding]; other site 340100011822 putative active site [active] 340100011823 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011824 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 340100011825 NAD binding site [chemical binding]; other site 340100011826 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100011827 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011828 DNA-binding site [nucleotide binding]; DNA binding site 340100011829 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 340100011830 thiamine pyrophosphate protein; Validated; Region: PRK08199 340100011831 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340100011832 PYR/PP interface [polypeptide binding]; other site 340100011833 dimer interface [polypeptide binding]; other site 340100011834 TPP binding site [chemical binding]; other site 340100011835 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 340100011836 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 340100011837 TPP-binding site [chemical binding]; other site 340100011838 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100011839 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011840 DNA-binding site [nucleotide binding]; DNA binding site 340100011841 FCD domain; Region: FCD; pfam07729 340100011842 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011843 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100011844 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011845 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100011846 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 340100011847 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100011848 DNA-binding site [nucleotide binding]; DNA binding site 340100011849 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 340100011850 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011851 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 340100011852 Fumarase C-terminus; Region: Fumerase_C; pfam05683 340100011853 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100011854 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100011855 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 340100011856 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 340100011857 Zn2+ binding site [ion binding]; other site 340100011858 Mg2+ binding site [ion binding]; other site 340100011859 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100011860 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 340100011861 active site 340100011862 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_8; cd12167 340100011863 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011864 putative ligand binding site [chemical binding]; other site 340100011865 putative NAD binding site [chemical binding]; other site 340100011866 catalytic site [active] 340100011867 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100011868 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100011869 DNA binding site [nucleotide binding] 340100011870 domain linker motif; other site 340100011871 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 340100011872 putative dimerization interface [polypeptide binding]; other site 340100011873 putative ligand binding site [chemical binding]; other site 340100011874 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100011875 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 340100011876 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100011877 DctM-like transporters; Region: DctM; pfam06808 340100011878 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100011879 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 340100011880 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 340100011881 putative substrate translocation pore; other site 340100011882 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100011883 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 340100011884 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 340100011885 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 340100011886 4Fe-4S binding domain; Region: Fer4; cl02805 340100011887 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 340100011888 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 340100011889 [4Fe-4S] binding site [ion binding]; other site 340100011890 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 340100011891 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 340100011892 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 340100011893 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 340100011894 molybdopterin cofactor binding site; other site 340100011895 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 340100011896 dimer interface [polypeptide binding]; other site 340100011897 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100011898 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 340100011899 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 340100011900 FMN binding site [chemical binding]; other site 340100011901 substrate binding site [chemical binding]; other site 340100011902 putative catalytic residue [active] 340100011903 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100011904 Helix-turn-helix domain; Region: HTH_18; pfam12833 340100011905 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100011906 EamA-like transporter family; Region: EamA; pfam00892 340100011907 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 340100011908 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 340100011909 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 340100011910 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 340100011911 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 340100011912 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 340100011913 Cytochrome c; Region: Cytochrom_C; cl11414 340100011914 Cytochrome c; Region: Cytochrom_C; cl11414 340100011915 putative acetyltransferase; Provisional; Region: PRK03624 340100011916 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100011917 Coenzyme A binding pocket [chemical binding]; other site 340100011918 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 340100011919 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 340100011920 N-terminal plug; other site 340100011921 ligand-binding site [chemical binding]; other site 340100011922 Protein of unknown function, DUF488; Region: DUF488; cl01246 340100011923 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 340100011924 Uncharacterized conserved protein [Function unknown]; Region: COG2353 340100011925 hypothetical protein; Provisional; Region: PRK06486 340100011926 active site 340100011927 intersubunit interface [polypeptide binding]; other site 340100011928 Zn2+ binding site [ion binding]; other site 340100011929 amidase; Provisional; Region: PRK07486 340100011930 Amidase; Region: Amidase; cl11426 340100011931 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 340100011932 putative acetyltransferase; Provisional; Region: PRK03624 340100011933 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100011934 Coenzyme A binding pocket [chemical binding]; other site 340100011935 Di- and tripeptidases [Amino acid transport and metabolism]; Region: PepD; COG2195 340100011936 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 340100011937 putative metal binding site [ion binding]; other site 340100011938 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 340100011939 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 340100011940 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 340100011941 E-class dimer interface [polypeptide binding]; other site 340100011942 P-class dimer interface [polypeptide binding]; other site 340100011943 active site 340100011944 Cu2+ binding site [ion binding]; other site 340100011945 Zn2+ binding site [ion binding]; other site 340100011946 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 340100011947 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 340100011948 Walker A motif; other site 340100011949 ATP binding site [chemical binding]; other site 340100011950 Walker B motif; other site 340100011951 arginine finger; other site 340100011952 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 340100011953 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 340100011954 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 340100011955 putative dimer interface [polypeptide binding]; other site 340100011956 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 340100011957 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100011958 active site 340100011959 catalytic tetrad [active] 340100011960 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 340100011961 intersubunit interface [polypeptide binding]; other site 340100011962 active site 340100011963 Zn2+ binding site [ion binding]; other site 340100011964 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100011965 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 340100011966 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011967 NAD binding site [chemical binding]; other site 340100011968 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 340100011969 Uncharacterized conserved protein [Function unknown]; Region: COG2128 340100011970 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 340100011971 Predicted transcriptional regulator [Transcription]; Region: COG1959 340100011972 Transcriptional regulator; Region: Rrf2; pfam02082 340100011973 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 340100011974 Domain of unknown function (DUF802); Region: DUF802; pfam05650 340100011975 hypothetical protein; Provisional; Region: PRK09040 340100011976 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100011977 ligand binding site [chemical binding]; other site 340100011978 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 340100011979 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 340100011980 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 340100011981 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 340100011982 active site 340100011983 Bacterial protein of unknown function (DUF899); Region: DUF899; pfam05988 340100011984 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_6; cd12165 340100011985 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 340100011986 putative ligand binding site [chemical binding]; other site 340100011987 NAD binding site [chemical binding]; other site 340100011988 dimer interface [polypeptide binding]; other site 340100011989 putative catalytic site [active] 340100011990 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 340100011991 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100011992 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100011993 Walker A/P-loop; other site 340100011994 ATP binding site [chemical binding]; other site 340100011995 Q-loop/lid; other site 340100011996 ABC transporter signature motif; other site 340100011997 Walker B; other site 340100011998 D-loop; other site 340100011999 H-loop/switch region; other site 340100012000 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100012001 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100012002 Walker A/P-loop; other site 340100012003 ATP binding site [chemical binding]; other site 340100012004 Q-loop/lid; other site 340100012005 ABC transporter signature motif; other site 340100012006 Walker B; other site 340100012007 D-loop; other site 340100012008 H-loop/switch region; other site 340100012009 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340100012010 D-ala-D-ala transporter subunit; Provisional; Region: PRK09881 340100012011 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 340100012012 dimer interface [polypeptide binding]; other site 340100012013 conserved gate region; other site 340100012014 putative PBP binding loops; other site 340100012015 ABC-ATPase subunit interface; other site 340100012016 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100012017 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 340100012018 dimer interface [polypeptide binding]; other site 340100012019 conserved gate region; other site 340100012020 putative PBP binding loops; other site 340100012021 ABC-ATPase subunit interface; other site 340100012022 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 340100012023 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 340100012024 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100012025 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 340100012026 putative active site [active] 340100012027 catalytic residue [active] 340100012028 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100012029 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100012030 DNA-binding site [nucleotide binding]; DNA binding site 340100012031 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 340100012032 cyanate transporter; Region: CynX; TIGR00896 340100012033 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012034 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012035 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 340100012036 putative effector binding pocket; other site 340100012037 dimerization interface [polypeptide binding]; other site 340100012038 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 340100012039 Argininosuccinate lyase [Amino acid transport and metabolism]; Region: ArgH; COG0165 340100012040 active sites [active] 340100012041 tetramer interface [polypeptide binding]; other site 340100012042 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100012043 NMT1-like family; Region: NMT1_2; pfam13379 340100012044 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100012045 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100012046 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 340100012047 membrane-bound complex binding site; other site 340100012048 hinge residues; other site 340100012049 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 340100012050 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 340100012051 substrate binding pocket [chemical binding]; other site 340100012052 membrane-bound complex binding site; other site 340100012053 hinge residues; other site 340100012054 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 340100012055 selenophosphate synthetase; Provisional; Region: PRK00943 340100012056 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 340100012057 dimerization interface [polypeptide binding]; other site 340100012058 putative ATP binding site [chemical binding]; other site 340100012059 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 340100012060 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 340100012061 active site residue [active] 340100012062 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 340100012063 putative hydrophobic ligand binding site [chemical binding]; other site 340100012064 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 340100012065 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 340100012066 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 340100012067 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100012068 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; cl17257 340100012069 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 340100012070 Clp protease; Region: CLP_protease; pfam00574 340100012071 oligomer interface [polypeptide binding]; other site 340100012072 active site residues [active] 340100012073 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100012074 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 340100012075 putative C-terminal domain interface [polypeptide binding]; other site 340100012076 putative GSH binding site (G-site) [chemical binding]; other site 340100012077 putative dimer interface [polypeptide binding]; other site 340100012078 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100012079 putative N-terminal domain interface [polypeptide binding]; other site 340100012080 putative dimer interface [polypeptide binding]; other site 340100012081 putative substrate binding pocket (H-site) [chemical binding]; other site 340100012082 Protein of unknown function (DUF1470); Region: DUF1470; pfam07336 340100012083 CGNR zinc finger; Region: zf-CGNR; pfam11706 340100012084 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 340100012085 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 340100012086 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100012087 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100012088 enoyl-CoA hydratase; Provisional; Region: PRK06495 340100012089 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 340100012090 substrate binding site [chemical binding]; other site 340100012091 oxyanion hole (OAH) forming residues; other site 340100012092 trimer interface [polypeptide binding]; other site 340100012093 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100012094 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100012095 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 340100012096 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 340100012097 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100012098 active site 340100012099 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 340100012100 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 340100012101 active site 340100012102 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012103 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012104 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012105 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 340100012106 putative dimerization interface [polypeptide binding]; other site 340100012107 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 340100012108 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 340100012109 active site 340100012110 putative glutathione S-transferase; Provisional; Region: PRK10357 340100012111 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 340100012112 putative C-terminal domain interface [polypeptide binding]; other site 340100012113 putative GSH binding site (G-site) [chemical binding]; other site 340100012114 putative dimer interface [polypeptide binding]; other site 340100012115 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 340100012116 dimer interface [polypeptide binding]; other site 340100012117 N-terminal domain interface [polypeptide binding]; other site 340100012118 putative substrate binding pocket (H-site) [chemical binding]; other site 340100012119 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 340100012120 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012121 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012122 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 340100012123 GAF domain; Region: GAF; pfam01590 340100012124 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2508 340100012125 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 340100012126 short chain dehydrogenase; Provisional; Region: PRK12829 340100012127 classical (c) SDRs; Region: SDR_c; cd05233 340100012128 NAD(P) binding site [chemical binding]; other site 340100012129 active site 340100012130 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100012131 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 340100012132 putative ligand binding site [chemical binding]; other site 340100012133 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 340100012134 TM-ABC transporter signature motif; other site 340100012135 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100012136 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 340100012137 TM-ABC transporter signature motif; other site 340100012138 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100012139 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100012140 Walker A/P-loop; other site 340100012141 ATP binding site [chemical binding]; other site 340100012142 Q-loop/lid; other site 340100012143 ABC transporter signature motif; other site 340100012144 Walker B; other site 340100012145 D-loop; other site 340100012146 H-loop/switch region; other site 340100012147 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100012148 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100012149 Walker A/P-loop; other site 340100012150 ATP binding site [chemical binding]; other site 340100012151 Q-loop/lid; other site 340100012152 ABC transporter signature motif; other site 340100012153 Walker B; other site 340100012154 D-loop; other site 340100012155 H-loop/switch region; other site 340100012156 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 340100012157 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100012158 This enzymatic domain is part of bacterial polyketide synthases; Region: PKS_KR; smart00822 340100012159 NAD(P) binding site [chemical binding]; other site 340100012160 active site 340100012161 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 340100012162 active site 340100012163 Zn binding site [ion binding]; other site 340100012164 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012165 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012166 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012167 The 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 340100012168 dimerization interface [polypeptide binding]; other site 340100012169 amino acid transporter; Region: 2A0306; TIGR00909 340100012170 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100012171 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012172 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100012173 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012174 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 340100012175 putative active site [active] 340100012176 putative metal binding site [ion binding]; other site 340100012177 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; pfam00596 340100012178 intersubunit interface [polypeptide binding]; other site 340100012179 active site 340100012180 Zn2+ binding site [ion binding]; other site 340100012181 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100012182 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 340100012183 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012184 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012185 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 340100012186 putative effector binding pocket; other site 340100012187 dimerization interface [polypeptide binding]; other site 340100012188 Response regulator receiver domain; Region: Response_reg; pfam00072 340100012189 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100012190 active site 340100012191 phosphorylation site [posttranslational modification] 340100012192 intermolecular recognition site; other site 340100012193 dimerization interface [polypeptide binding]; other site 340100012194 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 340100012195 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100012196 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100012197 active site 340100012198 phosphorylation site [posttranslational modification] 340100012199 intermolecular recognition site; other site 340100012200 dimerization interface [polypeptide binding]; other site 340100012201 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 340100012202 DNA binding residues [nucleotide binding] 340100012203 dimerization interface [polypeptide binding]; other site 340100012204 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 340100012205 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 340100012206 Catalytic domain of Protein Kinases; Region: PKc; cd00180 340100012207 active site 340100012208 ATP binding site [chemical binding]; other site 340100012209 substrate binding site [chemical binding]; other site 340100012210 activation loop (A-loop); other site 340100012211 AAA ATPase domain; Region: AAA_16; pfam13191 340100012212 Predicted ATPase [General function prediction only]; Region: COG3899 340100012213 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 340100012214 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 340100012215 PAS domain S-box; Region: sensory_box; TIGR00229 340100012216 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 340100012217 putative active site [active] 340100012218 heme pocket [chemical binding]; other site 340100012219 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 340100012220 dimer interface [polypeptide binding]; other site 340100012221 phosphorylation site [posttranslational modification] 340100012222 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 340100012223 ATP binding site [chemical binding]; other site 340100012224 Mg2+ binding site [ion binding]; other site 340100012225 G-X-G motif; other site 340100012226 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 340100012227 oligomerisation interface [polypeptide binding]; other site 340100012228 mobile loop; other site 340100012229 roof hairpin; other site 340100012230 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 340100012231 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 340100012232 ring oligomerisation interface [polypeptide binding]; other site 340100012233 ATP/Mg binding site [chemical binding]; other site 340100012234 stacking interactions; other site 340100012235 hinge regions; other site 340100012236 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 340100012237 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100012238 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 340100012239 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012240 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 340100012241 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 340100012242 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100012243 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 340100012244 catalytic loop [active] 340100012245 iron binding site [ion binding]; other site 340100012246 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100012247 Malate/L-lactate dehydrogenases [Energy production and conversion]; Region: COG2055 340100012248 putative transposase OrfB; Reviewed; Region: PHA02517 340100012249 HTH-like domain; Region: HTH_21; pfam13276 340100012250 Integrase core domain; Region: rve; pfam00665 340100012251 Integrase core domain; Region: rve_3; pfam13683 340100012252 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100012253 Transposase; Region: HTH_Tnp_1; pfam01527 340100012254 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 340100012255 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 340100012256 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 340100012257 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 340100012258 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 340100012259 putative active site pocket [active] 340100012260 putative metal binding site [ion binding]; other site 340100012261 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 340100012262 galactarate dehydratase; Region: galactar-dH20; TIGR03248 340100012263 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 340100012264 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 340100012265 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100012266 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 340100012267 human DHRS6-like, classical (c) SDRs; Region: DHRS6_like_SDR_c; cd05368 340100012268 NAD binding site [chemical binding]; other site 340100012269 homotetramer interface [polypeptide binding]; other site 340100012270 homodimer interface [polypeptide binding]; other site 340100012271 active site 340100012272 DctM-like transporters; Region: DctM; pfam06808 340100012273 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100012274 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100012275 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100012276 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100012277 L-idonate 5-dehydrogenase; Provisional; Region: PRK09880 340100012278 L-idonate 5-dehydrogenase; Region: idonate-5-DH; cd08232 340100012279 putative NAD(P) binding site [chemical binding]; other site 340100012280 catalytic Zn binding site [ion binding]; other site 340100012281 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100012282 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100012283 DNA-binding site [nucleotide binding]; DNA binding site 340100012284 FCD domain; Region: FCD; pfam07729 340100012285 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 340100012286 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 340100012287 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340100012288 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 340100012289 active site 340100012290 dimer interface [polypeptide binding]; other site 340100012291 Competence-damaged protein; Region: CinA; pfam02464 340100012292 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 340100012293 tetramer interfaces [polypeptide binding]; other site 340100012294 binuclear metal-binding site [ion binding]; other site 340100012295 thiamine monophosphate kinase; Provisional; Region: PRK05731 340100012296 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 340100012297 ATP binding site [chemical binding]; other site 340100012298 dimerization interface [polypeptide binding]; other site 340100012299 transcription antitermination factor NusB; Region: nusB; TIGR01951 340100012300 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 340100012301 homopentamer interface [polypeptide binding]; other site 340100012302 active site 340100012303 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 340100012304 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 340100012305 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 340100012306 dimerization interface [polypeptide binding]; other site 340100012307 active site 340100012308 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100012309 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 340100012310 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100012311 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 340100012312 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100012313 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012314 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012315 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 340100012316 4-hydroxybenzoyl-CoA reductase, gamma subunit; Region: 4hydroxCoAred; TIGR03193 340100012317 catalytic loop [active] 340100012318 iron binding site [ion binding]; other site 340100012319 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100012320 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012321 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 340100012322 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 340100012323 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100012324 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100012325 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100012326 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 340100012327 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 340100012328 substrate binding pocket [chemical binding]; other site 340100012329 membrane-bound complex binding site; other site 340100012330 hinge residues; other site 340100012331 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 340100012332 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 340100012333 Walker A/P-loop; other site 340100012334 ATP binding site [chemical binding]; other site 340100012335 Q-loop/lid; other site 340100012336 ABC transporter signature motif; other site 340100012337 Walker B; other site 340100012338 D-loop; other site 340100012339 H-loop/switch region; other site 340100012340 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 340100012341 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 340100012342 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 340100012343 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 340100012344 dimer interface [polypeptide binding]; other site 340100012345 conserved gate region; other site 340100012346 ABC-ATPase subunit interface; other site 340100012347 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 340100012348 putative active site; other site 340100012349 putative metal binding residues [ion binding]; other site 340100012350 signature motif; other site 340100012351 putative triphosphate binding site [ion binding]; other site 340100012352 CHAD domain; Region: CHAD; pfam05235 340100012353 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 340100012354 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 340100012355 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 340100012356 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 340100012357 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 340100012358 S-adenosylmethionine binding site [chemical binding]; other site 340100012359 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 340100012360 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 340100012361 active site 340100012362 (T/H)XGH motif; other site 340100012363 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100012364 Benzoate membrane transport protein; Region: BenE; pfam03594 340100012365 benzoate transporter; Region: benE; TIGR00843 340100012366 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 340100012367 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 340100012368 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 340100012369 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 340100012370 active site 340100012371 purine riboside binding site [chemical binding]; other site 340100012372 Transcriptional regulators [Transcription]; Region: MarR; COG1846 340100012373 MarR family; Region: MarR; pfam01047 340100012374 MarR family; Region: MarR_2; cl17246 340100012375 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 340100012376 Autotransporter beta-domain; Region: Autotransporter; pfam03797 340100012377 Predicted transcriptional regulators [Transcription]; Region: COG1695 340100012378 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 340100012379 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 340100012380 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 340100012381 FAD binding pocket [chemical binding]; other site 340100012382 FAD binding motif [chemical binding]; other site 340100012383 phosphate binding motif [ion binding]; other site 340100012384 NAD binding pocket [chemical binding]; other site 340100012385 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 340100012386 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 340100012387 NADP binding site [chemical binding]; other site 340100012388 dimer interface [polypeptide binding]; other site 340100012389 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012390 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012391 LysR substrate binding domain; Region: LysR_substrate; pfam03466 340100012392 dimerization interface [polypeptide binding]; other site 340100012393 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 340100012394 DNA-binding interface [nucleotide binding]; DNA binding site 340100012395 HTH-like domain; Region: HTH_21; pfam13276 340100012396 Integrase core domain; Region: rve; pfam00665 340100012397 Integrase core domain; Region: rve_3; pfam13683 340100012398 HTH-like domain; Region: HTH_21; pfam13276 340100012399 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100012400 Integrase core domain; Region: rve; pfam00665 340100012401 Integrase core domain; Region: rve_3; pfam13683 340100012402 Transposase; Region: HTH_Tnp_1; pfam01527 340100012403 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 340100012404 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 340100012405 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 340100012406 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 340100012407 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 340100012408 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 340100012409 HsdM N-terminal domain; Region: HsdM_N; pfam12161 340100012410 Methyltransferase domain; Region: Methyltransf_26; pfam13659 340100012411 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 340100012412 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100012413 Transposase; Region: HTH_Tnp_1; pfam01527 340100012414 putative transposase OrfB; Reviewed; Region: PHA02517 340100012415 HTH-like domain; Region: HTH_21; pfam13276 340100012416 Integrase core domain; Region: rve; pfam00665 340100012417 Integrase core domain; Region: rve_3; pfam13683 340100012418 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 340100012419 DEAD-like helicases superfamily; Region: DEXDc; smart00487 340100012420 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 340100012421 ATP binding site [chemical binding]; other site 340100012422 putative Mg++ binding site [ion binding]; other site 340100012423 Predicted transcriptional regulator [Transcription]; Region: COG4190 340100012424 MarR family; Region: MarR; pfam01047 340100012425 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 340100012426 GTP-binding protein YchF; Reviewed; Region: PRK09601 340100012427 YchF GTPase; Region: YchF; cd01900 340100012428 G1 box; other site 340100012429 GTP/Mg2+ binding site [chemical binding]; other site 340100012430 Switch I region; other site 340100012431 G2 box; other site 340100012432 Switch II region; other site 340100012433 G3 box; other site 340100012434 G4 box; other site 340100012435 G5 box; other site 340100012436 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 340100012437 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 340100012438 putative substrate translocation pore; other site 340100012439 Predicted transcriptional regulator [Transcription]; Region: COG2345 340100012440 CAAX protease self-immunity; Region: Abi; cl00558 340100012441 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 340100012442 putative active site [active] 340100012443 catalytic residue [active] 340100012444 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 340100012445 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 340100012446 5S rRNA interface [nucleotide binding]; other site 340100012447 CTC domain interface [polypeptide binding]; other site 340100012448 L16 interface [polypeptide binding]; other site 340100012449 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 340100012450 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 340100012451 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100012452 active site 340100012453 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 340100012454 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 340100012455 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 340100012456 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 340100012457 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 340100012458 TPR repeat; Region: TPR_11; pfam13414 340100012459 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 340100012460 binding surface 340100012461 TPR motif; other site 340100012462 TPR repeat; Region: TPR_11; pfam13414 340100012463 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 340100012464 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 340100012465 DNA binding site [nucleotide binding] 340100012466 catalytic residue [active] 340100012467 H2TH interface [polypeptide binding]; other site 340100012468 putative catalytic residues [active] 340100012469 turnover-facilitating residue; other site 340100012470 intercalation triad [nucleotide binding]; other site 340100012471 8OG recognition residue [nucleotide binding]; other site 340100012472 putative reading head residues; other site 340100012473 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 340100012474 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 340100012475 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 340100012476 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 340100012477 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100012478 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100012479 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 340100012480 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012481 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012482 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 340100012483 putative effector binding pocket; other site 340100012484 putative dimerization interface [polypeptide binding]; other site 340100012485 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 340100012486 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 340100012487 motif II; other site 340100012488 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012489 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 340100012490 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 340100012491 dimer interface [polypeptide binding]; other site 340100012492 active site 340100012493 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100012494 substrate binding site [chemical binding]; other site 340100012495 catalytic residue [active] 340100012496 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 340100012497 homotrimer interaction site [polypeptide binding]; other site 340100012498 putative active site [active] 340100012499 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 340100012500 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012501 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 340100012502 substrate binding pocket [chemical binding]; other site 340100012503 dimerization interface [polypeptide binding]; other site 340100012504 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 340100012505 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 340100012506 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 340100012507 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100012508 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100012509 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 340100012510 dimer interface [polypeptide binding]; other site 340100012511 phosphorylation site [posttranslational modification] 340100012512 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 340100012513 ATP binding site [chemical binding]; other site 340100012514 Mg2+ binding site [ion binding]; other site 340100012515 G-X-G motif; other site 340100012516 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100012517 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100012518 active site 340100012519 phosphorylation site [posttranslational modification] 340100012520 intermolecular recognition site; other site 340100012521 dimerization interface [polypeptide binding]; other site 340100012522 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 340100012523 DNA binding site [nucleotide binding] 340100012524 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100012525 FAD binding domain; Region: FAD_binding_4; pfam01565 340100012526 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 340100012527 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 340100012528 active site 340100012529 substrate binding site [chemical binding]; other site 340100012530 metal binding site [ion binding]; metal-binding site 340100012531 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 340100012532 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 340100012533 active site 340100012534 dimer interface [polypeptide binding]; other site 340100012535 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 340100012536 dimer interface [polypeptide binding]; other site 340100012537 active site 340100012538 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 340100012539 putative ADP-binding pocket [chemical binding]; other site 340100012540 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100012541 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 340100012542 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 340100012543 putative ADP-binding pocket [chemical binding]; other site 340100012544 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 340100012545 putative ADP-binding pocket [chemical binding]; other site 340100012546 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100012547 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 340100012548 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 340100012549 active site 340100012550 dimer interface [polypeptide binding]; other site 340100012551 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 340100012552 Ligand Binding Site [chemical binding]; other site 340100012553 Molecular Tunnel; other site 340100012554 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100012555 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 340100012556 putative ADP-binding pocket [chemical binding]; other site 340100012557 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 340100012558 Vi polysaccharide biosynthesis protein TviC; Provisional; Region: PRK15181 340100012559 UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs; Region: UDP_AE_SDR_e; cd05256 340100012560 NAD binding site [chemical binding]; other site 340100012561 substrate binding site [chemical binding]; other site 340100012562 homodimer interface [polypeptide binding]; other site 340100012563 active site 340100012564 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 340100012565 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 340100012566 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340100012567 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 340100012568 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 340100012569 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 340100012570 Mg++ binding site [ion binding]; other site 340100012571 putative catalytic motif [active] 340100012572 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 340100012573 diiron binding motif [ion binding]; other site 340100012574 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 340100012575 thymidylate synthase; Provisional; Region: thyA; PRK13821 340100012576 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 340100012577 dimerization interface [polypeptide binding]; other site 340100012578 active site 340100012579 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 340100012580 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 340100012581 folate binding site [chemical binding]; other site 340100012582 NADP+ binding site [chemical binding]; other site 340100012583 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 340100012584 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100012585 DNA-binding site [nucleotide binding]; DNA binding site 340100012586 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 340100012587 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012588 homodimer interface [polypeptide binding]; other site 340100012589 catalytic residue [active] 340100012590 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 340100012591 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 340100012592 inhibitor-cofactor binding pocket; inhibition site 340100012593 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012594 catalytic residue [active] 340100012595 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 340100012596 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 340100012597 tetrameric interface [polypeptide binding]; other site 340100012598 NAD binding site [chemical binding]; other site 340100012599 catalytic residues [active] 340100012600 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100012601 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100012602 MlrC C-terminus; Region: MlrC_C; pfam07171 340100012603 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 340100012604 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100012605 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100012606 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 340100012607 dimer interface [polypeptide binding]; other site 340100012608 conserved gate region; other site 340100012609 putative PBP binding loops; other site 340100012610 ABC-ATPase subunit interface; other site 340100012611 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100012612 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 340100012613 dimer interface [polypeptide binding]; other site 340100012614 conserved gate region; other site 340100012615 putative PBP binding loops; other site 340100012616 ABC-ATPase subunit interface; other site 340100012617 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 340100012618 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100012619 Walker A/P-loop; other site 340100012620 ATP binding site [chemical binding]; other site 340100012621 Q-loop/lid; other site 340100012622 ABC transporter signature motif; other site 340100012623 Walker B; other site 340100012624 D-loop; other site 340100012625 H-loop/switch region; other site 340100012626 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100012627 Walker A/P-loop; other site 340100012628 ATP binding site [chemical binding]; other site 340100012629 Q-loop/lid; other site 340100012630 ABC transporter signature motif; other site 340100012631 Walker B; other site 340100012632 D-loop; other site 340100012633 H-loop/switch region; other site 340100012634 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100012635 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100012636 MlrC C-terminus; Region: MlrC_C; pfam07171 340100012637 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 340100012638 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 340100012639 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 340100012640 siroheme synthase, N-terminal domain; Region: cysG_Nterm; TIGR01470 340100012641 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 340100012642 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 340100012643 S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase; cl00304 340100012644 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 340100012645 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 340100012646 ligand binding site [chemical binding]; other site 340100012647 flexible hinge region; other site 340100012648 helix_turn_helix, cAMP Regulatory protein; Region: HTH_CRP; smart00419 340100012649 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 340100012650 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 340100012651 metal ion-dependent adhesion site (MIDAS); other site 340100012652 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 340100012653 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 340100012654 Low-spin heme binding site [chemical binding]; other site 340100012655 D-pathway; other site 340100012656 Binuclear center (active site) [active] 340100012657 K-pathway; other site 340100012658 Putative proton exit pathway; other site 340100012659 Putative water exit pathway; other site 340100012660 Cytochrome c; Region: Cytochrom_C; pfam00034 340100012661 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 340100012662 Subunit I/III interface [polypeptide binding]; other site 340100012663 MoxR-like ATPases [General function prediction only]; Region: COG0714 340100012664 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 340100012665 Walker A motif; other site 340100012666 ATP binding site [chemical binding]; other site 340100012667 Walker B motif; other site 340100012668 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 340100012669 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100012670 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 340100012671 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 340100012672 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 340100012673 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 340100012674 Ethylbenzene dehydrogenase; Region: EB_dh; smart00887 340100012675 putative ligand binding site [chemical binding]; other site 340100012676 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 340100012677 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100012678 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100012679 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 340100012680 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; cl17220 340100012681 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100012682 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 340100012683 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 340100012684 FeS/SAM binding site; other site 340100012685 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 340100012686 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 340100012687 active site 340100012688 SAM binding site [chemical binding]; other site 340100012689 homodimer interface [polypeptide binding]; other site 340100012690 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 340100012691 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 340100012692 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 340100012693 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 340100012694 structural tetrad; other site 340100012695 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 340100012696 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100012697 Walker A/P-loop; other site 340100012698 ATP binding site [chemical binding]; other site 340100012699 Q-loop/lid; other site 340100012700 ABC transporter signature motif; other site 340100012701 Walker B; other site 340100012702 D-loop; other site 340100012703 H-loop/switch region; other site 340100012704 CcmB protein; Region: CcmB; cl17444 340100012705 heme exporter protein CcmC; Region: ccmC; TIGR01191 340100012706 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 340100012707 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 340100012708 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 340100012709 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 340100012710 catalytic residues [active] 340100012711 central insert; other site 340100012712 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 340100012713 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 340100012714 binding surface 340100012715 TPR motif; other site 340100012716 glycine dehydrogenase; Provisional; Region: PRK05367 340100012717 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 340100012718 tetramer interface [polypeptide binding]; other site 340100012719 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012720 catalytic residue [active] 340100012721 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 340100012722 tetramer interface [polypeptide binding]; other site 340100012723 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100012724 catalytic residue [active] 340100012725 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 340100012726 lipoyl attachment site [posttranslational modification]; other site 340100012727 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 340100012728 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 