-- dump date 20140619_145341 -- class Genbank::misc_feature -- table misc_feature_note -- id note 583345000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 583345000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 583345000003 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 583345000004 Walker A motif; other site 583345000005 ATP binding site [chemical binding]; other site 583345000006 Walker B motif; other site 583345000007 arginine finger; other site 583345000008 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 583345000009 DnaA box-binding interface [nucleotide binding]; other site 583345000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 583345000011 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 583345000012 putative DNA binding surface [nucleotide binding]; other site 583345000013 dimer interface [polypeptide binding]; other site 583345000014 beta-clamp/clamp loader binding surface; other site 583345000015 beta-clamp/translesion DNA polymerase binding surface; other site 583345000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 583345000017 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 583345000018 Mg2+ binding site [ion binding]; other site 583345000019 G-X-G motif; other site 583345000020 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 583345000021 anchoring element; other site 583345000022 dimer interface [polypeptide binding]; other site 583345000023 ATP binding site [chemical binding]; other site 583345000024 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 583345000025 active site 583345000026 putative metal-binding site [ion binding]; other site 583345000027 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 583345000028 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345000029 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345000030 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 583345000031 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345000032 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345000033 multidrug efflux protein; Reviewed; Region: PRK09577 583345000034 Protein export membrane protein; Region: SecD_SecF; cl14618 583345000035 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 583345000036 LysR family transcriptional regulator; Provisional; Region: PRK14997 583345000037 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345000038 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 583345000039 putative effector binding pocket; other site 583345000040 putative dimerization interface [polypeptide binding]; other site 583345000041 short chain dehydrogenase; Provisional; Region: PRK06500 583345000042 classical (c) SDRs; Region: SDR_c; cd05233 583345000043 NAD(P) binding site [chemical binding]; other site 583345000044 active site 583345000045 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 583345000046 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 583345000047 NADP binding site [chemical binding]; other site 583345000048 Predicted transcriptional regulators [Transcription]; Region: COG1733 583345000049 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 583345000050 Uncharacterized protein family (UPF0158); Region: UPF0158; pfam03682 583345000051 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 583345000052 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345000053 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 583345000054 putative dimerization interface [polypeptide binding]; other site 583345000055 heat shock protein HtpX; Provisional; Region: PRK05457 583345000056 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 583345000057 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 583345000058 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 583345000059 DoxX; Region: DoxX; pfam07681 583345000060 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 583345000061 PqqA family; Region: PqqA; cl15372 583345000062 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000063 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000064 metal binding site [ion binding]; metal-binding site 583345000065 active site 583345000066 I-site; other site 583345000067 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 583345000068 HPP family; Region: HPP; pfam04982 583345000069 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 583345000070 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 583345000071 YqjK-like protein; Region: YqjK; pfam13997 583345000072 Predicted membrane protein [Function unknown]; Region: COG5393 583345000073 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 583345000074 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 583345000075 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 583345000076 minor groove reading motif; other site 583345000077 helix-hairpin-helix signature motif; other site 583345000078 substrate binding pocket [chemical binding]; other site 583345000079 active site 583345000080 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 583345000081 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 583345000082 DNA binding and oxoG recognition site [nucleotide binding] 583345000083 AsmA family; Region: AsmA; pfam05170 583345000084 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 583345000085 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 583345000086 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 583345000087 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 583345000088 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 583345000089 RNA binding surface [nucleotide binding]; other site 583345000090 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 583345000091 active site 583345000092 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 583345000093 ThiC-associated domain; Region: ThiC-associated; pfam13667 583345000094 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 583345000095 short chain dehydrogenase; Provisional; Region: PRK09072 583345000096 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 583345000097 NAD(P) binding site [chemical binding]; other site 583345000098 active site 583345000099 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 583345000100 heme binding pocket [chemical binding]; other site 583345000101 heme ligand [chemical binding]; other site 583345000102 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 583345000103 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_3; cd05914 583345000104 acyl-activating enzyme (AAE) consensus motif; other site 583345000105 putative AMP binding site [chemical binding]; other site 583345000106 putative active site [active] 583345000107 putative CoA binding site [chemical binding]; other site 583345000108 Thermostable hemolysin; Region: T_hemolysin; pfam12261 583345000109 PBP superfamily domain; Region: PBP_like_2; cl17296 583345000110 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345000111 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 583345000112 dimerization interface [polypeptide binding]; other site 583345000113 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 583345000114 dimer interface [polypeptide binding]; other site 583345000115 phosphorylation site [posttranslational modification] 583345000116 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 583345000117 ATP binding site [chemical binding]; other site 583345000118 Mg2+ binding site [ion binding]; other site 583345000119 G-X-G motif; other site 583345000120 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 583345000121 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 583345000122 active site 583345000123 phosphorylation site [posttranslational modification] 583345000124 intermolecular recognition site; other site 583345000125 dimerization interface [polypeptide binding]; other site 583345000126 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 583345000127 Walker A motif; other site 583345000128 ATP binding site [chemical binding]; other site 583345000129 Walker B motif; other site 583345000130 arginine finger; other site 583345000131 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345000132 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 583345000133 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 583345000134 S-adenosylmethionine binding site [chemical binding]; other site 583345000135 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 583345000136 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 583345000137 Isochorismatase family; Region: Isochorismatase; pfam00857 583345000138 catalytic triad [active] 583345000139 dimer interface [polypeptide binding]; other site 583345000140 conserved cis-peptide bond; other site 583345000141 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 583345000142 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 583345000143 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 583345000144 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 583345000145 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 583345000146 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 583345000147 active site 583345000148 dimer interface [polypeptide binding]; other site 583345000149 effector binding site; other site 583345000150 TSCPD domain; Region: TSCPD; pfam12637 583345000151 Isochorismatase family; Region: Isochorismatase; pfam00857 583345000152 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 583345000153 catalytic triad [active] 583345000154 conserved cis-peptide bond; other site 583345000155 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 583345000156 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 583345000157 conserved cys residue [active] 583345000158 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 583345000159 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 583345000160 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 583345000161 DNA gyrase inhibitor [DNA replication, recombination, and repair]; Region: COG3449 583345000162 DsrE/DsrF-like family; Region: DrsE; cl00672 583345000163 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 583345000164 classical (c) SDRs; Region: SDR_c; cd05233 583345000165 NAD(P) binding site [chemical binding]; other site 583345000166 active site 583345000167 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345000168 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345000169 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 583345000170 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 583345000171 catalytic residues [active] 583345000172 OsmC-like protein; Region: OsmC; pfam02566 583345000173 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 583345000174 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 583345000175 FMN binding site [chemical binding]; other site 583345000176 active site 583345000177 substrate binding site [chemical binding]; other site 583345000178 catalytic residue [active] 583345000179 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 583345000180 dimerization interface [polypeptide binding]; other site 583345000181 putative DNA binding site [nucleotide binding]; other site 583345000182 putative Zn2+ binding site [ion binding]; other site 583345000183 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 583345000184 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 583345000185 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 583345000186 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 583345000187 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 583345000188 FMN binding site [chemical binding]; other site 583345000189 active site 583345000190 substrate binding site [chemical binding]; other site 583345000191 catalytic residue [active] 583345000192 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 583345000193 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 583345000194 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 583345000195 Cytochrome c; Region: Cytochrom_C; cl11414 583345000196 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 583345000197 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 583345000198 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 583345000199 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345000200 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345000201 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 583345000202 EamA-like transporter family; Region: EamA; pfam00892 583345000203 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 583345000204 Integrase core domain; Region: rve; pfam00665 583345000205 Integrase core domain; Region: rve_3; pfam13683 583345000206 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 583345000207 Bacterial TniB protein; Region: TniB; pfam05621 583345000208 AAA domain; Region: AAA_22; pfam13401 583345000209 TniQ; Region: TniQ; pfam06527 583345000210 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 583345000211 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 583345000212 non-specific DNA binding site [nucleotide binding]; other site 583345000213 salt bridge; other site 583345000214 sequence-specific DNA binding site [nucleotide binding]; other site 583345000215 Protein of unknown function (DUF1250); Region: DUF1250; cl11485 583345000216 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 583345000217 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345000218 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345000219 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345000220 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345000221 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345000222 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 583345000223 short chain dehydrogenase; Provisional; Region: PRK06179 583345000224 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 583345000225 NADP binding site [chemical binding]; other site 583345000226 active site 583345000227 steroid binding site; other site 583345000228 LrgA family; Region: LrgA; pfam03788 583345000229 LrgB-like family; Region: LrgB; pfam04172 583345000230 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; cl01544 583345000231 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 583345000232 Isochorismatase family; Region: Isochorismatase; pfam00857 583345000233 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 583345000234 catalytic triad [active] 583345000235 dimer interface [polypeptide binding]; other site 583345000236 conserved cis-peptide bond; other site 583345000237 CHASE domain; Region: CHASE; cl01369 583345000238 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000239 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000240 metal binding site [ion binding]; metal-binding site 583345000241 active site 583345000242 I-site; other site 583345000243 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 583345000244 putative heme binding pocket [chemical binding]; other site 583345000245 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 583345000246 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 583345000247 Walker A motif; other site 583345000248 ATP binding site [chemical binding]; other site 583345000249 Walker B motif; other site 583345000250 arginine finger; other site 583345000251 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 583345000252 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 583345000253 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 583345000254 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 583345000255 TolR protein; Region: tolR; TIGR02801 583345000256 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 583345000257 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 583345000258 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 583345000259 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 583345000260 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 583345000261 Walker A/P-loop; other site 583345000262 ATP binding site [chemical binding]; other site 583345000263 Q-loop/lid; other site 583345000264 ABC transporter signature motif; other site 583345000265 Walker B; other site 583345000266 D-loop; other site 583345000267 