340100012729 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100012730 4Fe-4S binding domain; Region: Fer4; cl02805 340100012731 NapD protein; Region: NapD; pfam03927 340100012732 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 340100012733 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 340100012734 [4Fe-4S] binding site [ion binding]; other site 340100012735 molybdopterin cofactor binding site; other site 340100012736 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 340100012737 molybdopterin cofactor binding site; other site 340100012738 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 340100012739 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 340100012740 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100012741 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100012742 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 340100012743 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 340100012744 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 340100012745 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 340100012746 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 340100012747 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 340100012748 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 340100012749 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 340100012750 Predicted flavoproteins [General function prediction only]; Region: COG2081 340100012751 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 340100012752 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 340100012753 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 340100012754 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100012755 catalytic residue [active] 340100012756 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 340100012757 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 340100012758 active site 340100012759 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 340100012760 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 340100012761 trimer interface [polypeptide binding]; other site 340100012762 active site 340100012763 Family of unknown function (DUF490); Region: DUF490; pfam04357 340100012764 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 340100012765 Surface antigen; Region: Bac_surface_Ag; pfam01103 340100012766 Domain of unknown function DUF59; Region: DUF59; pfam01883 340100012767 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 340100012768 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 340100012769 Walker A motif; other site 340100012770 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 340100012771 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 340100012772 active site 340100012773 HIGH motif; other site 340100012774 KMSKS motif; other site 340100012775 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 340100012776 anticodon binding site; other site 340100012777 tRNA binding surface [nucleotide binding]; other site 340100012778 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 340100012779 dimer interface [polypeptide binding]; other site 340100012780 putative tRNA-binding site [nucleotide binding]; other site 340100012781 rhodanese superfamily protein; Provisional; Region: PRK05320 340100012782 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 340100012783 active site residue [active] 340100012784 META domain; Region: META; pfam03724 340100012785 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 340100012786 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100012787 active site 340100012788 phosphorylation site [posttranslational modification] 340100012789 intermolecular recognition site; other site 340100012790 dimerization interface [polypeptide binding]; other site 340100012791 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 340100012792 DNA binding site [nucleotide binding] 340100012793 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100012794 PEGA domain; Region: PEGA; pfam08308 340100012795 Uncharacterized protein conserved in bacteria (DUF2094); Region: DUF2094; pfam09867 340100012796 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 340100012797 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 340100012798 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 340100012799 hypothetical protein; Provisional; Region: PRK07033 340100012800 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 340100012801 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340100012802 ligand binding site [chemical binding]; other site 340100012803 type VI secretion protein, VC_A0114 family; Region: VI_chp_4; TIGR03353 340100012804 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 340100012805 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 340100012806 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 340100012807 phosphopeptide binding site; other site 340100012808 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 340100012809 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 340100012810 Walker A motif; other site 340100012811 ATP binding site [chemical binding]; other site 340100012812 Walker B motif; other site 340100012813 arginine finger; other site 340100012814 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 340100012815 Walker A motif; other site 340100012816 ATP binding site [chemical binding]; other site 340100012817 Walker B motif; other site 340100012818 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 340100012819 Uncharacterized protein conserved in bacteria (DUF2195); Region: DUF2195; cl02042 340100012820 Protein of unknown function (DUF1305); Region: DUF1305; pfam06996 340100012821 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 340100012822 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 340100012823 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 340100012824 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 340100012825 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 340100012826 ImpE protein; Region: ImpE; pfam07024 340100012827 Protein of unknown function (DUF796); Region: DUF796; pfam05638 340100012828 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517 340100012829 Protein of unknown function (DUF877); Region: DUF877; pfam05943 340100012830 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3516 340100012831 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 340100012832 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 340100012833 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 340100012834 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 340100012835 dimerization interface [polypeptide binding]; other site 340100012836 BON domain; Region: BON; pfam04972 340100012837 Protein of unknwon function (DUF3008); Region: DUF3008; pfam11450 340100012838 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 340100012839 homotrimer interaction site [polypeptide binding]; other site 340100012840 putative active site [active] 340100012841 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 340100012842 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340100012843 minor groove reading motif; other site 340100012844 helix-hairpin-helix signature motif; other site 340100012845 substrate binding pocket [chemical binding]; other site 340100012846 active site 340100012847 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 340100012848 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012849 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 340100012850 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 340100012851 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 340100012852 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 340100012853 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 340100012854 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 340100012855 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 340100012856 dimer interface [polypeptide binding]; other site 340100012857 active site 340100012858 Fimbrial protein; Region: Fimbrial; pfam00419 340100012859 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 340100012860 PapC N-terminal domain; Region: PapC_N; pfam13954 340100012861 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100012862 PapC C-terminal domain; Region: PapC_C; pfam13953 340100012863 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 340100012864 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 340100012865 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 340100012866 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 340100012867 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 340100012868 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 340100012869 conserved cys residue [active] 340100012870 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012871 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100012872 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 340100012873 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 340100012874 tetramer interface [polypeptide binding]; other site 340100012875 heme binding pocket [chemical binding]; other site 340100012876 NADPH binding site [chemical binding]; other site 340100012877 HD domain protein, cyanamide hydratase family; Region: cyanamide_fam; TIGR03401 340100012878 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 340100012879 Isochorismatase family; Region: Isochorismatase; pfam00857 340100012880 catalytic triad [active] 340100012881 dimer interface [polypeptide binding]; other site 340100012882 conserved cis-peptide bond; other site 340100012883 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100012884 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100012885 Walker A/P-loop; other site 340100012886 ATP binding site [chemical binding]; other site 340100012887 Q-loop/lid; other site 340100012888 ABC transporter signature motif; other site 340100012889 Walker B; other site 340100012890 D-loop; other site 340100012891 H-loop/switch region; other site 340100012892 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 340100012893 dimer interface [polypeptide binding]; other site 340100012894 conserved gate region; other site 340100012895 putative PBP binding loops; other site 340100012896 ABC-ATPase subunit interface; other site 340100012897 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 340100012898 dimer interface [polypeptide binding]; other site 340100012899 conserved gate region; other site 340100012900 putative PBP binding loops; other site 340100012901 ABC-ATPase subunit interface; other site 340100012902 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100012903 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 340100012904 substrate binding pocket [chemical binding]; other site 340100012905 membrane-bound complex binding site; other site 340100012906 hinge residues; other site 340100012907 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 340100012908 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 340100012909 active site residue [active] 340100012910 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 340100012911 active site residue [active] 340100012912 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 340100012913 active site residue [active] 340100012914 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 340100012915 active site residue [active] 340100012916 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 340100012917 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 340100012918 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100012919 catalytic residue [active] 340100012920 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 340100012921 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012922 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012923 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 340100012924 putative dimerization interface [polypeptide binding]; other site 340100012925 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012926 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012927 The 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 340100012928 dimerization interface [polypeptide binding]; other site 340100012929 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 340100012930 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 340100012931 progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs; Region: 5beta-POR_like_SDR_a; cd08948 340100012932 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 340100012933 NAD(P) binding site [chemical binding]; other site 340100012934 active site 340100012935 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012936 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 340100012937 Strictosidine synthase; Region: Str_synth; pfam03088 340100012938 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 340100012939 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012940 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012941 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 340100012942 putative dimerization interface [polypeptide binding]; other site 340100012943 Repair protein; Region: Repair_PSII; pfam04536 340100012944 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 340100012945 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 340100012946 Autotransporter beta-domain; Region: Autotransporter; pfam03797 340100012947 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100012948 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 340100012949 DNA binding residues [nucleotide binding] 340100012950 dimerization interface [polypeptide binding]; other site 340100012951 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 340100012952 DctM-like transporters; Region: DctM; pfam06808 340100012953 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 340100012954 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 340100012955 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100012956 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 340100012957 substrate binding site [chemical binding]; other site 340100012958 oxyanion hole (OAH) forming residues; other site 340100012959 trimer interface [polypeptide binding]; other site 340100012960 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100012961 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100012962 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 340100012963 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012964 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100012965 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100012966 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 340100012967 putative dimerization interface [polypeptide binding]; other site 340100012968 LysE type translocator; Region: LysE; cl00565 340100012969 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 340100012970 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 340100012971 molybdopterin cofactor binding site [chemical binding]; other site 340100012972 substrate binding site [chemical binding]; other site 340100012973 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 340100012974 molybdopterin cofactor binding site; other site 340100012975 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100012976 short chain dehydrogenase; Provisional; Region: PRK06125 340100012977 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 340100012978 putative NAD(P) binding site [chemical binding]; other site 340100012979 putative active site [active] 340100012980 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100012981 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340100012982 dimer interface [polypeptide binding]; other site 340100012983 active site 340100012984 catalytic residue [active] 340100012985 cystathionine beta-lyase; Provisional; Region: PRK09028 340100012986 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 340100012987 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340100012988 catalytic residue [active] 340100012989 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 340100012990 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 340100012991 ligand binding site [chemical binding]; other site 340100012992 homodimer interface [polypeptide binding]; other site 340100012993 NAD(P) binding site [chemical binding]; other site 340100012994 trimer interface B [polypeptide binding]; other site 340100012995 trimer interface A [polypeptide binding]; other site 340100012996 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 340100012997 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 340100012998 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 340100012999 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013000 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013001 The 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 340100013002 dimerization interface [polypeptide binding]; other site 340100013003 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 340100013004 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 340100013005 putative DNA binding site [nucleotide binding]; other site 340100013006 putative Zn2+ binding site [ion binding]; other site 340100013007 AsnC family; Region: AsnC_trans_reg; pfam01037 340100013008 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100013009 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013010 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 340100013011 dimerization interface [polypeptide binding]; other site 340100013012 substrate binding pocket [chemical binding]; other site 340100013013 Predicted transcriptional regulator [Transcription]; Region: COG2378 340100013014 WYL domain; Region: WYL; pfam13280 340100013015 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 340100013016 putative active site [active] 340100013017 catalytic site [active] 340100013018 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 340100013019 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 340100013020 ATP binding site [chemical binding]; other site 340100013021 putative Mg++ binding site [ion binding]; other site 340100013022 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 340100013023 nucleotide binding region [chemical binding]; other site 340100013024 ATP-binding site [chemical binding]; other site 340100013025 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 340100013026 metal ion-dependent adhesion site (MIDAS); other site 340100013027 Proteins of 100 residues with WXG; Region: WXG100; pfam06013 340100013028 Transposase domain (DUF772); Region: DUF772; pfam05598 340100013029 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 340100013030 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 340100013031 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100013032 putative acyltransferase; Provisional; Region: PRK05790 340100013033 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 340100013034 dimer interface [polypeptide binding]; other site 340100013035 active site 340100013036 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 340100013037 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 340100013038 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 340100013039 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013040 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100013041 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013042 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100013043 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 340100013044 Ligand Binding Site [chemical binding]; other site 340100013045 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 340100013046 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100013047 Protein export membrane protein; Region: SecD_SecF; cl14618 340100013048 Protein export membrane protein; Region: SecD_SecF; cl14618 340100013049 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 340100013050 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100013051 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100013052 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013053 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100013054 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013055 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100013056 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 340100013057 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013058 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 340100013059 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 340100013060 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 340100013061 active site 340100013062 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 340100013063 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 340100013064 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 340100013065 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100013066 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100013067 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 340100013068 DNA-binding site [nucleotide binding]; DNA binding site 340100013069 FCD domain; Region: FCD; pfam07729 340100013070 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 340100013071 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100013072 active site 340100013073 catalytic tetrad [active] 340100013074 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 340100013075 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100013076 active site 340100013077 catalytic tetrad [active] 340100013078 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 340100013079 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 340100013080 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 340100013081 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 340100013082 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 340100013083 integrating conjugative element protein, PFL_4695 family; Region: ICE_PFL_4695; TIGR03765 340100013084 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100013085 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 340100013086 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 340100013087 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100013088 H-loop/switch region; other site 340100013089 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 340100013090 Walker A/P-loop; other site 340100013091 ATP binding site [chemical binding]; other site 340100013092 ABC transporter; Region: ABC_tran; pfam00005 340100013093 Q-loop/lid; other site 340100013094 ABC transporter signature motif; other site 340100013095 Walker B; other site 340100013096 D-loop; other site 340100013097 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 340100013098 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100013099 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 340100013100 Walker A/P-loop; other site 340100013101 ATP binding site [chemical binding]; other site 340100013102 Q-loop/lid; other site 340100013103 ABC transporter signature motif; other site 340100013104 Walker B; other site 340100013105 D-loop; other site 340100013106 H-loop/switch region; other site 340100013107 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 340100013108 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 340100013109 ABC-ATPase subunit interface; other site 340100013110 dimer interface [polypeptide binding]; other site 340100013111 putative PBP binding regions; other site 340100013112 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 340100013113 ABC-ATPase subunit interface; other site 340100013114 dimer interface [polypeptide binding]; other site 340100013115 putative PBP binding regions; other site 340100013116 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 340100013117 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 340100013118 intersubunit interface [polypeptide binding]; other site 340100013119 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 340100013120 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 340100013121 N-terminal plug; other site 340100013122 ligand-binding site [chemical binding]; other site 340100013123 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100013124 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100013125 Helix-turn-helix domain; Region: HTH_18; pfam12833 340100013126 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100013128 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100013129 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 340100013130 dimer interface [polypeptide binding]; other site 340100013131 ssDNA binding site [nucleotide binding]; other site 340100013132 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100013133 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100013134 ParB-like nuclease domain; Region: ParBc; pfam02195 340100013135 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 340100013136 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100013137 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 340100013138 P-loop; other site 340100013139 Magnesium ion binding site [ion binding]; other site 340100013140 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100013141 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013142 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100013143 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100013144 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 340100013145 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340100013146 substrate binding pocket [chemical binding]; other site 340100013147 chain length determination region; other site 340100013148 substrate-Mg2+ binding site; other site 340100013149 catalytic residues [active] 340100013150 aspartate-rich region 1; other site 340100013151 active site lid residues [active] 340100013152 aspartate-rich region 2; other site 340100013153 MarR family; Region: MarR_2; cl17246 340100013154 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100013155 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 340100013156 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 340100013157 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 340100013158 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 340100013159 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100013160 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100013161 The 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 340100013162 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013163 dimerization interface [polypeptide binding]; other site 340100013164 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100013165 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 340100013166 salt bridge; other site 340100013167 non-specific DNA binding site [nucleotide binding]; other site 340100013168 sequence-specific DNA binding site [nucleotide binding]; other site 340100013169 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013170 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013171 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 340100013172 dimerization interface [polypeptide binding]; other site 340100013173 substrate binding pocket [chemical binding]; other site 340100013174 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 340100013175 Ligand Binding Site [chemical binding]; other site 340100013176 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 340100013177 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 