H-loop/switch region; other site 583345000268 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 583345000269 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 583345000270 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 583345000271 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 583345000272 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 583345000273 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 583345000274 dimer interface [polypeptide binding]; other site 583345000275 conserved gate region; other site 583345000276 putative PBP binding loops; other site 583345000277 ABC-ATPase subunit interface; other site 583345000278 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 583345000279 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 583345000280 dimer interface [polypeptide binding]; other site 583345000281 conserved gate region; other site 583345000282 putative PBP binding loops; other site 583345000283 ABC-ATPase subunit interface; other site 583345000284 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 583345000285 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 583345000286 N-terminal plug; other site 583345000287 ligand-binding site [chemical binding]; other site 583345000288 Major Facilitator Superfamily; Region: MFS_1; pfam07690 583345000289 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 583345000290 putative substrate translocation pore; other site 583345000291 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 583345000292 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 583345000293 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 583345000294 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 583345000295 dimer interface [polypeptide binding]; other site 583345000296 active site 583345000297 non-prolyl cis peptide bond; other site 583345000298 insertion regions; other site 583345000299 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 583345000300 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 583345000301 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 583345000302 putative hydrophobic ligand binding site [chemical binding]; other site 583345000303 protein interface [polypeptide binding]; other site 583345000304 gate; other site 583345000305 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 583345000306 catalytic residues [active] 583345000307 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 583345000308 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 583345000309 Dodecin; Region: Dodecin; pfam07311 583345000310 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 583345000311 HD domain; Region: HD_4; pfam13328 583345000312 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 583345000313 synthetase active site [active] 583345000314 NTP binding site [chemical binding]; other site 583345000315 metal binding site [ion binding]; metal-binding site 583345000316 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 583345000317 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 583345000318 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 583345000319 NADP binding site [chemical binding]; other site 583345000320 dimer interface [polypeptide binding]; other site 583345000321 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 583345000322 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345000323 putative active site [active] 583345000324 heme pocket [chemical binding]; other site 583345000325 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 583345000326 putative active site [active] 583345000327 heme pocket [chemical binding]; other site 583345000328 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000329 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000330 metal binding site [ion binding]; metal-binding site 583345000331 active site 583345000332 I-site; other site 583345000333 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 583345000334 hypothetical protein; Provisional; Region: PRK09126 583345000335 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 583345000336 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 583345000337 Catalytic domain of Protein Kinases; Region: PKc; cd00180 583345000338 active site 583345000339 ATP binding site [chemical binding]; other site 583345000340 substrate binding site [chemical binding]; other site 583345000341 activation loop (A-loop); other site 583345000342 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 583345000343 HDOD domain; Region: HDOD; pfam08668 583345000344 GAF domain; Region: GAF; cl17456 583345000345 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 583345000346 heme-binding site [chemical binding]; other site 583345000347 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 583345000348 putative active site [active] 583345000349 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345000350 heme pocket [chemical binding]; other site 583345000351 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 583345000352 dimer interface [polypeptide binding]; other site 583345000353 phosphorylation site [posttranslational modification] 583345000354 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 583345000355 ATP binding site [chemical binding]; other site 583345000356 Mg2+ binding site [ion binding]; other site 583345000357 G-X-G motif; other site 583345000358 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 583345000359 Response regulator receiver domain; Region: Response_reg; pfam00072 583345000360 active site 583345000361 phosphorylation site [posttranslational modification] 583345000362 intermolecular recognition site; other site 583345000363 dimerization interface [polypeptide binding]; other site 583345000364 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 583345000365 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 583345000366 active site 583345000367 phosphorylation site [posttranslational modification] 583345000368 intermolecular recognition site; other site 583345000369 dimerization interface [polypeptide binding]; other site 583345000370 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000371 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000372 metal binding site [ion binding]; metal-binding site 583345000373 active site 583345000374 I-site; other site 583345000375 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 583345000376 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 583345000377 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 583345000378 active site 583345000379 phosphorylation site [posttranslational modification] 583345000380 intermolecular recognition site; other site 583345000381 dimerization interface [polypeptide binding]; other site 583345000382 PAS fold; Region: PAS_4; pfam08448 583345000383 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000384 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000385 metal binding site [ion binding]; metal-binding site 583345000386 active site 583345000387 I-site; other site 583345000388 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 583345000389 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 583345000390 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 583345000391 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000392 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000393 metal binding site [ion binding]; metal-binding site 583345000394 active site 583345000395 I-site; other site 583345000396 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 583345000397 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 583345000398 NnrS protein; Region: NnrS; pfam05940 583345000399 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 583345000400 enterobactin exporter EntS; Provisional; Region: PRK10489 583345000401 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 583345000402 putative substrate translocation pore; other site 583345000403 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 583345000404 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 583345000405 minor groove reading motif; other site 583345000406 helix-hairpin-helix signature motif; other site 583345000407 substrate binding pocket [chemical binding]; other site 583345000408 active site 583345000409 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 583345000410 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 583345000411 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 583345000412 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 583345000413 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 583345000414 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 583345000415 PAS domain; Region: PAS_9; pfam13426 583345000416 putative active site [active] 583345000417 heme pocket [chemical binding]; other site 583345000418 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000419 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000420 metal binding site [ion binding]; metal-binding site 583345000421 active site 583345000422 I-site; other site 583345000423 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 583345000424 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 583345000425 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 583345000426 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 583345000427 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 583345000428 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 583345000429 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 583345000430 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 583345000431 FAD binding pocket [chemical binding]; other site 583345000432 FAD binding motif [chemical binding]; other site 583345000433 phosphate binding motif [ion binding]; other site 583345000434 beta-alpha-beta structure motif; other site 583345000435 NAD binding pocket [chemical binding]; other site 583345000436 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 583345000437 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 583345000438 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 583345000439 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 583345000440 Ligand binding site [chemical binding]; other site 583345000441 Electron transfer flavoprotein domain; Region: ETF; pfam01012 583345000442 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 583345000443 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345000444 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 583345000445 putative dimerization interface [polypeptide binding]; other site 583345000446 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 583345000447 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 583345000448 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 583345000449 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 583345000450 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 583345000451 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 583345000452 dimer interface [polypeptide binding]; other site 583345000453 active site 583345000454 heme binding site [chemical binding]; other site 583345000455 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 583345000456 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 583345000457 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345000458 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 583345000459 dimerization interface [polypeptide binding]; other site 583345000460 PAS fold; Region: PAS_4; pfam08448 583345000461 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 583345000462 putative active site [active] 583345000463 heme pocket [chemical binding]; other site 583345000464 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 583345000465 PAS domain; Region: PAS_9; pfam13426 583345000466 putative active site [active] 583345000467 heme pocket [chemical binding]; other site 583345000468 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000469 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000470 metal binding site [ion binding]; metal-binding site 583345000471 active site 583345000472 I-site; other site 583345000473 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 583345000474 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 583345000475 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 583345000476 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 583345000477 S-adenosylmethionine binding site [chemical binding]; other site 583345000478 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 583345000479 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 583345000480 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 583345000481 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 583345000482 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 583345000483 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 583345000484 carboxyltransferase (CT) interaction site; other site 583345000485 biotinylation site [posttranslational modification]; other site 583345000486 Dehydroquinase class II; Region: DHquinase_II; pfam01220 583345000487 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 583345000488 trimer interface [polypeptide binding]; other site 583345000489 active site 583345000490 dimer interface [polypeptide binding]; other site 583345000491 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 583345000492 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 583345000493 catalytic residues [active] 583345000494 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 583345000495 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 583345000496 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 583345000497 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 583345000498 DsbD alpha interface [polypeptide binding]; other site 583345000499 catalytic residues [active] 583345000500 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 583345000501 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 583345000502 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 583345000503 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 583345000504 catalytic loop [active] 583345000505 iron binding site [ion binding]; other site 583345000506 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 583345000507 FAD binding pocket [chemical binding]; other site 583345000508 FAD binding motif [chemical binding]; other site 583345000509 phosphate binding motif [ion binding]; other site 583345000510 beta-alpha-beta structure motif; other site 583345000511 NAD binding pocket [chemical binding]; other site 583345000512 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 583345000513 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 583345000514 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 583345000515 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 583345000516 active site 583345000517 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 583345000518 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 583345000519 domain interfaces; other site 583345000520 active site 583345000521 Conserved TM helix; Region: TM_helix; pfam05552 583345000522 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 583345000523 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 583345000524 active site 583345000525 phosphorylation site [posttranslational modification] 583345000526 intermolecular recognition site; other site 583345000527 dimerization interface [polypeptide binding]; other site 583345000528 LytTr DNA-binding domain; Region: LytTR; smart00850 583345000529 Histidine kinase; Region: His_kinase; pfam06580 583345000530 argininosuccinate lyase; Provisional; Region: PRK00855 583345000531 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 583345000532 active sites [active] 583345000533 tetramer interface [polypeptide binding]; other site 583345000534 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 583345000535 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 583345000536 FeS/SAM binding site; other site 583345000537 HemN C-terminal domain; Region: HemN_C; pfam06969 583345000538 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 583345000539 active site 583345000540 dimerization interface [polypeptide binding]; other site 583345000541 ribonuclease PH; Reviewed; Region: rph; PRK00173 583345000542 Ribonuclease PH; Region: RNase_PH_bact; cd11362 583345000543 hexamer interface [polypeptide binding]; other site 583345000544 active site 583345000545 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 583345000546 active site 583345000547 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 583345000548 Catalytic domain of Protein Kinases; Region: PKc; cd00180 583345000549 active site 583345000550 ATP binding site [chemical binding]; other site 583345000551 substrate binding site [chemical binding]; other site 583345000552 activation loop (A-loop); other site 583345000553 hypothetical protein; Provisional; Region: PRK11820 583345000554 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 583345000555 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 583345000556 Uncharacterized conserved protein [Function unknown]; Region: COG2308 583345000557 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 583345000558 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 583345000559 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 583345000560 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 583345000561 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 583345000562 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 583345000563 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 583345000564 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 583345000565 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 583345000566 catalytic site [active] 583345000567 G-X2-G-X-G-K; other site 583345000568 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 583345000569 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 583345000570 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345000571 Zn2+ binding site [ion binding]; other site 583345000572 Mg2+ binding site [ion binding]; other site 583345000573 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 583345000574 synthetase active site [active] 583345000575 NTP binding site [chemical binding]; other site 583345000576 metal binding site [ion binding]; metal-binding site 583345000577 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 583345000578 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 583345000579 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 583345000580 homotrimer interaction site [polypeptide binding]; other site 583345000581 putative active site [active] 583345000582 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 583345000583 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 583345000584 generic binding surface II; other site 583345000585 ssDNA binding site; other site 583345000586 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 583345000587 ATP binding site [chemical binding]; other site 583345000588 putative Mg++ binding site [ion binding]; other site 583345000589 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 583345000590 nucleotide binding region [chemical binding]; other site 583345000591 ATP-binding site [chemical binding]; other site 583345000592 Chorismate lyase; Region: Chor_lyase; cl01230 583345000593 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 583345000594 UbiA prenyltransferase family; Region: UbiA; pfam01040 583345000595 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 583345000596 23S rRNA interface [nucleotide binding]; other site 583345000597 L3 interface [polypeptide binding]; other site 583345000598 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 583345000599 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 583345000600 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 583345000601 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 583345000602 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 583345000603 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 583345000604 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 583345000605 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 583345000606 dimer interface [polypeptide binding]; other site 583345000607 active site 583345000608 citrylCoA binding site [chemical binding]; other site 583345000609 NADH binding [chemical binding]; other site 583345000610 cationic pore residues; other site 583345000611 oxalacetate/citrate binding site [chemical binding]; other site 583345000612 coenzyme A binding site [chemical binding]; other site 583345000613 catalytic triad [active] 583345000614 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 583345000615 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 583345000616 Peptidase family M23; Region: Peptidase_M23; pfam01551 583345000617 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 583345000618 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 583345000619 active site 583345000620 HIGH motif; other site 583345000621 dimer interface [polypeptide binding]; other site 583345000622 KMSKS motif; other site 583345000623 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 583345000624 RNA binding surface [nucleotide binding]; other site 583345000625 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 583345000626 PAS fold; Region: PAS_3; pfam08447 583345000627 putative active site [active] 583345000628 heme pocket [chemical binding]; other site 583345000629 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345000630 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345000631 metal binding site [ion binding]; metal-binding site 583345000632 active site 583345000633 I-site; other site 583345000634 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 583345000635 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 583345000636 Walker A/P-loop; other site 583345000637 ATP binding site [chemical binding]; other site 583345000638 Q-loop/lid; other site 583345000639 ABC transporter signature motif; other site 583345000640 Walker B; other site 583345000641 D-loop; other site 583345000642 H-loop/switch region; other site 583345000643 TOBE-like domain; Region: TOBE_3; pfam12857 583345000644 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 583345000645 dimer interface [polypeptide binding]; other site 583345000646 conserved gate region; other site 583345000647 putative PBP binding loops; other site 583345000648 ABC-ATPase subunit interface; other site 583345000649 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 583345000650 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 583345000651 dimer interface [polypeptide binding]; other site 583345000652 conserved gate region; other site 583345000653 putative PBP binding loops; other site 583345000654 ABC-ATPase subunit interface; other site 583345000655 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 583345000656 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 583345000657 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 583345000658 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 583345000659 Uncharacterized small protein (DUF2292); Region: DUF2292; cl02371 583345000660 ribosome maturation protein RimP; Reviewed; Region: PRK00092 583345000661 Sm and related proteins; Region: Sm_like; cl00259 583345000662 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 583345000663 putative oligomer interface [polypeptide binding]; other site 583345000664 putative RNA binding site [nucleotide binding]; other site 583345000665 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 583345000666 NusA N-terminal domain; Region: NusA_N; pfam08529 583345000667 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 583345000668 RNA binding site [nucleotide binding]; other site 583345000669 homodimer interface [polypeptide binding]; other site 583345000670 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 583345000671 G-X-X-G motif; other site 583345000672 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 583345000673 G-X-X-G motif; other site 583345000674 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 583345000675 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 583345000676 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 583345000677 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 583345000678 translation initiation factor IF-2; Region: IF-2; TIGR00487 583345000679 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 583345000680 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 583345000681 G1 box; other site 583345000682 putative GEF interaction site [polypeptide binding]; other site 583345000683 GTP/Mg2+ binding site [chemical binding]; other site 583345000684 Switch I region; other site 583345000685 G2 box; other site 583345000686 G3 box; other site 583345000687 Switch II region; other site 583345000688 G4 box; other site 583345000689 G5 box; other site 583345000690 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 583345000691 Translation-initiation factor 2; Region: IF-2; pfam11987 583345000692 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 583345000693 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 583345000694 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 583345000695 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 583345000696 RNA binding site [nucleotide binding]; other site 583345000697 active site 583345000698 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 583345000699 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 583345000700 16S/18S rRNA binding site [nucleotide binding]; other site 583345000701 S13e-L30e interaction site [polypeptide binding]; other site 583345000702 25S rRNA binding site [nucleotide binding]; other site 583345000703 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 583345000704 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 583345000705 RNase E interface [polypeptide binding]; other site 583345000706 trimer interface [polypeptide binding]; other site 583345000707 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 583345000708 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 583345000709 RNase E interface [polypeptide binding]; other site 583345000710 trimer interface [polypeptide binding]; other site 583345000711 active site 583345000712 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 583345000713 putative nucleic acid binding region [nucleotide binding]; other site 583345000714 G-X-X-G motif; other site 583345000715 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 583345000716 RNA binding site [nucleotide binding]; other site 583345000717 domain interface; other site 583345000718 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 583345000719 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 583345000720 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 583345000721 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 583345000722 homodimer interface [polypeptide binding]; other site 583345000723 NADP binding site [chemical binding]; other site 583345000724 substrate binding site [chemical binding]; other site 583345000725 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 583345000726 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 583345000727 active site 583345000728 DNA binding site [nucleotide binding] 583345000729 Int/Topo IB signature motif; other site 583345000730 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 583345000731 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 583345000732 non-specific DNA binding site [nucleotide binding]; other site 583345000733 salt bridge; other site 583345000734 sequence-specific DNA binding site [nucleotide binding]; other site 583345000735 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 583345000736 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 583345000737 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 583345000738 ATP binding site [chemical binding]; other site 583345000739 putative Mg++ binding site [ion binding]; other site 583345000740 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 583345000741 PIN domain; Region: PIN_3; pfam13470 583345000742 DNA binding domain, excisionase family; Region: excise; TIGR01764 583345000743 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 583345000744 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 583345000745 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 583345000746 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 583345000747 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 583345000748 HsdM N-terminal domain; Region: HsdM_N; pfam12161 583345000749 Methyltransferase domain; Region: Methyltransf_26; pfam13659 583345000750 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 583345000751 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 583345000752 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 583345000753 ParB-like nuclease domain; Region: ParB; smart00470 583345000754 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 583345000755 Trp repressor protein; Region: Trp_repressor; cl17266 583345000756 MT-A70; Region: MT-A70; cl01947 583345000757 Replicase family; Region: Replicase; pfam03090 583345000758 Primase C terminal 1 (PriCT-1); Region: PriCT_1; pfam08708 583345000759 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 583345000760 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 583345000761 N-terminal plug; other site 583345000762 ligand-binding site [chemical binding]; other site 583345000763 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 583345000764 metal binding site [ion binding]; metal-binding site 583345000765 nucleotidyl binding site; other site 583345000766 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 583345000767 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 583345000768 active site 583345000769 phosphorylation site [posttranslational modification] 583345000770 intermolecular recognition site; other site 583345000771 dimerization interface [polypeptide binding]; other site 583345000772 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 583345000773 Walker A motif; other site 583345000774 ATP binding site [chemical binding]; other site 583345000775 Walker B motif; other site 583345000776 arginine finger; other site 583345000777 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345000778 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 583345000779 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 583345000780 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 583345000781 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 583345000782 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 583345000783 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 583345000784 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 583345000785 Walker A motif; other site 583345000786 ATP binding site [chemical binding]; other site 583345000787 Walker B motif; other site 583345000788 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 583345000789 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345000790 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345000791 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 583345000792 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 583345000793 ATP binding site [chemical binding]; other site 583345000794 substrate interface [chemical binding]; other site 583345000795 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 583345000796 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 583345000797 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 583345000798 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; cl00163 583345000799 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 583345000800 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 583345000801 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 583345000802 HIGH motif; other site 583345000803 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 583345000804 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 583345000805 active site 583345000806 KMSKS motif; other site 583345000807 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 583345000808 tRNA binding surface [nucleotide binding]; other site 583345000809 