340100013178 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013179 LysR substrate binding domain; Region: LysR_substrate; pfam03466 340100013180 dimerization interface [polypeptide binding]; other site 340100013181 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100013182 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 340100013183 sequence-specific DNA binding site [nucleotide binding]; other site 340100013184 salt bridge; other site 340100013185 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013186 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013187 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 340100013188 dimerization interface [polypeptide binding]; other site 340100013189 substrate binding pocket [chemical binding]; other site 340100013190 Predicted transcriptional regulator [Transcription]; Region: COG2378 340100013191 WYL domain; Region: WYL; pfam13280 340100013192 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 340100013193 putative active site [active] 340100013194 catalytic site [active] 340100013195 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 340100013196 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 340100013197 ATP binding site [chemical binding]; other site 340100013198 putative Mg++ binding site [ion binding]; other site 340100013199 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 340100013200 nucleotide binding region [chemical binding]; other site 340100013201 ATP-binding site [chemical binding]; other site 340100013202 Domain of unknown function (DUF4391); Region: DUF4391; pfam14335 340100013203 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 340100013204 DNA methylase; Region: N6_N4_Mtase; cl17433 340100013205 DNA methylase; Region: N6_N4_Mtase; pfam01555 340100013206 DNA methylase; Region: N6_N4_Mtase; cl17433 340100013207 Restriction endonuclease [Defense mechanisms]; Region: COG3587 340100013208 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 340100013209 ATP binding site [chemical binding]; other site 340100013210 putative Mg++ binding site [ion binding]; other site 340100013211 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 340100013212 metal ion-dependent adhesion site (MIDAS); other site 340100013213 Proteins of 100 residues with WXG; Region: WXG100; pfam06013 340100013214 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 340100013215 Integrase core domain; Region: rve_3; pfam13683 340100013216 Transposase; Region: HTH_Tnp_1; pfam01527 340100013217 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 340100013218 CRISPR/Cas system-associated protein Csx1; Region: Csx1_III-U; cl11817 340100013219 Domain of unknown function (DUF1887); Region: DUF1887; pfam09002 340100013220 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 340100013221 Protein phosphatase 2C; Region: PP2C_2; pfam13672 340100013222 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 340100013223 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100013224 active site 340100013225 ATP binding site [chemical binding]; other site 340100013226 substrate binding site [chemical binding]; other site 340100013227 activation loop (A-loop); other site 340100013228 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 340100013229 Walker A motif; other site 340100013230 ATP binding site [chemical binding]; other site 340100013231 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 340100013232 AAA domain; Region: AAA_30; pfam13604 340100013233 AAA domain; Region: AAA_12; pfam13087 340100013234 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 340100013235 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 340100013236 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 340100013237 RNA binding site [nucleotide binding]; other site 340100013238 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 340100013239 Putative helicase; Region: TraI_2; pfam07514 340100013240 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 340100013241 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340100013242 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 340100013243 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 340100013244 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 340100013245 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 340100013246 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 340100013247 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 340100013248 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 340100013249 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100013250 MPN+ (JAMM) motif; other site 340100013251 Zinc-binding site [ion binding]; other site 340100013252 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 340100013253 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 340100013254 catalytic residues [active] 340100013255 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 340100013256 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 340100013257 ParA/MinD ATPase like; Region: ParA; pfam10609 340100013258 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 340100013259 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 340100013260 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 340100013261 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 340100013262 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 340100013263 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 340100013264 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 340100013265 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 340100013266 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 340100013267 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 340100013268 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 340100013269 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 340100013270 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 340100013271 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 340100013272 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 340100013273 catalytic residue [active] 340100013274 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 340100013275 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 340100013276 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 340100013277 Part of AAA domain; Region: AAA_19; pfam13245 340100013278 Family description; Region: UvrD_C_2; pfam13538 340100013279 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 340100013280 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 340100013281 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100013282 ABC transporter signature motif; other site 340100013283 Walker B; other site 340100013284 D-loop; other site 340100013285 H-loop/switch region; other site 340100013286 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 340100013287 putative active site [active] 340100013288 putative metal-binding site [ion binding]; other site 340100013289 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 340100013290 nucleotide binding region [chemical binding]; other site 340100013291 ATP-binding site [chemical binding]; other site 340100013292 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 340100013293 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 340100013294 putative active site [active] 340100013295 putative NTP binding site [chemical binding]; other site 340100013296 putative nucleic acid binding site [nucleotide binding]; other site 340100013297 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100013298 Type II intron maturase; Region: Intron_maturas2; pfam01348 340100013299 Methyltransferase domain; Region: Methyltransf_26; pfam13659 340100013300 S-adenosylmethionine binding site [chemical binding]; other site 340100013301 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100013302 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 340100013303 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340100013304 putative active site [active] 340100013305 putative NTP binding site [chemical binding]; other site 340100013306 putative nucleic acid binding site [nucleotide binding]; other site 340100013307 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100013308 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 340100013309 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 340100013310 active site 340100013311 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100013312 Transposase; Region: HTH_Tnp_1; pfam01527 340100013313 putative transposase OrfB; Reviewed; Region: PHA02517 340100013314 HTH-like domain; Region: HTH_21; pfam13276 340100013315 Integrase core domain; Region: rve; pfam00665 340100013316 Integrase core domain; Region: rve_3; pfam13683 340100013317 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340100013318 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 340100013319 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 340100013320 putative active site [active] 340100013321 putative NTP binding site [chemical binding]; other site 340100013322 putative nucleic acid binding site [nucleotide binding]; other site 340100013323 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340100013324 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 340100013325 active site 340100013326 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 340100013327 Domain of unknown function (DUF932); Region: DUF932; pfam06067 340100013328 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100013329 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 340100013330 DNA topoisomerase III; Provisional; Region: PRK07726 340100013331 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 340100013332 active site 340100013333 putative interdomain interaction site [polypeptide binding]; other site 340100013334 putative metal-binding site [ion binding]; other site 340100013335 putative nucleotide binding site [chemical binding]; other site 340100013336 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 340100013337 domain I; other site 340100013338 DNA binding groove [nucleotide binding] 340100013339 phosphate binding site [ion binding]; other site 340100013340 domain II; other site 340100013341 domain III; other site 340100013342 nucleotide binding site [chemical binding]; other site 340100013343 catalytic site [active] 340100013344 domain IV; other site 340100013345 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340100013346 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100013347 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 340100013348 ssDNA binding site [nucleotide binding]; other site 340100013349 dimer interface [polypeptide binding]; other site 340100013350 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100013351 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 340100013352 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 340100013353 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 340100013354 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 340100013355 ParB-like nuclease domain; Region: ParBc; pfam02195 340100013356 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100013357 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 340100013358 Magnesium ion binding site [ion binding]; other site 340100013359 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 340100013360 integrase; Provisional; Region: PRK09692 340100013361 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 340100013362 active site 340100013363 Int/Topo IB signature motif; other site 340100013364 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013365 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100013366 active site 340100013367 catalytic residues [active] 340100013368 metal binding site [ion binding]; metal-binding site 340100013369 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100013370 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100013371 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013372 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013373 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 340100013374 putative dimerization interface [polypeptide binding]; other site 340100013375 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 340100013376 S-adenosylmethionine binding site [chemical binding]; other site 340100013377 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 340100013378 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 340100013379 thiS-thiF/thiG interaction site; other site 340100013380 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100013381 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 340100013382 BON domain; Region: BON; pfam04972 340100013383 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100013384 signal recognition particle protein; Provisional; Region: PRK10867 340100013385 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 340100013386 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 340100013387 P loop; other site 340100013388 GTP binding site [chemical binding]; other site 340100013389 Signal peptide binding domain; Region: SRP_SPB; pfam02978 340100013390 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340100013391 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 340100013392 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 340100013393 amidase catalytic site [active] 340100013394 Zn binding residues [ion binding]; other site 340100013395 substrate binding site [chemical binding]; other site 340100013396 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100013397 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 340100013398 putative C-terminal domain interface [polypeptide binding]; other site 340100013399 putative GSH binding site (G-site) [chemical binding]; other site 340100013400 putative dimer interface [polypeptide binding]; other site 340100013401 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 340100013402 putative N-terminal domain interface [polypeptide binding]; other site 340100013403 putative dimer interface [polypeptide binding]; other site 340100013404 putative substrate binding pocket (H-site) [chemical binding]; other site 340100013405 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 340100013406 MarR family; Region: MarR_2; pfam12802 340100013407 hypothetical protein; Provisional; Region: PRK07538 340100013408 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 340100013409 hypothetical protein; Provisional; Region: PRK00872 340100013410 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013411 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 340100013412 DNA-binding interface [nucleotide binding]; DNA binding site 340100013413 HTH-like domain; Region: HTH_21; pfam13276 340100013414 Integrase core domain; Region: rve; pfam00665 340100013415 Integrase core domain; Region: rve_3; pfam13683 340100013416 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013417 heat shock protein 90; Provisional; Region: PRK05218 340100013418 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 340100013419 ATP binding site [chemical binding]; other site 340100013420 Mg2+ binding site [ion binding]; other site 340100013421 G-X-G motif; other site 340100013422 azurin; Region: azurin; TIGR02695 340100013423 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 340100013424 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 340100013425 4Fe-4S binding domain; Region: Fer4_5; pfam12801 340100013426 nitrous-oxide reductase, TAT-dependent; Region: nitrous_NosZ_RR; TIGR04244 340100013427 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 340100013428 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 340100013429 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 340100013430 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340100013431 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 340100013432 Walker A/P-loop; other site 340100013433 ATP binding site [chemical binding]; other site 340100013434 Q-loop/lid; other site 340100013435 ABC transporter signature motif; other site 340100013436 Walker B; other site 340100013437 D-loop; other site 340100013438 H-loop/switch region; other site 340100013439 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 340100013440 NosL; Region: NosL; cl01769 340100013441 ApbE family; Region: ApbE; pfam02424 340100013442 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 340100013443 HTH-like domain; Region: HTH_21; pfam13276 340100013444 Integrase core domain; Region: rve; pfam00665 340100013445 Integrase core domain; Region: rve_3; pfam13683 340100013446 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 340100013447 DNA-binding interface [nucleotide binding]; DNA binding site 340100013448 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100013449 FAD binding domain; Region: FAD_binding_4; pfam01565 340100013450 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 340100013451 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 340100013452 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100013453 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100013454 DNA-binding site [nucleotide binding]; DNA binding site 340100013455 FCD domain; Region: FCD; pfam07729 340100013456 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 340100013457 homodimer interface [polypeptide binding]; other site 340100013458 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100013459 catalytic residue [active] 340100013460 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100013461 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100013462 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 340100013463 enoyl-CoA hydratase; Provisional; Region: PRK06127 340100013464 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 340100013465 substrate binding site [chemical binding]; other site 340100013466 oxyanion hole (OAH) forming residues; other site 340100013467 trimer interface [polypeptide binding]; other site 340100013468 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100013469 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100013470 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 340100013471 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 340100013472 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 340100013473 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 340100013474 Walker A/P-loop; other site 340100013475 ATP binding site [chemical binding]; other site 340100013476 Q-loop/lid; other site 340100013477 ABC transporter signature motif; other site 340100013478 Walker B; other site 340100013479 D-loop; other site 340100013480 H-loop/switch region; other site 340100013481 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 340100013482 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100013483 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 340100013484 TM-ABC transporter signature motif; other site 340100013485 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 340100013486 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 340100013487 nucleotide binding site [chemical binding]; other site 340100013488 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 340100013489 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 340100013490 classical (c) SDRs; Region: SDR_c; cd05233 340100013491 NAD(P) binding site [chemical binding]; other site 340100013492 active site 340100013493 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100013494 DctM-like transporters; Region: DctM; pfam06808 340100013495 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100013496 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100013497 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 340100013498 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100013499 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100013500 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100013501 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 340100013502 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 340100013503 active site 340100013504 acyl-CoA synthetase; Validated; Region: PRK07470 340100013505 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100013506 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 340100013507 acyl-activating enzyme (AAE) consensus motif; other site 340100013508 acyl-activating enzyme (AAE) consensus motif; other site 340100013509 putative AMP binding site [chemical binding]; other site 340100013510 putative active site [active] 340100013511 putative CoA binding site [chemical binding]; other site 340100013512 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 340100013513 trimer interface [polypeptide binding]; other site 340100013514 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 340100013515 classical (c) SDRs; Region: SDR_c; cd05233 340100013516 NAD(P) binding site [chemical binding]; other site 340100013517 active site 340100013518 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 340100013519 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 340100013520 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 340100013521 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340100013522 putative acyl-acceptor binding pocket; other site 340100013523 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340100013524 acyl carrier protein; Provisional; Region: PRK05350 340100013525 Predicted membrane protein [Function unknown]; Region: COG4648 340100013526 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100013527 AMP-binding enzyme; Region: AMP-binding; pfam00501 340100013528 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100013529 acyl-activating enzyme (AAE) consensus motif; other site 340100013530 acyl-activating enzyme (AAE) consensus motif; other site 340100013531 AMP binding site [chemical binding]; other site 340100013532 active site 340100013533 CoA binding site [chemical binding]; other site 340100013534 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases [Lipid metabolism]; Region: FabA; COG0764 340100013535 active site 2 [active] 340100013536 active site 1 [active] 340100013537 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 340100013538 Ligand binding site; other site 340100013539 Putative Catalytic site; other site 340100013540 DXD motif; other site 340100013541 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340100013542 putative acyl-acceptor binding pocket; other site 340100013543 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 340100013544 active site 340100013545 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 340100013546 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 340100013547 sequence-specific DNA binding site [nucleotide binding]; other site 340100013548 salt bridge; other site 340100013549 Winged helix-turn-helix DNA-binding; Region: HTH_35; cl17423 340100013550 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 340100013551 Mu DNA binding, I gamma subdomain; Region: HTH_Tnp_Mu_2; pfam09039 340100013552 Bacteriophage Mu transposase; Region: DDE_2; pfam02914 340100013553 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 340100013554 Uncharacterized ATPase, putative transposase [General function prediction only]; Region: COG2842 340100013555 AAA domain; Region: AAA_30; pfam13604 340100013556 Mu B transposition protein, C terminal; Region: Phage-MuB_C; pfam09077 340100013557 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 340100013558 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 340100013559 Mor transcription activator family; Region: Mor; cl02360 340100013560 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 340100013561 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100013562 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100013563 catalytic residue [active] 340100013564 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 340100013565 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 340100013566 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 340100013567 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 340100013568 Protein of unknown function (DUF935); Region: DUF935; pfam06074 340100013569 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 340100013570 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 340100013571 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 340100013572 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 340100013573 Domain of unknown function (DUF1834); Region: DUF1834; cl02087 340100013574 Protein of unknown function (DUF2635); Region: DUF2635; pfam10948 340100013575 Mu-like prophage tail sheath protein gpL [General function prediction only]; Region: COG4386 340100013576 Phage tail sheath protein; Region: Phage_sheath_1; pfam04984 340100013577 Phage tail tube protein; Region: Tail_tube; pfam10618 340100013578 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 340100013579 DNA circulation protein N-terminus; Region: DNA_circ_N; pfam07157 340100013580 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 340100013581 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 340100013582 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 340100013583 Phage protein GP46; Region: GP46; pfam07409 340100013584 Uncharacterized homolog of phage Mu protein gp47 [Function unknown]; Region: XkdT; COG3299 340100013585 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; pfam10076 340100013586 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 340100013587 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 340100013588 DNA methylase; Region: N6_N4_Mtase; pfam01555 340100013589 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 340100013590 active site 340100013591 DNA binding site [nucleotide binding] 340100013592 Int/Topo IB signature motif; other site 340100013593 Predicted exporter [General function prediction only]; Region: COG4258 340100013594 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 340100013595 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 340100013596 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 340100013597 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 340100013598 active site 340100013599 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 340100013600 putative active site 1 [active] 340100013601 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013602 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 340100013603 NAD(P) binding site [chemical binding]; other site 340100013604 active site 340100013605 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 340100013606 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 340100013607 dimer interface [polypeptide binding]; other site 340100013608 active site 340100013609 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013610 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013611 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013612 The 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 340100013613 dimerization interface [polypeptide binding]; other site 340100013614 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100013615 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 340100013616 Walker A/P-loop; other site 340100013617 ATP binding site [chemical binding]; other site 340100013618 Q-loop/lid; other site 340100013619 ABC transporter signature motif; other site 340100013620 Walker B; other site 340100013621 D-loop; other site 340100013622 H-loop/switch region; other site 340100013623 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340100013624 