anticodon binding site; other site 583345000810 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 583345000811 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 583345000812 CPxP motif; other site 583345000813 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 583345000814 active site residue [active] 583345000815 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 583345000816 dimer interface [polypeptide binding]; other site 583345000817 Alkaline phosphatase homologues; Region: alkPPc; smart00098 583345000818 active site 583345000819 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 583345000820 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg6; cd04781 583345000821 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 583345000822 DNA binding residues [nucleotide binding] 583345000823 putative dimer interface [polypeptide binding]; other site 583345000824 putative metal binding residues [ion binding]; other site 583345000825 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 583345000826 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 583345000827 putative dimer interface [polypeptide binding]; other site 583345000828 active site pocket [active] 583345000829 putative cataytic base [active] 583345000830 cobalamin synthase; Reviewed; Region: cobS; PRK00235 583345000831 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 583345000832 catalytic core [active] 583345000833 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 583345000834 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 583345000835 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345000836 homodimer interface [polypeptide binding]; other site 583345000837 catalytic residue [active] 583345000838 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 583345000839 cobyric acid synthase; Provisional; Region: PRK00784 583345000840 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 583345000841 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 583345000842 catalytic triad [active] 583345000843 S4 domain; Region: S4_2; pfam13275 583345000844 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 583345000845 homotrimer interface [polypeptide binding]; other site 583345000846 Walker A motif; other site 583345000847 GTP binding site [chemical binding]; other site 583345000848 Walker B motif; other site 583345000849 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 583345000850 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 583345000851 cobalamin binding residues [chemical binding]; other site 583345000852 putative BtuC binding residues; other site 583345000853 dimer interface [polypeptide binding]; other site 583345000854 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 583345000855 putative FMN binding site [chemical binding]; other site 583345000856 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 583345000857 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 583345000858 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 583345000859 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 583345000860 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 583345000861 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 583345000862 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 583345000863 catalytic triad [active] 583345000864 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 583345000865 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 583345000866 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 583345000867 homodimer interface [polypeptide binding]; other site 583345000868 Walker A motif; other site 583345000869 ATP binding site [chemical binding]; other site 583345000870 hydroxycobalamin binding site [chemical binding]; other site 583345000871 Walker B motif; other site 583345000872 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 583345000873 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 583345000874 N-terminal plug; other site 583345000875 ligand-binding site [chemical binding]; other site 583345000876 Cell division protein ZapA; Region: ZapA; pfam05164 583345000877 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 583345000878 EVE domain; Region: EVE; cl00728 583345000879 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 583345000880 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 583345000881 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 583345000882 structural tetrad; other site 583345000883 threonine dehydratase; Reviewed; Region: PRK09224 583345000884 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 583345000885 tetramer interface [polypeptide binding]; other site 583345000886 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345000887 catalytic residue [active] 583345000888 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 583345000889 putative Ile/Val binding site [chemical binding]; other site 583345000890 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 583345000891 putative Ile/Val binding site [chemical binding]; other site 583345000892 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 583345000893 tetramer (dimer of dimers) interface [polypeptide binding]; other site 583345000894 active site 583345000895 dimer interface [polypeptide binding]; other site 583345000896 transcriptional regulator PhoU; Provisional; Region: PRK11115 583345000897 PhoU domain; Region: PhoU; pfam01895 583345000898 PhoU domain; Region: PhoU; pfam01895 583345000899 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 583345000900 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 583345000901 active site 583345000902 interdomain interaction site; other site 583345000903 putative metal-binding site [ion binding]; other site 583345000904 nucleotide binding site [chemical binding]; other site 583345000905 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 583345000906 domain I; other site 583345000907 DNA binding groove [nucleotide binding] 583345000908 phosphate binding site [ion binding]; other site 583345000909 domain II; other site 583345000910 domain III; other site 583345000911 nucleotide binding site [chemical binding]; other site 583345000912 catalytic site [active] 583345000913 domain IV; other site 583345000914 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 583345000915 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 583345000916 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 583345000917 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 583345000918 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 583345000919 Ligand Binding Site [chemical binding]; other site 583345000920 pteridine reductase; Provisional; Region: PRK09135 583345000921 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 583345000922 NADP binding site [chemical binding]; other site 583345000923 substrate binding pocket [chemical binding]; other site 583345000924 active site 583345000925 Uncharacterized conserved protein [Function unknown]; Region: COG1565 583345000926 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 583345000927 S-adenosylmethionine binding site [chemical binding]; other site 583345000928 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 583345000929 G1 box; other site 583345000930 GTP/Mg2+ binding site [chemical binding]; other site 583345000931 Switch I region; other site 583345000932 G2 box; other site 583345000933 G3 box; other site 583345000934 Switch II region; other site 583345000935 G4 box; other site 583345000936 G5 box; other site 583345000937 Cytochrome c553 [Energy production and conversion]; Region: COG2863 583345000938 Cytochrome c; Region: Cytochrom_C; cl11414 583345000939 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 583345000940 ResB-like family; Region: ResB; pfam05140 583345000941 ResB-like family; Region: ResB; pfam05140 583345000942 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 583345000943 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 583345000944 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345000945 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 583345000946 ATP binding site [chemical binding]; other site 583345000947 Mg2+ binding site [ion binding]; other site 583345000948 G-X-G motif; other site 583345000949 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 583345000950 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 583345000951 Walker A/P-loop; other site 583345000952 ATP binding site [chemical binding]; other site 583345000953 Q-loop/lid; other site 583345000954 ABC transporter signature motif; other site 583345000955 Walker B; other site 583345000956 D-loop; other site 583345000957 H-loop/switch region; other site 583345000958 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 583345000959 Permease; Region: Permease; pfam02405 583345000960 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 583345000961 mce related protein; Region: MCE; pfam02470 583345000962 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 583345000963 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 583345000964 anti sigma factor interaction site; other site 583345000965 regulatory phosphorylation site [posttranslational modification]; other site 583345000966 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 583345000967 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 583345000968 Walker A/P-loop; other site 583345000969 ATP binding site [chemical binding]; other site 583345000970 Q-loop/lid; other site 583345000971 ABC transporter signature motif; other site 583345000972 Walker B; other site 583345000973 D-loop; other site 583345000974 H-loop/switch region; other site 583345000975 ABC-2 type transporter; Region: ABC2_membrane; cl17235 583345000976 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 583345000977 BolA-like protein; Region: BolA; pfam01722 583345000978 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 583345000979 putative GSH binding site [chemical binding]; other site 583345000980 catalytic residues [active] 583345000981 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 583345000982 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 583345000983 hinge; other site 583345000984 active site 583345000985 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 583345000986 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 583345000987 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 583345000988 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 583345000989 NAD binding site [chemical binding]; other site 583345000990 dimerization interface [polypeptide binding]; other site 583345000991 product binding site; other site 583345000992 substrate binding site [chemical binding]; other site 583345000993 zinc binding site [ion binding]; other site 583345000994 catalytic residues [active] 583345000995 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 583345000996 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 583345000997 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345000998 homodimer interface [polypeptide binding]; other site 583345000999 catalytic residue [active] 583345001000 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 583345001001 active site 583345001002 dimer interface [polypeptide binding]; other site 583345001003 magnesium binding site [ion binding]; other site 583345001004 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 583345001005 putative active site pocket [active] 583345001006 4-fold oligomerization interface [polypeptide binding]; other site 583345001007 metal binding residues [ion binding]; metal-binding site 583345001008 3-fold/trimer interface [polypeptide binding]; other site 583345001009 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 583345001010 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 583345001011 putative active site [active] 583345001012 oxyanion strand; other site 583345001013 catalytic triad [active] 583345001014 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 583345001015 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 583345001016 catalytic residues [active] 583345001017 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 583345001018 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 583345001019 substrate binding site [chemical binding]; other site 583345001020 glutamase interaction surface [polypeptide binding]; other site 583345001021 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 583345001022 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 583345001023 metal binding site [ion binding]; metal-binding site 583345001024 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 583345001025 nucleotide binding site/active site [active] 583345001026 HIT family signature motif; other site 583345001027 catalytic residue [active] 583345001028 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 583345001029 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 583345001030 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 583345001031 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 583345001032 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 583345001033 protein binding site [polypeptide binding]; other site 583345001034 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 583345001035 Uncharacterized conserved protein [Function unknown]; Region: COG0327 583345001036 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 583345001037 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 583345001038 [2Fe-2S] cluster binding site [ion binding]; other site 583345001039 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 583345001040 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 583345001041 Qi binding site; other site 583345001042 intrachain domain interface; other site 583345001043 interchain domain interface [polypeptide binding]; other site 583345001044 heme bH binding site [chemical binding]; other site 583345001045 heme bL binding site [chemical binding]; other site 583345001046 Qo binding site; other site 583345001047 interchain domain interface [polypeptide binding]; other site 583345001048 intrachain domain interface; other site 583345001049 Qi binding site; other site 583345001050 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 583345001051 Qo binding site; other site 583345001052 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 583345001053 stringent starvation protein A; Provisional; Region: sspA; PRK09481 583345001054 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 583345001055 C-terminal domain interface [polypeptide binding]; other site 583345001056 putative GSH binding site (G-site) [chemical binding]; other site 583345001057 dimer interface [polypeptide binding]; other site 583345001058 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 583345001059 dimer interface [polypeptide binding]; other site 583345001060 N-terminal domain interface [polypeptide binding]; other site 583345001061 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 583345001062 elongation factor Tu; Reviewed; Region: PRK00049 583345001063 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 583345001064 G1 box; other site 583345001065 GEF interaction site [polypeptide binding]; other site 583345001066 GTP/Mg2+ binding site [chemical binding]; other site 583345001067 Switch I region; other site 583345001068 G2 box; other site 583345001069 G3 box; other site 583345001070 Switch II region; other site 583345001071 G4 box; other site 583345001072 G5 box; other site 583345001073 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 583345001074 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 583345001075 Antibiotic Binding Site [chemical binding]; other site 583345001076 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 583345001077 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 583345001078 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 583345001079 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 583345001080 putative homodimer interface [polypeptide binding]; other site 583345001081 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 583345001082 heterodimer interface [polypeptide binding]; other site 583345001083 