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 340100013625 dimer interface [polypeptide binding]; other site 340100013626 conserved gate region; other site 340100013627 putative PBP binding loops; other site 340100013628 ABC-ATPase subunit interface; other site 340100013629 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 340100013630 dimer interface [polypeptide binding]; other site 340100013631 conserved gate region; other site 340100013632 putative PBP binding loops; other site 340100013633 ABC-ATPase subunit interface; other site 340100013634 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100013635 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 340100013636 substrate binding pocket [chemical binding]; other site 340100013637 membrane-bound complex binding site; other site 340100013638 hinge residues; other site 340100013639 aspartate aminotransferase; Provisional; Region: PRK06107 340100013640 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 340100013641 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100013642 homodimer interface [polypeptide binding]; other site 340100013643 catalytic residue [active] 340100013644 hypothetical protein; Validated; Region: PRK06201 340100013645 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 340100013646 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013647 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013648 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 340100013649 putative dimerization interface [polypeptide binding]; other site 340100013650 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 340100013651 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100013652 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100013653 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013654 Putative cyclase; Region: Cyclase; cl00814 340100013655 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 340100013656 homodimer interface [polypeptide binding]; other site 340100013657 chemical substrate binding site [chemical binding]; other site 340100013658 oligomer interface [polypeptide binding]; other site 340100013659 metal binding site [ion binding]; metal-binding site 340100013660 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 340100013661 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100013662 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 340100013663 DNA binding residues [nucleotide binding] 340100013664 fec operon regulator FecR; Reviewed; Region: PRK09774 340100013665 FecR protein; Region: FecR; pfam04773 340100013666 Secretin and TonB N terminus short domain; Region: STN; smart00965 340100013667 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 340100013668 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 340100013669 N-terminal plug; other site 340100013670 ligand-binding site [chemical binding]; other site 340100013671 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100013672 short chain dehydrogenase; Provisional; Region: PRK07577 340100013673 classical (c) SDRs; Region: SDR_c; cd05233 340100013674 NAD(P) binding site [chemical binding]; other site 340100013675 active site 340100013676 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013677 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 340100013678 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 340100013679 substrate binding pocket [chemical binding]; other site 340100013680 active site 340100013681 iron coordination sites [ion binding]; other site 340100013682 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 340100013683 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013684 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 340100013685 dimerization interface [polypeptide binding]; other site 340100013686 substrate binding pocket [chemical binding]; other site 340100013687 Kynureninase [Amino acid transport and metabolism]; Region: COG3844 340100013688 kynureninase; Region: kynureninase; TIGR01814 340100013689 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 340100013690 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 340100013691 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 340100013692 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 340100013693 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 340100013694 PapC N-terminal domain; Region: PapC_N; pfam13954 340100013695 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 340100013696 PapC C-terminal domain; Region: PapC_C; pfam13953 340100013697 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 340100013698 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340100013699 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 340100013700 dimer interface [polypeptide binding]; other site 340100013701 phosphorylation site [posttranslational modification] 340100013702 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 340100013703 ATP binding site [chemical binding]; other site 340100013704 Mg2+ binding site [ion binding]; other site 340100013705 G-X-G motif; other site 340100013706 Response regulator receiver domain; Region: Response_reg; pfam00072 340100013707 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100013708 active site 340100013709 phosphorylation site [posttranslational modification] 340100013710 intermolecular recognition site; other site 340100013711 dimerization interface [polypeptide binding]; other site 340100013712 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 340100013713 putative binding surface; other site 340100013714 active site 340100013715 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100013716 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100013717 active site 340100013718 phosphorylation site [posttranslational modification] 340100013719 intermolecular recognition site; other site 340100013720 dimerization interface [polypeptide binding]; other site 340100013721 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 340100013722 DNA binding residues [nucleotide binding] 340100013723 dimerization interface [polypeptide binding]; other site 340100013724 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 340100013725 dimer interface [polypeptide binding]; other site 340100013726 phosphorylation site [posttranslational modification] 340100013727 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 340100013728 ATP binding site [chemical binding]; other site 340100013729 Mg2+ binding site [ion binding]; other site 340100013730 G-X-G motif; other site 340100013731 Response regulator receiver domain; Region: Response_reg; pfam00072 340100013732 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100013733 active site 340100013734 phosphorylation site [posttranslational modification] 340100013735 intermolecular recognition site; other site 340100013736 dimerization interface [polypeptide binding]; other site 340100013737 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013738 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013739 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 340100013740 putative effector binding pocket; other site 340100013741 dimerization interface [polypeptide binding]; other site 340100013742 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 340100013743 dimer interface [polypeptide binding]; other site 340100013744 FMN binding site [chemical binding]; other site 340100013745 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 340100013746 EamA-like transporter family; Region: EamA; pfam00892 340100013747 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 340100013748 tartrate dehydrogenase; Region: TTC; TIGR02089 340100013749 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100013750 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100013751 Helix-turn-helix domain; Region: HTH_28; pfam13518 340100013752 Transposase; Region: HTH_Tnp_1; cl17663 340100013753 putative transposase OrfB; Reviewed; Region: PHA02517 340100013754 HTH-like domain; Region: HTH_21; pfam13276 340100013755 Integrase core domain; Region: rve; pfam00665 340100013756 Integrase core domain; Region: rve_2; pfam13333 340100013757 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013758 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013759 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 340100013760 putative effector binding pocket; other site 340100013761 putative dimerization interface [polypeptide binding]; other site 340100013762 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 340100013763 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 340100013764 ABC-ATPase subunit interface; other site 340100013765 dimer interface [polypeptide binding]; other site 340100013766 putative PBP binding regions; other site 340100013767 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 340100013768 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 340100013769 Walker A/P-loop; other site 340100013770 ATP binding site [chemical binding]; other site 340100013771 Q-loop/lid; other site 340100013772 ABC transporter signature motif; other site 340100013773 Walker B; other site 340100013774 D-loop; other site 340100013775 H-loop/switch region; other site 340100013776 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 340100013777 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 340100013778 putative active site pocket [active] 340100013779 metal binding site [ion binding]; metal-binding site 340100013780 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013781 cell density-dependent motility repressor; Provisional; Region: PRK10082 340100013782 The 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 340100013783 dimerization interface [polypeptide binding]; other site 340100013784 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 340100013785 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 340100013786 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 340100013787 lysine transporter; Provisional; Region: PRK10836 340100013788 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 340100013789 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100013790 active site 340100013791 catalytic tetrad [active] 340100013792 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013793 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013794 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 340100013795 putative effector binding pocket; other site 340100013796 putative dimerization interface [polypeptide binding]; other site 340100013797 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100013798 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 340100013799 putative ligand binding site [chemical binding]; other site 340100013800 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100013801 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 340100013802 TM-ABC transporter signature motif; other site 340100013803 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100013804 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 340100013805 TM-ABC transporter signature motif; other site 340100013806 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100013807 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100013808 Walker A/P-loop; other site 340100013809 ATP binding site [chemical binding]; other site 340100013810 Q-loop/lid; other site 340100013811 ABC transporter signature motif; other site 340100013812 Walker B; other site 340100013813 D-loop; other site 340100013814 H-loop/switch region; other site 340100013815 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100013816 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100013817 Walker A/P-loop; other site 340100013818 ATP binding site [chemical binding]; other site 340100013819 Q-loop/lid; other site 340100013820 ABC transporter signature motif; other site 340100013821 Walker B; other site 340100013822 D-loop; other site 340100013823 H-loop/switch region; other site 340100013824 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 340100013825 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 340100013826 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 340100013827 active site 340100013828 DNA binding site [nucleotide binding] 340100013829 Int/Topo IB signature motif; other site 340100013830 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100013831 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100013832 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100013833 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 340100013834 N-terminal domain interface [polypeptide binding]; other site 340100013835 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 340100013836 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 340100013837 Domain of unknown function DUF20; Region: UPF0118; pfam01594 340100013838 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013839 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013840 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 340100013841 putative effector binding pocket; other site 340100013842 putative dimerization interface [polypeptide binding]; other site 340100013843 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 340100013844 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 340100013845 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100013846 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 340100013847 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 340100013848 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 340100013849 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); Region: NT5C; cl17836 340100013850 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]; Region: COG4091 340100013851 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 340100013852 SAF domain of putative dehydrogenases or oxidoreductases; Region: SAF_DH_OX_like; cd11616 340100013853 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013854 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013855 The 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 340100013856 dimerization interface [polypeptide binding]; other site 340100013857 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 340100013858 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 340100013859 putative substrate translocation pore; other site 340100013860 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 340100013861 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 340100013862 active site 340100013863 catalytic tetrad [active] 340100013864 short chain dehydrogenase; Provisional; Region: PRK06125 340100013865 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100013866 NAD(P) binding site [chemical binding]; other site 340100013867 active site 340100013868 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 340100013869 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100013870 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100013871 The 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 340100013872 dimerization interface [polypeptide binding]; other site 340100013873 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 340100013874 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100013875 Coenzyme A binding pocket [chemical binding]; other site 340100013876 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100013877 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 340100013878 putative substrate translocation pore; other site 340100013879 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 340100013880 Ligand Binding Site [chemical binding]; other site 340100013881 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 340100013882 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 340100013883 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 340100013884 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 340100013885 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 340100013886 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 340100013887 short chain dehydrogenase; Provisional; Region: PRK07577 340100013888 classical (c) SDRs; Region: SDR_c; cd05233 340100013889 NAD(P) binding site [chemical binding]; other site 340100013890 active site 340100013891 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 340100013892 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100013893 Bacterial transcriptional regulator; Region: IclR; pfam01614 340100013894 Coenzyme A transferase; Region: CoA_trans; cl17247 340100013895 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 340100013896 Muconolactone delta-isomerase; Region: MIase; cl01992 340100013897 YciI-like protein; Reviewed; Region: PRK12863 340100013898 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 340100013899 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 340100013900 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 340100013901 Putative cyclase; Region: Cyclase; cl00814 340100013902 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 340100013903 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 340100013904 active site clefts [active] 340100013905 zinc binding site [ion binding]; other site 340100013906 dimer interface [polypeptide binding]; other site 340100013907 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100013908 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 340100013909 putative C-terminal domain interface [polypeptide binding]; other site 340100013910 putative GSH binding site (G-site) [chemical binding]; other site 340100013911 putative dimer interface [polypeptide binding]; other site 340100013912 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 340100013913 N-terminal domain interface [polypeptide binding]; other site 340100013914 dimer interface [polypeptide binding]; other site 340100013915 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 340100013916 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100013917 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 340100013918 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 340100013919 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 340100013920 Flavoprotein; Region: Flavoprotein; pfam02441 340100013921 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 340100013922 putative GSH binding site [chemical binding]; other site 340100013923 catalytic residues [active] 340100013924 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 340100013925 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 340100013926 S-adenosylmethionine binding site [chemical binding]; other site 340100013927 peptide chain release factor 1; Validated; Region: prfA; PRK00591 340100013928 This domain is found in peptide chain release factors; Region: PCRF; smart00937 340100013929 RF-1 domain; Region: RF-1; pfam00472 340100013930 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 340100013931 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 340100013932 tRNA; other site 340100013933 putative tRNA binding site [nucleotide binding]; other site 340100013934 putative NADP binding site [chemical binding]; other site 340100013935 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 340100013936 integrase; Provisional; Region: PRK09692 340100013937 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 340100013938 active site 340100013939 Int/Topo IB signature motif; other site 340100013940 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 340100013941 Protein of unknown function (DUF497); Region: DUF497; cl01108 340100013942 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 340100013943 Antirestriction protein; Region: Antirestrict; pfam03230 340100013944 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 340100013945 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 340100013946 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 340100013947 ArsC family; Region: ArsC; pfam03960 340100013948 catalytic residues [active] 340100013949 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 340100013950 arsenical-resistance protein; Region: acr3; TIGR00832 340100013951 Low molecular weight phosphatase family; Region: LMWPc; cd00115 340100013952 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 340100013953 active site 340100013954 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 340100013955 dimerization interface [polypeptide binding]; other site 340100013956 putative DNA binding site [nucleotide binding]; other site 340100013957 putative Zn2+ binding site [ion binding]; other site 340100013958 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340100013959 MPN+ (JAMM) motif; other site 340100013960 Zinc-binding site [ion binding]; other site 340100013961 ParB-like nuclease domain; Region: ParBc; pfam02195 340100013962 Uncharacterized conserved protein [Function unknown]; Region: COG5489 340100013963 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100013964 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 340100013965 non-specific DNA binding site [nucleotide binding]; other site 340100013966 salt bridge; other site 340100013967 sequence-specific DNA binding site [nucleotide binding]; other site 340100013968 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 340100013969 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 340100013970 Helix-turn-helix domain; Region: HTH_17; pfam12728 340100013971 Replication initiator protein A; Region: RPA; pfam10134 340100013972 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100013973 AAA domain; Region: AAA_31; pfam13614 340100013974 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 340100013975 Walker A motif; other site 340100013976 ATP binding site [chemical binding]; other site 340100013977 P-loop; other site 340100013978 Magnesium ion binding site [ion binding]; other site 340100013979 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 340100013980 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 340100013981 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 340100013982 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 340100013983 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 340100013984 FtsI repressor; Provisional; Region: PRK10883 340100013985 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 340100013986 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 340100013987 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 340100013988 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340100013989 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 340100013990 motif II; other site 340100013991 Outer membrane efflux protein; Region: OEP; pfam02321 340100013992 Outer membrane efflux protein; Region: OEP; pfam02321 340100013993 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 340100013994 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100013995 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 340100013996 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 340100013997 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 340100013998 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100013999 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 340100014000 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 340100014001 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340100014002 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 340100014003 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 340100014004 Protein of unknown function, DUF; Region: DUF411; cl01142 340100014005 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 340100014006 Cytochrome c; Region: Cytochrom_C; pfam00034 340100014007 Putative copper export protein [Inorganic ion transport and metabolism]; Region: PcoD; COG1276 340100014008 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 340100014009 DNA-binding interface [nucleotide binding]; DNA binding site 340100014010 HTH-like domain; Region: HTH_21; pfam13276 340100014011 Integrase core domain; Region: rve; pfam00665 340100014012 Integrase core domain; Region: rve_3; pfam13683 340100014013 CopC domain; Region: CopC; pfam04234 340100014014 Domain of unknown function (DUF305); Region: DUF305; cl17794 340100014015 Predicted metal-binding protein [General function prediction only]; Region: COG3019 340100014016 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 340100014017 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 340100014018 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 340100014019 Multicopper oxidase; Region: Cu-oxidase; pfam00394 340100014020 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 340100014021 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 340100014022 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 340100014023 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 340100014024 dimerization interface [polypeptide binding]; other site 340100014025 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 340100014026 dimer interface [polypeptide binding]; other site 340100014027 phosphorylation site [posttranslational modification] 340100014028 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 340100014029 ATP binding site [chemical binding]; other site 340100014030 Mg2+ binding site [ion binding]; other site 340100014031 G-X-G motif; other site 340100014032 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 340100014033 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100014034 active site 340100014035 phosphorylation site [posttranslational modification] 340100014036 intermolecular recognition site; other site 340100014037 dimerization interface [polypeptide binding]; other site 340100014038 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 340100014039 DNA binding site [nucleotide binding] 340100014040 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100014041 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100014042 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014043 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 340100014044 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 340100014045 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 340100014046 Transposase; Region: HTH_Tnp_1; pfam01527 340100014047 Homeodomain-like domain; Region: HTH_32; pfam13565 340100014048 Integrase core domain; Region: rve; pfam00665 340100014049 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340100014050 Integrase core domain; Region: rve_3; pfam13683 340100014051 Predicted membrane protein [Function unknown]; Region: COG2246 340100014052 GtrA-like protein; Region: GtrA; pfam04138 340100014053 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 340100014054 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 340100014055 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 340100014056 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 340100014057 Ligand binding site; other site 340100014058 Putative Catalytic site; other site 340100014059 DXD motif; other site 340100014060 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 340100014061 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 340100014062 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 340100014063 HlyD family secretion protein; Region: HlyD_3; pfam13437 340100014064 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 340100014065 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 340100014066 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100014067 active site 340100014068 phosphorylation site [posttranslational modification] 340100014069 intermolecular recognition