homodimer interface [polypeptide binding]; other site 583345001084 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 583345001085 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 583345001086 23S rRNA interface [nucleotide binding]; other site 583345001087 L7/L12 interface [polypeptide binding]; other site 583345001088 putative thiostrepton binding site; other site 583345001089 L25 interface [polypeptide binding]; other site 583345001090 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 583345001091 mRNA/rRNA interface [nucleotide binding]; other site 583345001092 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 583345001093 23S rRNA interface [nucleotide binding]; other site 583345001094 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 583345001095 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 583345001096 peripheral dimer interface [polypeptide binding]; other site 583345001097 core dimer interface [polypeptide binding]; other site 583345001098 L10 interface [polypeptide binding]; other site 583345001099 L11 interface [polypeptide binding]; other site 583345001100 putative EF-Tu interaction site [polypeptide binding]; other site 583345001101 putative EF-G interaction site [polypeptide binding]; other site 583345001102 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 583345001103 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 583345001104 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 583345001105 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 583345001106 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 583345001107 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 583345001108 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 583345001109 RPB3 interaction site [polypeptide binding]; other site 583345001110 RPB1 interaction site [polypeptide binding]; other site 583345001111 RPB11 interaction site [polypeptide binding]; other site 583345001112 RPB10 interaction site [polypeptide binding]; other site 583345001113 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 583345001114 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 583345001115 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 583345001116 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 583345001117 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 583345001118 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 583345001119 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 583345001120 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 583345001121 G-loop; other site 583345001122 DNA binding site [nucleotide binding] 583345001123 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 583345001124 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 583345001125 S17 interaction site [polypeptide binding]; other site 583345001126 S8 interaction site; other site 583345001127 16S rRNA interaction site [nucleotide binding]; other site 583345001128 streptomycin interaction site [chemical binding]; other site 583345001129 23S rRNA interaction site [nucleotide binding]; other site 583345001130 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 583345001131 30S ribosomal protein S7; Validated; Region: PRK05302 583345001132 elongation factor G; Reviewed; Region: PRK00007 583345001133 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 583345001134 G1 box; other site 583345001135 putative GEF interaction site [polypeptide binding]; other site 583345001136 GTP/Mg2+ binding site [chemical binding]; other site 583345001137 Switch I region; other site 583345001138 G2 box; other site 583345001139 G3 box; other site 583345001140 Switch II region; other site 583345001141 G4 box; other site 583345001142 G5 box; other site 583345001143 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 583345001144 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 583345001145 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 583345001146 elongation factor Tu; Reviewed; Region: PRK00049 583345001147 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 583345001148 G1 box; other site 583345001149 GEF interaction site [polypeptide binding]; other site 583345001150 GTP/Mg2+ binding site [chemical binding]; other site 583345001151 Switch I region; other site 583345001152 G2 box; other site 583345001153 G3 box; other site 583345001154 Switch II region; other site 583345001155 G4 box; other site 583345001156 G5 box; other site 583345001157 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 583345001158 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 583345001159 Antibiotic Binding Site [chemical binding]; other site 583345001160 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 583345001161 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 583345001162 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 583345001163 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 583345001164 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 583345001165 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 583345001166 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 583345001167 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 583345001168 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 583345001169 putative translocon binding site; other site 583345001170 protein-rRNA interface [nucleotide binding]; other site 583345001171 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 583345001172 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 583345001173 G-X-X-G motif; other site 583345001174 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 583345001175 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 583345001176 23S rRNA interface [nucleotide binding]; other site 583345001177 5S rRNA interface [nucleotide binding]; other site 583345001178 putative antibiotic binding site [chemical binding]; other site 583345001179 L25 interface [polypeptide binding]; other site 583345001180 L27 interface [polypeptide binding]; other site 583345001181 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 583345001182 23S rRNA interface [nucleotide binding]; other site 583345001183 putative translocon interaction site; other site 583345001184 signal recognition particle (SRP54) interaction site; other site 583345001185 L23 interface [polypeptide binding]; other site 583345001186 trigger factor interaction site; other site 583345001187 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 583345001188 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 583345001189 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 583345001190 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 583345001191 RNA binding site [nucleotide binding]; other site 583345001192 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 583345001193 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 583345001194 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 583345001195 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 583345001196 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 583345001197 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 583345001198 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 583345001199 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 583345001200 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 583345001201 5S rRNA interface [nucleotide binding]; other site 583345001202 23S rRNA interface [nucleotide binding]; other site 583345001203 L5 interface [polypeptide binding]; other site 583345001204 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 583345001205 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 583345001206 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 583345001207 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 583345001208 23S rRNA binding site [nucleotide binding]; other site 583345001209 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 583345001210 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 583345001211 SecY translocase; Region: SecY; pfam00344 583345001212 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 583345001213 rRNA binding site [nucleotide binding]; other site 583345001214 predicted 30S ribosome binding site; other site 583345001215 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 583345001216 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 583345001217 30S ribosomal protein S13; Region: bact_S13; TIGR03631 583345001218 30S ribosomal protein S11; Validated; Region: PRK05309 583345001219 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 583345001220 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 583345001221 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 583345001222 RNA binding surface [nucleotide binding]; other site 583345001223 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 583345001224 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 583345001225 alphaNTD homodimer interface [polypeptide binding]; other site 583345001226 alphaNTD - beta interaction site [polypeptide binding]; other site 583345001227 alphaNTD - beta' interaction site [polypeptide binding]; other site 583345001228 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 583345001229 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 583345001230 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 583345001231 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 583345001232 MgtE intracellular N domain; Region: MgtE_N; smart00924 583345001233 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 583345001234 Divalent cation transporter; Region: MgtE; cl00786 583345001235 Mechanosensitive ion channel; Region: MS_channel; pfam00924 583345001236 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 583345001237 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 583345001238 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 583345001239 trimer interface [polypeptide binding]; other site 583345001240 active site 583345001241 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 583345001242 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 583345001243 N-terminal plug; other site 583345001244 ligand-binding site [chemical binding]; other site 583345001245 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 583345001246 Flavoprotein; Region: Flavoprotein; pfam02441 583345001247 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 583345001248 hypothetical protein; Reviewed; Region: PRK00024 583345001249 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 583345001250 MPN+ (JAMM) motif; other site 583345001251 Zinc-binding site [ion binding]; other site 583345001252 Predicted membrane protein [Function unknown]; Region: COG3174 583345001253 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 583345001254 carbon starvation protein A; Provisional; Region: PRK15015 583345001255 Carbon starvation protein CstA; Region: CstA; pfam02554 583345001256 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 583345001257 Protein of unknown function (DUF466); Region: DUF466; cl01082 583345001258 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 583345001259 Molybdenum cofactor biosynthesis protein F; Region: MoaF; pfam10703 583345001260 TfoX N-terminal domain; Region: TfoX_N; pfam04993 583345001261 integron integrase; Region: integrase_gron; TIGR02249 583345001262 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 583345001263 Int/Topo IB signature motif; other site 583345001264 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 583345001265 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 583345001266 active site 583345001267 phosphate binding residues; other site 583345001268 catalytic residues [active] 583345001269 Cytochrome c; Region: Cytochrom_C; cl11414 583345001270 amino acid transporter; Region: 2A0306; TIGR00909 583345001271 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 583345001272 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 583345001273 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 583345001274 active site 583345001275 metal binding site [ion binding]; metal-binding site 583345001276 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 583345001277 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 583345001278 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 583345001279 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 583345001280 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 583345001281 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 583345001282 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 583345001283 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 583345001284 purine monophosphate binding site [chemical binding]; other site 583345001285 dimer interface [polypeptide binding]; other site 583345001286 putative catalytic residues [active] 583345001287 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 583345001288 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 583345001289 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 583345001290 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 583345001291 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 583345001292 FMN binding site [chemical binding]; other site 583345001293 active site 583345001294 catalytic residues [active] 583345001295 substrate binding site [chemical binding]; other site 583345001296 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 583345001297 metabolite-proton symporter; Region: 2A0106; TIGR00883 583345001298 putative substrate translocation pore; other site 583345001299 Flagellin N-methylase; Region: FliB; pfam03692 583345001300 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 583345001301 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 583345001302 putative MPT binding site; other site 583345001303 DNA polymerase I; Provisional; Region: PRK05755 583345001304 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 583345001305 active site 583345001306 metal binding site 1 [ion binding]; metal-binding site 583345001307 putative 5' ssDNA interaction site; other site 583345001308 metal binding site 3; metal-binding site 583345001309 metal binding site 2 [ion binding]; metal-binding site 583345001310 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 583345001311 putative DNA binding site [nucleotide binding]; other site 583345001312 putative metal binding site [ion binding]; other site 583345001313 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 583345001314 active site 583345001315 catalytic site [active] 583345001316 substrate binding site [chemical binding]; other site 583345001317 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 583345001318 active site 583345001319 DNA binding site [nucleotide binding] 583345001320 catalytic site [active] 583345001321 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 583345001322 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 583345001323 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 583345001324 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 583345001325 putative active site [active] 583345001326 putative substrate binding site [chemical binding]; other site 583345001327 ATP binding site [chemical binding]; other site 583345001328 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 583345001329 Part of AAA domain; Region: AAA_19; pfam13245 583345001330 Family description; Region: UvrD_C_2; pfam13538 583345001331 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 583345001332 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 583345001333 putative active site [active] 583345001334 metal binding site [ion binding]; metal-binding site 583345001335 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 583345001336 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 583345001337 NADP binding site [chemical binding]; other site 583345001338 Pirin-related protein [General function prediction only]; Region: COG1741 583345001339 Pirin; Region: Pirin; pfam02678 583345001340 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 583345001341 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345001342 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 583345001343 