site; other site 340100014070 dimerization interface [polypeptide binding]; other site 340100014071 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 340100014072 DNA binding site [nucleotide binding] 340100014073 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 340100014074 dimer interface [polypeptide binding]; other site 340100014075 phosphorylation site [posttranslational modification] 340100014076 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 340100014077 ATP binding site [chemical binding]; other site 340100014078 Mg2+ binding site [ion binding]; other site 340100014079 G-X-G motif; other site 340100014080 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100014081 active site 340100014082 phosphorylation site [posttranslational modification] 340100014083 intermolecular recognition site; other site 340100014084 dimerization interface [polypeptide binding]; other site 340100014085 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 340100014086 DNA binding site [nucleotide binding] 340100014087 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 340100014088 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 340100014089 trimer interface [polypeptide binding]; other site 340100014090 eyelet of channel; other site 340100014091 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100014092 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100014093 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100014094 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 340100014095 dimerization interface [polypeptide binding]; other site 340100014096 substrate binding pocket [chemical binding]; other site 340100014097 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 340100014098 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100014099 Walker A motif; other site 340100014100 ATP binding site [chemical binding]; other site 340100014101 Walker B motif; other site 340100014102 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 340100014103 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 340100014104 ATP binding site [chemical binding]; other site 340100014105 Walker A motif; other site 340100014106 hexamer interface [polypeptide binding]; other site 340100014107 Walker B motif; other site 340100014108 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 340100014109 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 340100014110 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 340100014111 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 340100014112 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 340100014113 Walker A motif; other site 340100014114 ATP binding site [chemical binding]; other site 340100014115 Walker B motif; other site 340100014116 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 340100014117 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 340100014118 conjugal transfer protein TrbL; Provisional; Region: PRK13875 340100014119 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340100014120 conjugal transfer protein TrbF; Provisional; Region: PRK13872 340100014121 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340100014122 VirB7 interaction site; other site 340100014123 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 340100014124 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 340100014125 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 340100014126 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100014127 AAA domain; Region: AAA_23; pfam13476 340100014128 Walker A/P-loop; other site 340100014129 ATP binding site [chemical binding]; other site 340100014130 Q-loop/lid; other site 340100014131 ABC transporter signature motif; other site 340100014132 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100014133 ABC transporter signature motif; other site 340100014134 Walker B; other site 340100014135 D-loop; other site 340100014136 H-loop/switch region; other site 340100014137 putative transposase OrfB; Reviewed; Region: PHA02517 340100014138 HTH-like domain; Region: HTH_21; pfam13276 340100014139 Integrase core domain; Region: rve; pfam00665 340100014140 Integrase core domain; Region: rve_3; pfam13683 340100014141 Transposase; Region: HTH_Tnp_1; pfam01527 340100014142 Transposase; Region: HTH_Tnp_1; pfam01527 340100014143 putative transposase OrfB; Reviewed; Region: PHA02517 340100014144 HTH-like domain; Region: HTH_21; pfam13276 340100014145 Integrase core domain; Region: rve; pfam00665 340100014146 Integrase core domain; Region: rve_3; pfam13683 340100014147 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 340100014148 Domain of unknown function (DUF955); Region: DUF955; pfam06114 340100014149 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 340100014150 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 340100014151 non-specific DNA binding site [nucleotide binding]; other site 340100014152 salt bridge; other site 340100014153 sequence-specific DNA binding site [nucleotide binding]; other site 340100014154 Amidase; Region: Amidase; cl11426 340100014155 Cupin; Region: Cupin_6; pfam12852 340100014156 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100014157 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100014158 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100014159 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 340100014160 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 340100014161 dimer interface [polypeptide binding]; other site 340100014162 FMN binding site [chemical binding]; other site 340100014163 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 340100014164 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 340100014165 Trp docking motif [polypeptide binding]; other site 340100014166 putative active site [active] 340100014167 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 340100014168 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 340100014169 N-terminal plug; other site 340100014170 ligand-binding site [chemical binding]; other site 340100014171 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 340100014172 Predicted membrane protein (DUF2231); Region: DUF2231; pfam09990 340100014173 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 340100014174 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 340100014175 tetramer interface [polypeptide binding]; other site 340100014176 active site 340100014177 Mg2+/Mn2+ binding site [ion binding]; other site 340100014178 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340100014179 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 340100014180 DNA binding site [nucleotide binding] 340100014181 active site 340100014182 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 340100014183 META domain; Region: META; pfam03724 340100014184 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 340100014185 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 340100014186 The 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 340100014187 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 340100014188 dimerization interface [polypeptide binding]; other site 340100014189 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340100014190 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 340100014191 Walker A/P-loop; other site 340100014192 ATP binding site [chemical binding]; other site 340100014193 Q-loop/lid; other site 340100014194 ABC transporter signature motif; other site 340100014195 Walker B; other site 340100014196 D-loop; other site 340100014197 H-loop/switch region; other site 340100014198 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 340100014199 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 340100014200 PBP superfamily domain; Region: PBP_like; pfam12727 340100014201 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 340100014202 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 340100014203 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 340100014204 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 340100014205 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 340100014206 [4Fe-4S] binding site [ion binding]; other site 340100014207 molybdopterin cofactor binding site; other site 340100014208 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 340100014209 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 340100014210 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 340100014211 molybdopterin cofactor binding site; other site 340100014212 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 340100014213 4Fe-4S binding domain; Region: Fer4; pfam00037 340100014214 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100014215 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 340100014216 4Fe-4S binding domain; Region: Fer4; pfam00037 340100014217 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 340100014218 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 340100014219 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 340100014220 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 340100014221 antiporter inner membrane protein; Provisional; Region: PRK11670 340100014222 Domain of unknown function DUF59; Region: DUF59; pfam01883 340100014223 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 340100014224 Walker A motif; other site 340100014225 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 340100014226 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 340100014227 GTP binding site; other site 340100014228 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 340100014229 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 340100014230 dimer interface [polypeptide binding]; other site 340100014231 putative functional site; other site 340100014232 putative MPT binding site; other site 340100014233 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 340100014234 Walker A motif; other site 340100014235 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 340100014236 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 340100014237 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 340100014238 putative NADH binding site [chemical binding]; other site 340100014239 putative active site [active] 340100014240 nudix motif; other site 340100014241 putative metal binding site [ion binding]; other site 340100014242 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 340100014243 Sulfatase; Region: Sulfatase; pfam00884 340100014244 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 340100014245 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340100014246 substrate binding pocket [chemical binding]; other site 340100014247 chain length determination region; other site 340100014248 substrate-Mg2+ binding site; other site 340100014249 catalytic residues [active] 340100014250 aspartate-rich region 1; other site 340100014251 active site lid residues [active] 340100014252 aspartate-rich region 2; other site 340100014253 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 340100014254 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 340100014255 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 340100014256 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100014257 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 340100014258 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 340100014259 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 340100014260 GTPase CgtA; Reviewed; Region: obgE; PRK12299 340100014261 GTP1/OBG; Region: GTP1_OBG; pfam01018 340100014262 Obg GTPase; Region: Obg; cd01898 340100014263 G1 box; other site 340100014264 GTP/Mg2+ binding site [chemical binding]; other site 340100014265 Switch I region; other site 340100014266 G2 box; other site 340100014267 G3 box; other site 340100014268 Switch II region; other site 340100014269 G4 box; other site 340100014270 G5 box; other site 340100014271 gamma-glutamyl kinase; Provisional; Region: PRK05429 340100014272 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 340100014273 nucleotide binding site [chemical binding]; other site 340100014274 homotetrameric interface [polypeptide binding]; other site 340100014275 putative phosphate binding site [ion binding]; other site 340100014276 putative allosteric binding site; other site 340100014277 PUA domain; Region: PUA; pfam01472 340100014278 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100014279 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 340100014280 DNA binding site [nucleotide binding] 340100014281 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 340100014282 non-specific DNA binding site [nucleotide binding]; other site 340100014283 salt bridge; other site 340100014284 sequence-specific DNA binding site [nucleotide binding]; other site 340100014285 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 340100014286 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 340100014287 ThiC-associated domain; Region: ThiC-associated; pfam13667 340100014288 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 340100014289 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 340100014290 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100014291 NAD(P) binding site [chemical binding]; other site 340100014292 catalytic residues [active] 340100014293 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 340100014294 FAD binding domain; Region: FAD_binding_4; pfam01565 340100014295 Transcriptional regulators [Transcription]; Region: FadR; COG2186 340100014296 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100014297 DNA-binding site [nucleotide binding]; DNA binding site 340100014298 FCD domain; Region: FCD; pfam07729 340100014299 Isochorismatase family; Region: Isochorismatase; pfam00857 340100014300 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 340100014301 catalytic triad [active] 340100014302 conserved cis-peptide bond; other site 340100014303 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 340100014304 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340100014305 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 340100014306 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 340100014307 Methyltransferase domain; Region: Methyltransf_24; pfam13578 340100014308 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 340100014309 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 340100014310 ATP binding site [chemical binding]; other site 340100014311 substrate interface [chemical binding]; other site 340100014312 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 340100014313 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 340100014314 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 340100014315 protein binding site [polypeptide binding]; other site 340100014316 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 340100014317 Catalytic dyad [active] 340100014318 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 340100014319 Peptidase family M23; Region: Peptidase_M23; pfam01551 340100014320 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 340100014321 catalytic core [active] 340100014322 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 340100014323 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 340100014324 active site residue [active] 340100014325 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 340100014326 GSH binding site [chemical binding]; other site 340100014327 catalytic residues [active] 340100014328 preprotein translocase subunit SecB; Validated; Region: PRK05751 340100014329 SecA binding site; other site 340100014330 Preprotein binding site; other site 340100014331 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 340100014332 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 340100014333 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 340100014334 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100014335 Uncharacterized conserved protein [Function unknown]; Region: COG5476 340100014336 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 340100014337 MlrC C-terminus; Region: MlrC_C; pfam07171 340100014338 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 340100014339 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100014340 Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like; Region: ALDH_DhaS; cd07114 340100014341 NAD(P) binding site [chemical binding]; other site 340100014342 catalytic residues [active] 340100014343 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 340100014344 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340100014345 active site 340100014346 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 340100014347 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 340100014348 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 340100014349 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 340100014350 Cation transport protein; Region: TrkH; cl17365 340100014351 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 340100014352 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 340100014353 TrkA-N domain; Region: TrkA_N; pfam02254 340100014354 TrkA-C domain; Region: TrkA_C; pfam02080 340100014355 TrkA-N domain; Region: TrkA_N; pfam02254 340100014356 TrkA-C domain; Region: TrkA_C; pfam02080 340100014357 Response regulator receiver domain; Region: Response_reg; pfam00072 340100014358 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100014359 active site 340100014360 phosphorylation site [posttranslational modification] 340100014361 intermolecular recognition site; other site 340100014362 dimerization interface [polypeptide binding]; other site 340100014363 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 340100014364 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 340100014365 dimerization interface [polypeptide binding]; other site 340100014366 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 340100014367 dimer interface [polypeptide binding]; other site 340100014368 phosphorylation site [posttranslational modification] 340100014369 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 340100014370 ATP binding site [chemical binding]; other site 340100014371 Mg2+ binding site [ion binding]; other site 340100014372 G-X-G motif; other site 340100014373 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 340100014374 16S rRNA methyltransferase B; Provisional; Region: PRK10901 340100014375 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 340100014376 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 340100014377 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100014378 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100014379 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 340100014380 putative effector binding pocket; other site 340100014381 putative dimerization interface [polypeptide binding]; other site 340100014382 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100014383 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 340100014384 putative C-terminal domain interface [polypeptide binding]; other site 340100014385 putative GSH binding site (G-site) [chemical binding]; other site 340100014386 putative dimer interface [polypeptide binding]; other site 340100014387 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 340100014388 putative N-terminal domain interface [polypeptide binding]; other site 340100014389 putative dimer interface [polypeptide binding]; other site 340100014390 putative substrate binding pocket (H-site) [chemical binding]; other site 340100014391 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340100014392 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340100014393 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 340100014394 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 340100014395 FAD binding pocket [chemical binding]; other site 340100014396 FAD binding motif [chemical binding]; other site 340100014397 phosphate binding motif [ion binding]; other site 340100014398 beta-alpha-beta structure motif; other site 340100014399 NAD binding pocket [chemical binding]; other site 340100014400 Heme binding pocket [chemical binding]; other site 340100014401 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 340100014402 catalytic loop [active] 340100014403 iron binding site [ion binding]; other site 340100014404 Uncharacterized protein involved in propionate catabolism [General function prediction only]; Region: PrpD; COG2079 340100014405 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100014406 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 340100014407 CoA binding domain; Region: CoA_binding_2; pfam13380 340100014408 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 340100014409 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 340100014410 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 340100014411 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 340100014412 substrate binding site [chemical binding]; other site 340100014413 oxyanion hole (OAH) forming residues; other site 340100014414 trimer interface [polypeptide binding]; other site 340100014415 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 340100014416 Transcriptional regulator [Transcription]; Region: IclR; COG1414 340100014417 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 340100014418 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 340100014419 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 340100014420 FeS/SAM binding site; other site 340100014421 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 340100014422 Ferritin-like domain; Region: Ferritin; pfam00210 340100014423 dinuclear metal binding motif [ion binding]; other site 340100014424 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 340100014425 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 340100014426 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 340100014427 motif II; other site 340100014428 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 340100014429 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 340100014430 putative active site [active] 340100014431 substrate binding site [chemical binding]; other site 340100014432 putative cosubstrate binding site; other site 340100014433 catalytic site [active] 340100014434 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 340100014435 substrate binding site [chemical binding]; other site 340100014436 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 340100014437 active site 340100014438 catalytic residues [active] 340100014439 metal binding site [ion binding]; metal-binding site 340100014440 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 340100014441 DNA protecting protein DprA; Region: dprA; TIGR00732 340100014442 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 340100014443 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 340100014444 active site 340100014445 catalytic residues [active] 340100014446 metal binding site [ion binding]; metal-binding site 340100014447 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 340100014448 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 340100014449 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014450 homodimer interface [polypeptide binding]; other site 340100014451 catalytic residue [active] 340100014452 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 340100014453 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100014454 catalytic residue [active] 340100014455 Protein of unknown function (DUF461); Region: DUF461; pfam04314 340100014456 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 340100014457 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100014458 The 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 340100014459 dimerization interface [polypeptide binding]; other site 340100014460 LysE type translocator; Region: LysE; cl00565 340100014461 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340100014462 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340100014463 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 340100014464 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340100014465 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 340100014466 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100014467 acyl-activating enzyme (AAE) consensus motif; other site 340100014468 AMP binding site [chemical binding]; other site 340100014469 active site 340100014470 CoA binding site [chemical binding]; other site 340100014471 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100014472 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100014473 Walker A/P-loop; other site 340100014474 ATP binding site [chemical binding]; other site 340100014475 Q-loop/lid; other site 340100014476 ABC transporter signature motif; other site 340100014477 Walker B; other site 340100014478 D-loop; other site 340100014479 H-loop/switch region; other site 340100014480 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 340100014481 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 340100014482 putative ligand binding site [chemical binding]; other site 340100014483 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 340100014484 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 340100014485 TM-ABC transporter signature motif; other site 340100014486 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100014487 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 340100014488 TM-ABC transporter signature motif; other site 340100014489 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100014490 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100014491 Walker A/P-loop; other site 340100014492 ATP binding site [chemical binding]; other site 340100014493 Q-loop/lid; other site 340100014494 ABC transporter signature motif; other site 340100014495 Walker B; other site 340100014496 D-loop; other site 340100014497 H-loop/switch region; other site 340100014498 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 340100014499 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 340100014500 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 340100014501 acyl-activating enzyme (AAE) consensus motif; other site 340100014502 putative AMP binding site [chemical binding]; other site 340100014503 putative active site [active] 340100014504 putative CoA binding site [chemical binding]; other site 340100014505 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 340100014506 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 340100014507 ligand binding site [chemical binding]; other site 340100014508 flexible hinge region; other site 340100014509 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 340100014510 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 340100014511 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 340100014512 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 340100014513 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340100014514 Coenzyme A binding pocket [chemical binding]; other site 340100014515 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 340100014516 nucleotide binding site/active site [active] 340100014517 HIT family signature motif; other site 340100014518 catalytic residue [active] 340100014519 NnrS protein; Region: NnrS; pfam05940 340100014520 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 340100014521 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 340100014522 substrate binding pocket [chemical binding]; other site 340100014523 membrane-bound complex binding site; other site 340100014524 hinge residues; other site 340100014525 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 340100014526 ligand binding site [chemical binding]; other site 340100014527 active site 340100014528 UGI interface [polypeptide binding]; other site 340100014529 catalytic site [active] 340100014530 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 340100014531 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 340100014532 ATP binding site [chemical binding]; other site 340100014533 Mg++ binding site [ion binding]; other site 340100014534 motif III; other site 340100014535 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 340100014536 nucleotide binding region [chemical binding]; other site 340100014537 ATP-binding site [chemical binding]; other site 340100014538 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 340100014539 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13297 340100014540 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 340100014541 active site 340100014542 NTP binding site [chemical binding]; other site 340100014543 metal binding triad [ion binding]; metal-binding site 340100014544 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 340100014545 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 340100014546 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 340100014547 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340100014548 catalytic residue [active] 340100014549 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 340100014550 Uncharacterized conserved protein [Function unknown]; Region: COG2308 340100014551 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 340100014552 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 340100014553 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 340100014554 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 340100014555 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 340100014556 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 340100014557 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 340100014558 active site 340100014559 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 340100014560 FAD binding site [chemical binding]; other site 340100014561 Membrane protein of unknown function; Region: DUF360; pfam04020 340100014562 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 340100014563 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 340100014564 homotetramer interface [polypeptide binding]; other site 340100014565 ligand binding site [chemical binding]; other site 340100014566 catalytic site [active] 340100014567 NAD binding site [chemical binding]; other site 340100014568 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 340100014569 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100014570 active site 340100014571 phosphorylation site [posttranslational modification] 340100014572 intermolecular recognition site; other site 340100014573 dimerization interface [polypeptide binding]; other site 340100014574 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 340100014575 DNA binding residues [nucleotide binding] 340100014576 dimerization interface [polypeptide binding]; other site 340100014577 PAS domain; Region: PAS_9; pfam13426 340100014578 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 340100014579 putative active site [active] 340100014580 heme pocket [chemical binding]; other site 340100014581 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 340100014582 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 340100014583 ATP binding site [chemical binding]; other site 340100014584 Mg2+ binding site [ion binding]; other site 340100014585 G-X-G motif; other site 340100014586 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100014587 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 340100014588 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 340100014589 DctM-like transporters; Region: DctM; pfam06808 340100014590 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100014591 DctM-like transporters; Region: DctM; pfam06808 340100014592 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 340100014593 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014594 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 340100014595 Predicted Fe-S protein [General function prediction only]; Region: COG3313 340100014596 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 340100014597 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 340100014598 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 340100014599 substrate binding site [chemical binding]; other site 340100014600 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 340100014601 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 340100014602 substrate binding site [chemical binding]; other site 340100014603 ligand binding site [chemical binding]; other site 340100014604 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100014605 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100014606 transcriptional activator TtdR; Provisional; Region: PRK09801 340100014607 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 340100014608 putative effector binding pocket; other site 340100014609 putative dimerization interface [polypeptide binding]; other site 340100014610 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 340100014611 CoA-transferase family III; Region: CoA_transf_3; pfam02515 340100014612 Transcriptional regulator [Transcription]; Region: LysR; COG0583 340100014613 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 340100014614 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 340100014615 putative dimerization interface [polypeptide binding]; other site 340100014616 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100014617 (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 340100014618 active site 340100014619 catalytic site [active] 340100014620 S-adenosylmethionine synthetase; Validated; Region: PRK05250 340100014621 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 340100014622 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 340100014623 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 340100014624 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340100014625 putative acyl-acceptor binding pocket; other site 340100014626 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 340100014627 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340100014628 putative acyl-acceptor binding pocket; other site 340100014629 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 340100014630 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 340100014631 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 340100014632 Protein of unknown function, DUF484; Region: DUF484; cl17449 340100014633 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 340100014634 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 340100014635 active site 340100014636 DNA binding site [nucleotide binding] 340100014637 Int/Topo IB signature motif; other site 340100014638 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 340100014639 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 340100014640 N-terminal plug; other site 340100014641 ligand-binding site [chemical binding]; other site 340100014642 High-affinity nickel-transport protein; Region: NicO; cl00964 340100014643 Protein of unknown function (DUF1007); Region: DUF1007; cl01487 340100014644 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 340100014645 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 340100014646 metal binding site [ion binding]; metal-binding site 340100014647 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 340100014648 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 340100014649 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 340100014650 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 340100014651 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 340100014652 metal binding site 2 [ion binding]; metal-binding site 340100014653 putative DNA binding helix; other site 340100014654 metal binding site 1 [ion binding]; metal-binding site 340100014655 dimer interface [polypeptide binding]; other site 340100014656 structural Zn2+ binding site [ion binding]; other site 340100014657 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 340100014658 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 340100014659 P-loop, Walker A motif; other site 340100014660 Base recognition motif; other site 340100014661 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 340100014662 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 340100014663 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 340100014664 active site 340100014665 HslU subunit interaction site [polypeptide binding]; other site 340100014666 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 340100014667 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 340100014668 Walker A motif; other site 340100014669 ATP binding site [chemical binding]; other site 340100014670 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 340100014671 Walker B motif; other site 340100014672 arginine finger; other site 340100014673 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 340100014674 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 340100014675 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 340100014676 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 340100014677 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 340100014678 NAD binding site [chemical binding]; other site 340100014679 substrate binding site [chemical binding]; other site 340100014680 homodimer interface [polypeptide binding]; other site 340100014681 active site 340100014682 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 340100014683 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 340100014684 NADP binding site [chemical binding]; other site 340100014685 active site 340100014686 putative substrate binding site [chemical binding]; other site 340100014687 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 340100014688 lipoyl synthase; Provisional; Region: PRK05481 340100014689 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 340100014690 FeS/SAM binding site; other site 340100014691 lipoate-protein ligase B; Provisional; Region: PRK14349 340100014692 hypothetical protein; Provisional; Region: PRK02047 340100014693 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 340100014694 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 340100014695 homodimer interface [polypeptide binding]; other site 340100014696 substrate-cofactor binding pocket; other site 340100014697 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014698 catalytic residue [active] 340100014699 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 340100014700 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 340100014701 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 340100014702 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 340100014703 Serine hydrolase (FSH1); Region: FSH1; pfam03959 340100014704 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 340100014705 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 340100014706 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 340100014707 pantothenate kinase; Reviewed; Region: PRK13328 340100014708 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 340100014709 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 340100014710 lipopolysaccharide heptosyltransferase I; Region: heptsyl_trn_I; TIGR02193 340100014711 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 340100014712 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 340100014713 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 340100014714 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 340100014715 putative transposase OrfB; Reviewed; Region: PHA02517 340100014716 HTH-like domain; Region: HTH_21; pfam13276 340100014717 Integrase core domain; Region: rve; pfam00665 340100014718 Integrase core domain; Region: rve_3; pfam13683 340100014719 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340100014720 Transposase; Region: HTH_Tnp_1; pfam01527 340100014721 putative trimer interface [polypeptide binding]; other site 340100014722 Bacterial transferase hexapeptide (six repeats); Region: Hexapep; pfam00132 340100014723 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 340100014724 putative CoA binding site [chemical binding]; other site 340100014725 putative trimer interface [polypeptide binding]; other site 340100014726 putative active site [active] 340100014727 putative substrate binding site [chemical binding]; other site 340100014728 putative CoA binding site [chemical binding]; other site 340100014729 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 340100014730 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 340100014731 inhibitor-cofactor binding pocket; inhibition site 340100014732 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014733 catalytic residue [active] 340100014734 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 340100014735 active site 340100014736 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 340100014737 homodimer interface [polypeptide binding]; other site 340100014738 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 340100014739 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 340100014740 Mg++ binding site [ion binding]; other site 340100014741 putative catalytic motif [active] 340100014742 putative substrate binding site [chemical binding]; other site 340100014743 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 340100014744 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014745 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 340100014746 N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA; Region: thiol_BshA; TIGR03999 340100014747 Protein of unknown function (DUF2837); Region: DUF2837; pfam10997 340100014748 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 340100014749 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014750 NAD(P) binding site [chemical binding]; other site 340100014751 active site 340100014752 Transposase; Region: HTH_Tnp_1; pfam01527 340100014753 putative transposase OrfB; Reviewed; Region: PHA02517 340100014754 HTH-like domain; Region: HTH_21; pfam13276 340100014755 Integrase core domain; Region: rve; pfam00665 340100014756 Integrase core domain; Region: rve_3; pfam13683 340100014757 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014758 active site 340100014759 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 340100014760 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014761 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014762 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 340100014763 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 340100014764 active site 340100014765 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 340100014766 homodimer interface [polypeptide binding]; other site 340100014767 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 340100014768 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014769 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 340100014770 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 340100014771 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 340100014772 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 340100014773 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 340100014774 Walker A/P-loop; other site 340100014775 ATP binding site [chemical binding]; other site 340100014776 Q-loop/lid; other site 340100014777 ABC transporter signature motif; other site 340100014778 Walker B; other site 340100014779 D-loop; other site 340100014780 H-loop/switch region; other site 340100014781 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340100014782 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340100014783 NAD(P) binding site [chemical binding]; other site 340100014784 active site 340100014785 O-Antigen ligase; Region: Wzy_C; pfam04932 340100014786 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 340100014787 putative hydrophobic ligand binding site [chemical binding]; other site 340100014788 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 340100014789 putative substrate translocation pore; other site 340100014790 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 340100014791 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100014792 EamA-like transporter family; Region: EamA; pfam00892 340100014793 EamA-like transporter family; Region: EamA; pfam00892 340100014794 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 340100014795 putative active site [active] 340100014796 catalytic site [active] 340100014797 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 340100014798 putative active site [active] 340100014799 catalytic site [active] 340100014800 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 340100014801 putative catalytic site [active] 340100014802 putative metal binding site [ion binding]; other site 340100014803 putative phosphate binding site [ion binding]; other site 340100014804 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 340100014805 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 340100014806 dimer interface [polypeptide binding]; other site 340100014807 anticodon binding site; other site 340100014808 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 340100014809 homodimer interface [polypeptide binding]; other site 340100014810 motif 1; other site 340100014811 active site 340100014812 motif 2; other site 340100014813 GAD domain; Region: GAD; pfam02938 340100014814 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 340100014815 motif 3; other site 340100014816 Uncharacterized conserved protein [Function unknown]; Region: COG2928 340100014817 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2331 340100014818 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 340100014819 choline dehydrogenase; Validated; Region: PRK02106 340100014820 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 340100014821 Methyltransferase domain; Region: Methyltransf_31; pfam13847 340100014822 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 340100014823 S-adenosylmethionine binding site [chemical binding]; other site 340100014824 L-type amino acid transporter; Region: 2A0308; TIGR00911 340100014825 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 340100014826 "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...; Region: init_cond_enzymes; cd00827 340100014827 dimer interface [polypeptide binding]; other site 340100014828 active site 340100014829 Fatty acid desaturase; Region: FA_desaturase; pfam00487 340100014830 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 340100014831 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 340100014832 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340100014833 dimer interface [polypeptide binding]; other site 340100014834 active site 340100014835 catalytic residue [active] 340100014836 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 340100014837 GAF domain; Region: GAF_2; pfam13185 340100014838 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 340100014839 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 340100014840 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014841 homodimer interface [polypeptide binding]; other site 340100014842 catalytic residue [active] 340100014843 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 340100014844 UbiA prenyltransferase family; Region: UbiA; pfam01040 340100014845 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 340100014846 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 340100014847 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 340100014848 TrkA-N domain; Region: TrkA_N; pfam02254 340100014849 DNA-binding transcriptional regulator GlcC; Provisional; Region: PRK09990 340100014850 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 340100014851 DNA-binding site [nucleotide binding]; DNA binding site 340100014852 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 340100014853 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 340100014854 active site 340100014855 Transcriptional regulators [Transcription]; Region: GntR; COG1802 340100014856 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl17414 340100014857 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 340100014858 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 340100014859 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 340100014860 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 340100014861 Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs; Region: Gne_like_SDR_e; cd05238 340100014862 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340100014863 putative NAD(P) binding site [chemical binding]; other site 340100014864 active site 340100014865 putative substrate binding site [chemical binding]; other site 340100014866 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 340100014867 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 340100014868 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 340100014869 DctM-like transporters; Region: DctM; pfam06808 340100014870 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 340100014871 The 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 340100014872 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 340100014873 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 340100014874 putative ligand binding site [chemical binding]; other site 340100014875 NAD binding site [chemical binding]; other site 340100014876 dimerization interface [polypeptide binding]; other site 340100014877 catalytic site [active] 340100014878 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 340100014879 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340100014880 substrate binding pocket [chemical binding]; other site 340100014881 membrane-bound complex binding site; other site 340100014882 hinge residues; other site 340100014883 quinolinate synthetase; Provisional; Region: PRK09375 340100014884 L-aspartate oxidase; Provisional; Region: PRK09077 340100014885 L-aspartate oxidase; Provisional; Region: PRK06175 340100014886 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340100014887 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 340100014888 oligomerization interface [polypeptide binding]; other site 340100014889 active site 340100014890 metal binding site [ion binding]; metal-binding site 340100014891 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 340100014892 CoenzymeA binding site [chemical binding]; other site 340100014893 subunit interaction site [polypeptide binding]; other site 340100014894 PHB binding site; other site 340100014895 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 340100014896 putative FMN binding site [chemical binding]; other site 340100014897 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 340100014898 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100014899 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 340100014900 homotrimer interaction site [polypeptide binding]; other site 340100014901 putative active site [active] 340100014902 acetylornithine deacetylase; Provisional; Region: PRK07522 340100014903 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 340100014904 metal binding site [ion binding]; metal-binding site 340100014905 putative dimer interface [polypeptide binding]; other site 340100014906 metabolite-proton symporter; Region: 2A0106; TIGR00883 340100014907 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 340100014908 putative substrate translocation pore; other site 340100014909 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 340100014910 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 340100014911 tetramer interface [polypeptide binding]; other site 340100014912 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100014913 catalytic residue [active] 340100014914 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 340100014915 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 340100014916 active site 340100014917 Zn binding site [ion binding]; other site 340100014918 Predicted membrane protein [Function unknown]; Region: COG4541 340100014919 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 340100014920 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 340100014921 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 340100014922 Amidase; Region: Amidase; pfam01425 340100014923 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 340100014924 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340100014925 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 340100014926 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 340100014927 Walker A/P-loop; other site 340100014928 ATP binding site [chemical binding]; other site 340100014929 Q-loop/lid; other site 340100014930 ABC transporter signature motif; other site 340100014931 Walker B; other site 340100014932 D-loop; other site 340100014933 H-loop/switch region; other site 340100014934 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 340100014935 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 340100014936 Walker A/P-loop; other site 340100014937 ATP binding site [chemical binding]; other site 340100014938 Q-loop/lid; other site 340100014939 ABC transporter signature motif; other site 340100014940 Walker B; other site 340100014941 D-loop; other site 340100014942 H-loop/switch region; other site 340100014943 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100014944 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 340100014945 TM-ABC transporter signature motif; other site 340100014946 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 340100014947 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 340100014948 TM-ABC transporter signature motif; other site 340100014949 Transcriptional regulators [Transcription]; Region: PurR; COG1609 340100014950 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 340100014951 DNA binding site [nucleotide binding] 340100014952 domain linker motif; other site 340100014953 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 340100014954 putative dimerization interface [polypeptide binding]; other site 340100014955 putative ligand binding site [chemical binding]; other site 340100014956 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 340100014957 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 340100014958 putative heme binding pocket [chemical binding]; other site 340100014959 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340100014960 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 340100014961 DNA binding residues [nucleotide binding] 340100014962 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 340100014963 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 340100014964 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 340100014965 classical (c) SDRs; Region: SDR_c; cd05233 340100014966 NAD(P) binding site [chemical binding]; other site 340100014967 active site 340100014968 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 340100014969 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 340100014970 motif II; other site 340100014971 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340100014972 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 340100014973 dimer interface [polypeptide binding]; other site 340100014974 ssDNA binding site [nucleotide