dimerization interface [polypeptide binding]; other site 583345001344 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 583345001345 acyl-CoA esterase; Provisional; Region: PRK10673 583345001346 PGAP1-like protein; Region: PGAP1; pfam07819 583345001347 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 583345001348 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 583345001349 putative active site [active] 583345001350 PAS fold; Region: PAS_3; pfam08447 583345001351 heme pocket [chemical binding]; other site 583345001352 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 583345001353 PAS domain; Region: PAS_9; pfam13426 583345001354 putative active site [active] 583345001355 heme pocket [chemical binding]; other site 583345001356 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345001357 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345001358 metal binding site [ion binding]; metal-binding site 583345001359 active site 583345001360 I-site; other site 583345001361 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 583345001362 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 583345001363 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 583345001364 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 583345001365 N-terminal plug; other site 583345001366 ligand-binding site [chemical binding]; other site 583345001367 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 583345001368 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 583345001369 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 583345001370 AIPR protein; Region: AIPR; pfam10592 583345001371 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 583345001372 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 583345001373 ring oligomerisation interface [polypeptide binding]; other site 583345001374 ATP/Mg binding site [chemical binding]; other site 583345001375 stacking interactions; other site 583345001376 hinge regions; other site 583345001377 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 583345001378 oligomerisation interface [polypeptide binding]; other site 583345001379 mobile loop; other site 583345001380 roof hairpin; other site 583345001381 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 583345001382 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 583345001383 active site 583345001384 catalytic tetrad [active] 583345001385 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 583345001386 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 583345001387 PhnA protein; Region: PhnA; pfam03831 583345001388 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 583345001389 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345001390 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345001391 metal binding site [ion binding]; metal-binding site 583345001392 active site 583345001393 I-site; other site 583345001394 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 583345001395 Peptidase family U32; Region: Peptidase_U32; pfam01136 583345001396 Collagenase; Region: DUF3656; pfam12392 583345001397 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 583345001398 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 583345001399 inhibitor-cofactor binding pocket; inhibition site 583345001400 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345001401 catalytic residue [active] 583345001402 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 583345001403 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 583345001404 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 583345001405 OsmC-like protein; Region: OsmC; cl00767 583345001406 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 583345001407 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 583345001408 diiron binding motif [ion binding]; other site 583345001409 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 583345001410 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 583345001411 Cysteine-rich domain; Region: CCG; pfam02754 583345001412 Cysteine-rich domain; Region: CCG; pfam02754 583345001413 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 583345001414 C-terminal peptidase (prc); Region: prc; TIGR00225 583345001415 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 583345001416 protein binding site [polypeptide binding]; other site 583345001417 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 583345001418 Catalytic dyad [active] 583345001419 Rdx family; Region: Rdx; cl01407 583345001420 Ferritin-like domain; Region: Ferritin; pfam00210 583345001421 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 583345001422 dinuclear metal binding motif [ion binding]; other site 583345001423 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 583345001424 NlpC/P60 family; Region: NLPC_P60; pfam00877 583345001425 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 583345001426 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 583345001427 DEAD_2; Region: DEAD_2; pfam06733 583345001428 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 583345001429 hypothetical protein; Provisional; Region: PRK09256 583345001430 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 583345001431 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 583345001432 Glycoprotease family; Region: Peptidase_M22; pfam00814 583345001433 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 583345001434 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 583345001435 Coenzyme A binding pocket [chemical binding]; other site 583345001436 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 583345001437 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 583345001438 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 583345001439 Repair protein; Region: Repair_PSII; pfam04536 583345001440 Repair protein; Region: Repair_PSII; cl01535 583345001441 prolyl-tRNA synthetase; Provisional; Region: PRK09194 583345001442 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 583345001443 dimer interface [polypeptide binding]; other site 583345001444 motif 1; other site 583345001445 active site 583345001446 motif 2; other site 583345001447 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 583345001448 putative deacylase active site [active] 583345001449 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 583345001450 active site 583345001451 motif 3; other site 583345001452 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 583345001453 anticodon binding site; other site 583345001454 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 583345001455 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 583345001456 N-acetyl-D-glucosamine binding site [chemical binding]; other site 583345001457 catalytic residue [active] 583345001458 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 583345001459 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 583345001460 PqqA family; Region: PqqA; cl15372 583345001461 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 583345001462 catalytic residues [active] 583345001463 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 583345001464 Catalytic site [active] 583345001465 protein structure with unknown function; Region: DUF4144; pfam13642 583345001466 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 583345001467 Isochorismatase family; Region: Isochorismatase; pfam00857 583345001468 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 583345001469 catalytic triad [active] 583345001470 dimer interface [polypeptide binding]; other site 583345001471 conserved cis-peptide bond; other site 583345001472 Pirin-related protein [General function prediction only]; Region: COG1741 583345001473 Pirin; Region: Pirin; pfam02678 583345001474 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 583345001475 Transcriptional regulator [Transcription]; Region: LysR; COG0583 583345001476 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345001477 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 583345001478 putative effector binding pocket; other site 583345001479 dimerization interface [polypeptide binding]; other site 583345001480 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 583345001481 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 583345001482 DNA-binding site [nucleotide binding]; DNA binding site 583345001483 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 583345001484 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345001485 homodimer interface [polypeptide binding]; other site 583345001486 catalytic residue [active] 583345001487 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 583345001488 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 583345001489 putative molybdopterin cofactor binding site [chemical binding]; other site 583345001490 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 583345001491 putative molybdopterin cofactor binding site; other site 583345001492 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 583345001493 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345001494 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345001495 dimer interface [polypeptide binding]; other site 583345001496 putative CheW interface [polypeptide binding]; other site 583345001497 Uncharacterized protein conserved in bacteria (DUF2188); Region: DUF2188; pfam09954 583345001498 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 583345001499 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 583345001500 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345001501 Walker A/P-loop; other site 583345001502 ATP binding site [chemical binding]; other site 583345001503 Q-loop/lid; other site 583345001504 ABC transporter signature motif; other site 583345001505 Walker B; other site 583345001506 D-loop; other site 583345001507 H-loop/switch region; other site 583345001508 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 583345001509 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001510 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001511 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001512 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 583345001513 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001514 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001515 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 583345001516 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001517 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001518 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001519 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 583345001520 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001521 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 583345001522 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 583345001523 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345001524 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345001525 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 583345001526 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 583345001527 non-specific DNA binding site [nucleotide binding]; other site 583345001528 salt bridge; other site 583345001529 sequence-specific DNA binding site [nucleotide binding]; other site 583345001530 TniQ; Region: TniQ; pfam06527 583345001531 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 583345001532 AAA domain; Region: AAA_22; pfam13401 583345001533 Walker A motif; other site 583345001534 ATP binding site [chemical binding]; other site 583345001535 Walker B motif; other site 583345001536 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 583345001537 Mu DNA binding, I gamma subdomain; Region: HTH_Tnp_Mu_2; pfam09039 583345001538 Integrase core domain; Region: rve; pfam00665 583345001539 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 583345001540 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 583345001541 cofactor binding site; other site 583345001542 DNA binding site [nucleotide binding] 583345001543 substrate interaction site [chemical binding]; other site 583345001544 Protein of unknown function DUF262; Region: DUF262; pfam03235 583345001545 Uncharacterized conserved protein [Function unknown]; Region: COG4938 583345001546 Protein of unknown function (DUF3696); Region: DUF3696; pfam12476 583345001547 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 583345001548 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 583345001549 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 583345001550 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 583345001551 active site 583345001552 metal binding site [ion binding]; metal-binding site 583345001553 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 583345001554 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 583345001555 putative acyl-acceptor binding pocket; other site 583345001556 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 583345001557 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 583345001558 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 583345001559 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 583345001560 substrate binding site [chemical binding]; other site 583345001561 ATP binding site [chemical binding]; other site 583345001562 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345001563 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345001564 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 583345001565 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 583345001566 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 583345001567 catalytic residues [active] 583345001568 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 583345001569 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 583345001570 FAD binding domain; Region: FAD_binding_4; pfam01565 583345001571 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 583345001572 Cysteine-rich domain; Region: CCG; pfam02754 583345001573 Cysteine-rich domain; Region: CCG; pfam02754 583345001574 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 583345001575 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 583345001576 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 583345001577 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 583345001578 dimer interface [polypeptide binding]; other site 583345001579 phosphorylation site [posttranslational modification] 583345001580 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 583345001581 ATP binding site [chemical binding]; other site 583345001582 Mg2+ binding site [ion binding]; other site 583345001583 G-X-G motif; other site 583345001584 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 583345001585 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 583345001586 active site 583345001587 phosphorylation site [posttranslational modification] 583345001588 intermolecular recognition site; other site 583345001589 dimerization interface [polypeptide binding]; other site 583345001590 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 583345001591 DNA binding site [nucleotide binding] 583345001592 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 583345001593 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 583345001594 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 583345001595 homopentamer interface [polypeptide binding]; other site 583345001596 active site 583345001597 transcription antitermination factor NusB; Region: nusB; TIGR01951 583345001598 putative RNA binding site [nucleotide binding]; other site 583345001599 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 583345001600 active site 583345001601 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 583345001602 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 583345001603 phosphopeptide binding site; other site 583345001604 GAF domain; Region: GAF; pfam01590 583345001605 GAF domain; Region: GAF_2; pfam13185 583345001606 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 583345001607 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345001608 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 583345001609 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 583345001610 putative active site [active] 583345001611 