binding]; other site 340100014975 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340100014976 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 340100014977 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340100014978 putative substrate translocation pore; other site 340100014979 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 340100014980 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 340100014981 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 340100014982 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 340100014983 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 340100014984 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 340100014985 putative C-terminal domain interface [polypeptide binding]; other site 340100014986 putative GSH binding site (G-site) [chemical binding]; other site 340100014987 putative dimer interface [polypeptide binding]; other site 340100014988 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 340100014989 putative substrate binding pocket (H-site) [chemical binding]; other site 340100014990 putative N-terminal domain interface [polypeptide binding]; other site 340100014991 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 340100014992 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 340100014993 Zn2+ binding site [ion binding]; other site 340100014994 Mg2+ binding site [ion binding]; other site 340100014995 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 340100014996 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 340100014997 active site 340100014998 dimer interface [polypeptide binding]; other site 340100014999 metal binding site [ion binding]; metal-binding site 340100015000 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 340100015001 shikimate kinase; Reviewed; Region: aroK; PRK00131 340100015002 ADP binding site [chemical binding]; other site 340100015003 magnesium binding site [ion binding]; other site 340100015004 putative shikimate binding site; other site 340100015005 Transglycosylase; Region: Transgly; pfam00912 340100015006 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 340100015007 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...; Region: Frataxin; cd00503 340100015008 putative iron binding site [ion binding]; other site 340100015009 diaminopimelate decarboxylase; Region: lysA; TIGR01048 340100015010 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 340100015011 active site 340100015012 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340100015013 substrate binding site [chemical binding]; other site 340100015014 catalytic residues [active] 340100015015 dimer interface [polypeptide binding]; other site 340100015016 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 340100015017 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 340100015018 ResB-like family; Region: ResB; pfam05140 340100015019 ResB-like family; Region: ResB; pfam05140 340100015020 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 340100015021 Cytochrome c; Region: Cytochrom_C; cl11414 340100015022 Cytochrome c; Region: Cytochrom_C; cl11414 340100015023 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 340100015024 G1 box; other site 340100015025 GTP/Mg2+ binding site [chemical binding]; other site 340100015026 Switch I region; other site 340100015027 G2 box; other site 340100015028 G3 box; other site 340100015029 Switch II region; other site 340100015030 G4 box; other site 340100015031 G5 box; other site 340100015032 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 340100015033 dimer interface [polypeptide binding]; other site 340100015034 active site 340100015035 aspartate-rich active site metal binding site; other site 340100015036 allosteric magnesium binding site [ion binding]; other site 340100015037 Schiff base residues; other site 340100015038 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 340100015039 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 340100015040 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 340100015041 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 340100015042 DsbD alpha interface [polypeptide binding]; other site 340100015043 catalytic residues [active] 340100015044 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 340100015045 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 340100015046 nucleotide binding site/active site [active] 340100015047 HIT family signature motif; other site 340100015048 catalytic residue [active] 340100015049 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 340100015050 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 340100015051 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 340100015052 alphaNTD homodimer interface [polypeptide binding]; other site 340100015053 alphaNTD - beta interaction site [polypeptide binding]; other site 340100015054 alphaNTD - beta' interaction site [polypeptide binding]; other site 340100015055 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 340100015056 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 340100015057 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 340100015058 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 340100015059 RNA binding surface [nucleotide binding]; other site 340100015060 30S ribosomal protein S11; Validated; Region: PRK05309 340100015061 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 340100015062 30S ribosomal protein S13; Region: bact_S13; TIGR03631 340100015063 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 340100015064 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 340100015065 rRNA binding site [nucleotide binding]; other site 340100015066 predicted 30S ribosome binding site; other site 340100015067 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 340100015068 SecY translocase; Region: SecY; pfam00344 340100015069 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 340100015070 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 340100015071 23S rRNA binding site [nucleotide binding]; other site 340100015072 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 340100015073 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 340100015074 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 340100015075 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 340100015076 5S rRNA interface [nucleotide binding]; other site 340100015077 L27 interface [polypeptide binding]; other site 340100015078 23S rRNA interface [nucleotide binding]; other site 340100015079 L5 interface [polypeptide binding]; other site 340100015080 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 340100015081 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 340100015082 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 340100015083 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 340100015084 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 340100015085 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 340100015086 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 340100015087 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 340100015088 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 340100015089 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 340100015090 RNA binding site [nucleotide binding]; other site 340100015091 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 340100015092 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 340100015093 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 340100015094 tetramerization interface [polypeptide binding]; other site 340100015095 NAD(P) binding site [chemical binding]; other site 340100015096 catalytic residues [active] 340100015097 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 340100015098 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 340100015099 23S rRNA interface [nucleotide binding]; other site 340100015100 putative translocon interaction site; other site 340100015101 signal recognition particle (SRP54) interaction site; other site 340100015102 L23 interface [polypeptide binding]; other site 340100015103 trigger factor interaction site; other site 340100015104 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 340100015105 23S rRNA interface [nucleotide binding]; other site 340100015106 5S rRNA interface [nucleotide binding]; other site 340100015107 putative antibiotic binding site [chemical binding]; other site 340100015108 L25 interface [polypeptide binding]; other site 340100015109 L27 interface [polypeptide binding]; other site 340100015110 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 340100015111 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 340100015112 G-X-X-G motif; other site 340100015113 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 340100015114 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 340100015115 putative translocon binding site; other site 340100015116 protein-rRNA interface [nucleotide binding]; other site 340100015117 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 340100015118 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 340100015119 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 340100015120 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 340100015121 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 340100015122 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 340100015123 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 340100015124 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 340100015125 elongation factor Tu; Reviewed; Region: PRK00049 340100015126 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 340100015127 G1 box; other site 340100015128 GEF interaction site [polypeptide binding]; other site 340100015129 GTP/Mg2+ binding site [chemical binding]; other site 340100015130 Switch I region; other site 340100015131 G2 box; other site 340100015132 G3 box; other site 340100015133 Switch II region; other site 340100015134 G4 box; other site 340100015135 G5 box; other site 340100015136 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 340100015137 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 340100015138 Antibiotic Binding Site [chemical binding]; other site 340100015139 elongation factor G; Reviewed; Region: PRK00007 340100015140 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 340100015141 G1 box; other site 340100015142 putative GEF interaction site [polypeptide binding]; other site 340100015143 GTP/Mg2+ binding site [chemical binding]; other site 340100015144 Switch I region; other site 340100015145 G2 box; other site 340100015146 G3 box; other site 340100015147 Switch II region; other site 340100015148 G4 box; other site 340100015149 G5 box; other site 340100015150 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 340100015151 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 340100015152 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 340100015153 30S ribosomal protein S7; Validated; Region: PRK05302 340100015154 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 340100015155 S17 interaction site [polypeptide binding]; other site 340100015156 S8 interaction site; other site 340100015157 16S rRNA interaction site [nucleotide binding]; other site 340100015158 streptomycin interaction site [chemical binding]; other site 340100015159 23S rRNA interaction site [nucleotide binding]; other site 340100015160 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 340100015161 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 340100015162 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 340100015163 active site 340100015164 phosphorylation site [posttranslational modification] 340100015165 intermolecular recognition site; other site 340100015166 dimerization interface [polypeptide binding]; other site 340100015167 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 340100015168 DNA binding site [nucleotide binding] 340100015169 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 340100015170 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100015171 active site 340100015172 phosphorylation site [posttranslational modification] 340100015173 intermolecular recognition site; other site 340100015174 dimerization interface [polypeptide binding]; other site 340100015175 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 340100015176 DNA binding site [nucleotide binding] 340100015177 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 340100015178 FecR protein; Region: FecR; pfam04773 340100015179 CHASE2 domain; Region: CHASE2; pfam05226 340100015180 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 340100015181 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 340100015182 dimer interface [polypeptide binding]; other site 340100015183 phosphorylation site [posttranslational modification] 340100015184 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 340100015185 ATP binding site [chemical binding]; other site 340100015186 Mg2+ binding site [ion binding]; other site 340100015187 G-X-G motif; other site 340100015188 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340100015189 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 340100015190 substrate binding site [chemical binding]; other site 340100015191 PEGA domain; Region: PEGA; pfam08308 340100015192 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 340100015193 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 340100015194 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 340100015195 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 340100015196 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 340100015197 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 340100015198 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 340100015199 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 340100015200 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 340100015201 DNA binding site [nucleotide binding] 340100015202 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 340100015203 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 340100015204 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 340100015205 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 340100015206 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 340100015207 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 340100015208 RPB3 interaction site [polypeptide binding]; other site 340100015209 RPB1 interaction site [polypeptide binding]; other site 340100015210 RPB11 interaction site [polypeptide binding]; other site 340100015211 RPB10 interaction site [polypeptide binding]; other site 340100015212 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 340100015213 core dimer interface [polypeptide binding]; other site 340100015214 peripheral dimer interface [polypeptide binding]; other site 340100015215 L10 interface [polypeptide binding]; other site 340100015216 L11 interface [polypeptide binding]; other site 340100015217 putative EF-Tu interaction site [polypeptide binding]; other site 340100015218 putative EF-G interaction site [polypeptide binding]; other site 340100015219 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 340100015220 23S rRNA interface [nucleotide binding]; other site 340100015221 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 340100015222 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 340100015223 mRNA/rRNA interface [nucleotide binding]; other site 340100015224 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 340100015225 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 340100015226 23S rRNA interface [nucleotide binding]; other site 340100015227 L7/L12 interface [polypeptide binding]; other site 340100015228 putative thiostrepton binding site; other site 340100015229 L25 interface [polypeptide binding]; other site 340100015230 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 340100015231 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 340100015232 putative homodimer interface [polypeptide binding]; other site 340100015233 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 340100015234 heterodimer interface [polypeptide binding]; other site 340100015235 homodimer interface [polypeptide binding]; other site 340100015236 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 340100015237 elongation factor Tu; Reviewed; Region: PRK00049 340100015238 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 340100015239 G1 box; other site 340100015240 GEF interaction site [polypeptide binding]; other site 340100015241 GTP/Mg2+ binding site [chemical binding]; other site 340100015242 Switch I region; other site 340100015243 G2 box; other site 340100015244 G3 box; other site 340100015245 Switch II region; other site 340100015246 G4 box; other site 340100015247 G5 box; other site 340100015248 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 340100015249 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 340100015250 Antibiotic Binding Site [chemical binding]; other site 340100015251 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 340100015252 active site 340100015253 homotetramer interface [polypeptide binding]; other site 340100015254 homodimer interface [polypeptide binding]; other site 340100015255 ParB-like nuclease domain; Region: ParB; smart00470 340100015256 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 340100015257 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340100015258 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 340100015259 P-loop; other site 340100015260 Magnesium ion binding site [ion binding]; other site 340100015261 transport-energizing ATPase, TRC40/GET3/ArsA family; Region: GET3_arsA_TRC40; TIGR00345 340100015262 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 340100015263 Magnesium ion binding site [ion binding]; other site 340100015264 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 340100015265 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 340100015266 S-adenosylmethionine binding site [chemical binding]; other site 340100015267 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 340100015268 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 340100015269 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 340100015270 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 340100015271 DNA-binding site [nucleotide binding]; DNA binding site 340100015272 RNA-binding motif; other site 340100015273 methionine aminotransferase; Validated; Region: PRK09082 340100015274 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 340100015275 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340100015276 homodimer interface [polypeptide binding]; other site 340100015277 catalytic residue [active] 340100015278 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 340100015279 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 340100015280 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 340100015281 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 340100015282 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 340100015283 dimer interface [polypeptide binding]; other site 340100015284 phosphorylation site [posttranslational modification] 340100015285 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 340100015286 ATP binding site [chemical binding]; other site 340100015287 Mg2+ binding site [ion binding]; other site 340100015288 G-X-G motif; other site 340100015289 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 340100015290 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100015291 active site 340100015292 phosphorylation site [posttranslational modification] 340100015293 intermolecular recognition site; other site 340100015294 dimerization interface [polypeptide binding]; other site 340100015295 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 340100015296 DNA binding site [nucleotide binding] 340100015297 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 340100015298 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 340100015299 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340100015300 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340100015301 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 340100015302 DNA binding site [nucleotide binding] 340100015303 active site 340100015304 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 340100015305 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 340100015306 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 340100015307 putative substrate translocation pore; other site 340100015308 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 340100015309 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 340100015310 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 340100015311 [4Fe-4S] binding site [ion binding]; other site 340100015312 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 340100015313 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 340100015314 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 340100015315 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 340100015316 molybdopterin cofactor binding site; other site 340100015317 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 340100015318 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 340100015319 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 340100015320 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 340100015321 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 340100015322 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 340100015323 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 340100015324 FeS/SAM binding site; other site 340100015325 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 340100015326 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 340100015327 active site clefts [active] 340100015328 zinc binding site [ion binding]; other site 340100015329 dimer interface [polypeptide binding]; other site 340100015330 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 340100015331 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 340100015332 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 340100015333 dimerization interface [polypeptide binding]; other site 340100015334 GAF domain; Region: GAF; pfam01590 340100015335 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 340100015336 ATP binding site [chemical binding]; other site 340100015337 Mg2+ binding site [ion binding]; other site 340100015338 G-X-G motif; other site 340100015339 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340100015340 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 340100015341 active site 340100015342 phosphorylation site [posttranslational modification] 340100015343 intermolecular recognition site; other site 340100015344 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 340100015345 dimerization interface [polypeptide binding]; other site 340100015346 DNA binding residues [nucleotide binding] 340100015347 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 340100015348 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 340100015349 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 340100015350 TrkA-N domain; Region: TrkA_N; pfam02254 340100015351 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 340100015352 active site 340100015353 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 340100015354 Catalytic domain of Protein Kinases; Region: PKc; cd00180 340100015355 active site 340100015356 ATP binding site [chemical binding]; other site 340100015357 substrate binding site [chemical binding]; other site 340100015358 activation loop (A-loop); other site 340100015359 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 340100015360 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 340100015361 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 340100015362 trmE is a tRNA modification GTPase; Region: trmE; cd04164 340100015363 G1 box; other site 340100015364 GTP/Mg2+ binding site [chemical binding]; other site 340100015365 Switch I region; other site 340100015366 G2 box; other site 340100015367 Switch II region; other site 340100015368 G3 box; other site 340100015369 G4 box; other site 340100015370 G5 box; other site 340100015371 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 340100015372 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 340100015373 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 340100015374 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 340100015375 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 340100015376 dimer interface [polypeptide binding]; other site 340100015377 conserved gate region; other site 340100015378 putative PBP binding loops; other site 340100015379 ABC-ATPase subunit interface; other site 340100015380 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 340100015381 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 340100015382 dimer interface [polypeptide binding]; other site 340100015383 conserved gate region; other site 340100015384 putative PBP binding loops; other site 340100015385 ABC-ATPase subunit interface; other site 340100015386 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 340100015387 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100015388 Walker A/P-loop; other site 340100015389 ATP binding site [chemical binding]; other site 340100015390 Q-loop/lid; other site 340100015391 ABC transporter signature motif; other site 340100015392 Walker B; other site 340100015393 D-loop; other site 340100015394 H-loop/switch region; other site 340100015395 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 340100015396 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 340100015397 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 340100015398 Walker A/P-loop; other site 340100015399 ATP binding site [chemical binding]; other site 340100015400 Q-loop/lid; other site 340100015401 ABC transporter signature motif; other site 340100015402 Walker B; other site 340100015403 D-loop; other site 340100015404 H-loop/switch region; other site 340100015405 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 340100015406 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 340100015407 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 340100015408 metal binding site [ion binding]; metal-binding site 340100015409 putative dimer interface [polypeptide binding]; other site 340100015410 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 340100015411 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 340100015412 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 340100015413 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 340100015414 Walker A/P-loop; other site 340100015415 ATP binding site [chemical binding]; other site 340100015416 Q-loop/lid; other site 340100015417 ABC transporter signature motif; other site 340100015418 Walker B; other site 340100015419 D-loop; other site 340100015420 H-loop/switch region; other site 340100015421 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 340100015422 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 340100015423 putative PBP binding loops; other site 340100015424 dimer interface [polypeptide binding]; other site 340100015425 ABC-ATPase subunit interface; other site 340100015426 membrane protein insertase; Provisional; Region: PRK01318 340100015427 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 340100015428 Haemolytic domain; Region: Haemolytic; pfam01809 340100015429 ribonuclease P; Reviewed; Region: rnpA; PRK00038 340100015430 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399