putative metal binding site [ion binding]; other site 583345001612 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 583345001613 substrate binding site [chemical binding]; other site 583345001614 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 583345001615 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 583345001616 substrate binding site [chemical binding]; other site 583345001617 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 583345001618 TPR repeat; Region: TPR_11; pfam13414 583345001619 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 583345001620 binding surface 583345001621 TPR motif; other site 583345001622 Tetratricopeptide repeat; Region: TPR_12; pfam13424 583345001623 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 583345001624 SnoaL-like domain; Region: SnoaL_3; pfam13474 583345001625 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 583345001626 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 583345001627 active site 583345001628 HIGH motif; other site 583345001629 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 583345001630 KMSKS motif; other site 583345001631 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 583345001632 tRNA binding surface [nucleotide binding]; other site 583345001633 anticodon binding site; other site 583345001634 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 583345001635 heterotetramer interface [polypeptide binding]; other site 583345001636 active site pocket [active] 583345001637 cleavage site 583345001638 hypothetical protein; Provisional; Region: PRK08999 583345001639 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 583345001640 active site 583345001641 8-oxo-dGMP binding site [chemical binding]; other site 583345001642 nudix motif; other site 583345001643 metal binding site [ion binding]; metal-binding site 583345001644 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 583345001645 thiamine phosphate binding site [chemical binding]; other site 583345001646 active site 583345001647 pyrophosphate binding site [ion binding]; other site 583345001648 Protein of unknown function (DUF461); Region: DUF461; pfam04314 583345001649 Domain of unknown function (DUF329); Region: DUF329; pfam03884 583345001650 hypothetical protein; Provisional; Region: PRK05287 583345001651 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 583345001652 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 583345001653 CoA-binding site [chemical binding]; other site 583345001654 ATP-binding [chemical binding]; other site 583345001655 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 583345001656 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 583345001657 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 583345001658 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 583345001659 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 583345001660 substrate binding pocket [chemical binding]; other site 583345001661 chain length determination region; other site 583345001662 substrate-Mg2+ binding site; other site 583345001663 catalytic residues [active] 583345001664 aspartate-rich region 1; other site 583345001665 active site lid residues [active] 583345001666 aspartate-rich region 2; other site 583345001667 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 583345001668 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 583345001669 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 583345001670 GTPase CgtA; Reviewed; Region: obgE; PRK12299 583345001671 GTP1/OBG; Region: GTP1_OBG; pfam01018 583345001672 Obg GTPase; Region: Obg; cd01898 583345001673 G1 box; other site 583345001674 GTP/Mg2+ binding site [chemical binding]; other site 583345001675 Switch I region; other site 583345001676 G2 box; other site 583345001677 G3 box; other site 583345001678 Switch II region; other site 583345001679 G4 box; other site 583345001680 G5 box; other site 583345001681 gamma-glutamyl kinase; Provisional; Region: PRK05429 583345001682 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 583345001683 nucleotide binding site [chemical binding]; other site 583345001684 homotetrameric interface [polypeptide binding]; other site 583345001685 putative phosphate binding site [ion binding]; other site 583345001686 putative allosteric binding site; other site 583345001687 PUA domain; Region: PUA; pfam01472 583345001688 AIR carboxylase; Region: AIRC; pfam00731 583345001689 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 583345001690 ATP-grasp domain; Region: ATP-grasp; pfam02222 583345001691 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 583345001692 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 583345001693 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 583345001694 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 583345001695 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 583345001696 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 583345001697 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 583345001698 active site 583345001699 Riboflavin kinase; Region: Flavokinase; smart00904 583345001700 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 583345001701 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 583345001702 active site 583345001703 HIGH motif; other site 583345001704 nucleotide binding site [chemical binding]; other site 583345001705 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 583345001706 active site 583345001707 KMSKS motif; other site 583345001708 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 583345001709 tRNA binding surface [nucleotide binding]; other site 583345001710 anticodon binding site; other site 583345001711 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 583345001712 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 583345001713 lipoprotein signal peptidase; Provisional; Region: PRK14787 583345001714 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 583345001715 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 583345001716 Moco binding site; other site 583345001717 metal coordination site [ion binding]; other site 583345001718 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 583345001719 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 583345001720 active site 583345001721 phosphorylation site [posttranslational modification] 583345001722 intermolecular recognition site; other site 583345001723 dimerization interface [polypeptide binding]; other site 583345001724 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345001725 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345001726 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 583345001727 phosphorylation site [posttranslational modification] 583345001728 dimer interface [polypeptide binding]; other site 583345001729 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 583345001730 ATP binding site [chemical binding]; other site 583345001731 Mg2+ binding site [ion binding]; other site 583345001732 G-X-G motif; other site 583345001733 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 583345001734 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 583345001735 N-terminal plug; other site 583345001736 ligand-binding site [chemical binding]; other site 583345001737 Family description; Region: DsbD_2; pfam13386 583345001738 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 583345001739 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 583345001740 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 583345001741 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 583345001742 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 583345001743 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 583345001744 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 583345001745 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 583345001746 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 583345001747 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 583345001748 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 583345001749 Low-spin heme binding site [chemical binding]; other site 583345001750 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 583345001751 Putative water exit pathway; other site 583345001752 Binuclear center (active site) [active] 583345001753 Putative proton exit pathway; other site 583345001754 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 583345001755 UbiA prenyltransferase family; Region: UbiA; pfam01040 583345001756 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 583345001757 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 583345001758 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 583345001759 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 583345001760 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 583345001761 Subunit III/VIIa interface [polypeptide binding]; other site 583345001762 Phospholipid binding site [chemical binding]; other site 583345001763 Subunit I/III interface [polypeptide binding]; other site 583345001764 Subunit III/VIb interface [polypeptide binding]; other site 583345001765 Subunit III/VIa interface; other site 583345001766 Subunit III/Vb interface [polypeptide binding]; other site 583345001767 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 583345001768 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 583345001769 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 583345001770 Subunit I/III interface [polypeptide binding]; other site 583345001771 D-pathway; other site 583345001772 Subunit I/VIIc interface [polypeptide binding]; other site 583345001773 Subunit I/IV interface [polypeptide binding]; other site 583345001774 Subunit I/II interface [polypeptide binding]; other site 583345001775 Low-spin heme (heme a) binding site [chemical binding]; other site 583345001776 Subunit I/VIIa interface [polypeptide binding]; other site 583345001777 Subunit I/VIa interface [polypeptide binding]; other site 583345001778 Dimer interface; other site 583345001779 Putative water exit pathway; other site 583345001780 Binuclear center (heme a3/CuB) [ion binding]; other site 583345001781 K-pathway; other site 583345001782 Subunit I/Vb interface [polypeptide binding]; other site 583345001783 Putative proton exit pathway; other site 583345001784 Subunit I/VIb interface; other site 583345001785 Subunit I/VIc interface [polypeptide binding]; other site 583345001786 Electron transfer pathway; other site 583345001787 Subunit I/VIIIb interface [polypeptide binding]; other site 583345001788 Subunit I/VIIb interface [polypeptide binding]; other site 583345001789 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 583345001790 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 583345001791 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 583345001792 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 583345001793 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 583345001794 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 583345001795 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 583345001796 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 583345001797 metal-binding site [ion binding] 583345001798 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 583345001799 Soluble P-type ATPase [General function prediction only]; Region: COG4087 583345001800 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 583345001801 Clp amino terminal domain; Region: Clp_N; pfam02861 583345001802 Clp amino terminal domain; Region: Clp_N; pfam02861 583345001803 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 583345001804 Walker A motif; other site 583345001805 ATP binding site [chemical binding]; other site 583345001806 Walker B motif; other site 583345001807 arginine finger; other site 583345001808 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 583345001809 Walker A motif; other site 583345001810 ATP binding site [chemical binding]; other site 583345001811 Walker B motif; other site 583345001812 arginine finger; other site 583345001813 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 583345001814 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 583345001815 Sel1-like repeats; Region: SEL1; smart00671 583345001816 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 583345001817 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 583345001818 N-acetyl-D-glucosamine binding site [chemical binding]; other site 583345001819 catalytic residue [active] 583345001820 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 583345001821 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 583345001822 Peptidase family M23; Region: Peptidase_M23; pfam01551 583345001823 phosphoglyceromutase; Provisional; Region: PRK05434 583345001824 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 583345001825 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 583345001826 active site residue [active] 583345001827 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 583345001828 GSH binding site [chemical binding]; other site 583345001829 catalytic residues [active] 583345001830 preprotein translocase subunit SecB; Validated; Region: PRK05751 583345001831 SecA binding site; other site 583345001832 Preprotein binding site; other site 583345001833 Bacterial SH3 domain; Region: SH3_4; pfam06347 583345001834 Bacterial SH3 domain; Region: SH3_4; pfam06347 583345001835 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 583345001836 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 583345001837 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 583345001838 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 583345001839 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 583345001840 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345001841 active site 583345001842 biotin synthase; Region: bioB; TIGR00433 583345001843 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 583345001844 FeS/SAM binding site; other site 583345001845 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 583345001846 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 583345001847 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 583345001848 substrate-cofactor binding pocket; other site 583345001849 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345001850 catalytic residue [active] 583345001851 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 583345001852 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 583345001853 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 583345001854 S-adenosylmethionine binding site [chemical binding]; other site 583345001855 AAA domain; Region: AAA_26; pfam13500 583345001856 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 583345001857 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 583345001858 Peptidase family M48; Region: Peptidase_M48; pfam01435 583345001859 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 583345001860 TPR motif; other site 583345001861 binding surface 583345001862 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 583345001863 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 583345001864 active site 583345001865 (T/H)XGH motif; other site 583345001866 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 583345001867 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 583345001868 putative catalytic cysteine [active] 583345001869 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 583345001870 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 583345001871 Lipopolysaccharide-assembly; Region: LptE; cl01125 583345001872 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 583345001873 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 583345001874 HIGH motif; other site 583345001875 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 583345001876 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 583345001877 active site 583345001878 KMSKS motif; other site 583345001879 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 583345001880 tRNA binding surface [nucleotide binding]; other site 583345001881 adenylate kinase; Reviewed; Region: adk; PRK00279 583345001882 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 583345001883 AMP-binding site [chemical binding]; other site 583345001884 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 583345001885 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 583345001886 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 583345001887 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 583345001888 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 583345001889 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 583345001890 SurA N-terminal domain; Region: SurA_N; pfam09312 583345001891 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 583345001892 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 583345001893 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 583345001894 OstA-like protein; Region: OstA; cl00844 583345001895 Organic solvent tolerance protein; Region: OstA_C; pfam04453 583345001896 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 583345001897 Phosphotransferase enzyme family; Region: APH; pfam01636 583345001898 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 583345001899 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 583345001900 Substrate binding site; other site 583345001901 metal-binding site 583345001902 proline aminopeptidase P II; Provisional; Region: PRK10879 583345001903 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 583345001904 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 583345001905 active site 583345001906 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 583345001907 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 583345001908 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 583345001909 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 583345001910 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 583345001911 dimerization domain [polypeptide binding]; other site 583345001912 dimer interface [polypeptide binding]; other site 583345001913 catalytic residues [active] 583345001914 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 583345001915 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345001916 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345001917 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 583345001918 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 583345001919 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 583345001920 Walker A motif; other site 583345001921 ATP binding site [chemical binding]; other site 583345001922 Walker B motif; other site 583345001923 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 583345001924 DNA-binding site [nucleotide binding]; DNA binding site 583345001925 RNA-binding motif; other site 583345001926 isocitrate dehydrogenase; Validated; Region: PRK07362 583345001927 isocitrate dehydrogenase; Reviewed; Region: PRK07006 583345001928 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 583345001929 pseudouridine synthase; Region: TIGR00093 583345001930 active site 583345001931 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 583345001932 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 583345001933 catalytic triad [active] 583345001934 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 583345001935 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 583345001936 Tetramer interface [polypeptide binding]; other site 583345001937 active site 583345001938 FMN-binding site [chemical binding]; other site 583345001939 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 583345001940 Major Facilitator Superfamily; Region: MFS_1; pfam07690 583345001941 putative substrate translocation pore; other site 583345001942 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 583345001943 catalytic motif [active] 583345001944 Catalytic residue [active] 583345001945 putative GTP cyclohydrolase; Provisional; Region: PRK13674 583345001946 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 583345001947 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 583345001948 TPP-binding site; other site 583345001949 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 583345001950 PYR/PP interface [polypeptide binding]; other site 583345001951 dimer interface [polypeptide binding]; other site 583345001952 TPP binding site [chemical binding]; other site 583345001953 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 583345001954 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 583345001955 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 583345001956 substrate binding pocket [chemical binding]; other site 583345001957 chain length determination region; other site 583345001958 substrate-Mg2+ binding site; other site 583345001959 catalytic residues [active] 583345001960 aspartate-rich region 1; other site 583345001961 active site lid residues [active] 583345001962 aspartate-rich region 2; other site 583345001963 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 583345001964 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 583345001965 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 583345001966 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 583345001967 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 583345001968 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 583345001969 ligand binding site [chemical binding]; other site 583345001970 flexible hinge region; other site 583345001971 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 583345001972 active site residue [active] 583345001973 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 583345001974 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 583345001975 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 583345001976 putative hydrophobic ligand binding site [chemical binding]; other site 583345001977 protein interface [polypeptide binding]; other site 583345001978 gate; other site 583345001979 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 583345001980 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 583345001981 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 583345001982 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 583345001983 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 583345001984 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 583345001985 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 583345001986 putative active site [active] 583345001987 Ap4A binding site [chemical binding]; other site 583345001988 nudix motif; other site 583345001989 putative metal binding site [ion binding]; other site 583345001990 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 583345001991 ketol-acid reductoisomerase; Provisional; Region: PRK05479 583345001992 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 583345001993 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 583345001994 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 583345001995 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 583345001996 putative valine binding site [chemical binding]; other site 583345001997 dimer interface [polypeptide binding]; other site 583345001998 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 583345001999 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 583345002000 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 583345002001 PYR/PP interface [polypeptide binding]; other site 583345002002 dimer interface [polypeptide binding]; other site 583345002003 TPP binding site [chemical binding]; other site 583345002004 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 583345002005 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 583345002006 TPP-binding site [chemical binding]; other site 583345002007 dimer interface [polypeptide binding]; other site 583345002008 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 583345002009 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 583345002010 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 583345002011 Walker A motif; other site 583345002012 ATP binding site [chemical binding]; other site 583345002013 Walker B motif; other site 583345002014 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 583345002015 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 583345002016 dimerization interface [polypeptide binding]; other site 583345002017 active site 583345002018 putative glutathione S-transferase; Provisional; Region: PRK10357 583345002019 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 583345002020 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 583345002021 dimer interface [polypeptide binding]; other site 583345002022 N-terminal domain interface [polypeptide binding]; other site 583345002023 putative substrate binding pocket (H-site) [chemical binding]; other site 583345002024 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 583345002025 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 583345002026 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 583345002027 nudix motif; other site 583345002028 MarC family integral membrane protein; Region: MarC; cl00919 583345002029 Maf-like protein; Region: Maf; pfam02545 583345002030 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 583345002031 active site 583345002032 dimer interface [polypeptide binding]; other site 583345002033 ribonuclease G; Provisional; Region: PRK11712 583345002034 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 583345002035 homodimer interface [polypeptide binding]; other site 583345002036 oligonucleotide binding site [chemical binding]; other site 583345002037 Dynamin family; Region: Dynamin_N; pfam00350 583345002038 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 583345002039 G1 box; other site 583345002040 GTP/Mg2+ binding site [chemical binding]; other site 583345002041 G2 box; other site 583345002042 Switch I region; other site 583345002043 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 583345002044 G3 box; other site 583345002045 Switch II region; other site 583345002046 GTP/Mg2+ binding site [chemical binding]; other site 583345002047 G4 box; other site 583345002048 G5 box; other site 583345002049 YGGT family; Region: YGGT; pfam02325 583345002050 YGGT family; Region: YGGT; pfam02325 583345002051 pyrroline-5-carboxylate reductase; Region: PLN02688 583345002052 pyrroline-5-carboxylate reductase; Region: proC; TIGR00112 583345002053 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 583345002054 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 583345002055 catalytic residue [active] 583345002056 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 583345002057 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 583345002058 Walker A motif; other site 583345002059 ATP binding site [chemical binding]; other site 583345002060 Walker B motif; other site 583345002061 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 583345002062 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 583345002063 Walker A motif; other site 583345002064 ATP binding site [chemical binding]; other site 583345002065 Walker B motif; other site 583345002066 dihydroorotase; Provisional; Region: PRK07627 583345002067 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 583345002068 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 583345002069 active site 583345002070 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 583345002071 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 583345002072 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 583345002073 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345002074 active site 583345002075 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 583345002076 hypothetical protein; Validated; Region: PRK00228 583345002077 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 583345002078 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 583345002079 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 583345002080 dimerization interface [polypeptide binding]; other site 583345002081 active site 583345002082 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 583345002083 Lumazine binding domain; Region: Lum_binding; pfam00677 583345002084 Lumazine binding domain; Region: Lum_binding; pfam00677 583345002085 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 583345002086 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 583345002087 FtsX-like permease family; Region: FtsX; pfam02687 583345002088 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 583345002089 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 583345002090 Walker A/P-loop; other site 583345002091 ATP binding site [chemical binding]; other site 583345002092 Q-loop/lid; other site 583345002093 ABC transporter signature motif; other site 583345002094 Walker B; other site 583345002095 D-loop; other site 583345002096 H-loop/switch region; other site 583345002097 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 583345002098 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 583345002099 Competence protein; Region: Competence; pfam03772 583345002100 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 583345002101 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 583345002102 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 583345002103 active site 583345002104 phosphorylation site [posttranslational modification] 583345002105 intermolecular recognition site; other site 583345002106 dimerization interface [polypeptide binding]; other site 583345002107 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345002108 Zn2+ binding site [ion binding]; other site 583345002109 Mg2+ binding site [ion binding]; other site 583345002110 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 583345002111 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 583345002112 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 583345002113 PAS domain S-box; Region: sensory_box; TIGR00229 583345002114 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 583345002115 putative active site [active] 583345002116 heme pocket [chemical binding]; other site 583345002117 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 583345002118 PAS fold; Region: PAS_3; pfam08447 583345002119 putative active site [active] 583345002120 heme pocket [chemical binding]; other site 583345002121 PAS domain; Region: PAS_9; pfam13426 583345002122 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 583345002123 putative active site [active] 583345002124 heme pocket [chemical binding]; other site 583345002125 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345002126 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 583345002127 dimer interface [polypeptide binding]; other site 583345002128 phosphorylation site [posttranslational modification] 583345002129 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 583345002130 ATP binding site [chemical binding]; other site 583345002131 Mg2+ binding site [ion binding]; other site 583345002132 G-X-G motif; other site 583345002133 Response regulator receiver domain; Region: Response_reg; pfam00072 583345002134 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 583345002135 active site 583345002136 phosphorylation site [posttranslational modification] 583345002137 intermolecular recognition site; other site 583345002138 dimerization interface [polypeptide binding]; other site 583345002139 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 583345002140 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 583345002141 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 583345002142 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 583345002143 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 583345002144 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 583345002145 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 583345002146 Walker A/P-loop; other site 583345002147 ATP binding site [chemical binding]; other site 583345002148 Q-loop/lid; other site 583345002149 ABC transporter signature motif; other site 583345002150 Walker B; other site 583345002151 D-loop; other site 583345002152 H-loop/switch region; other site 583345002153 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 583345002154 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 583345002155 Uncharacterized conserved protein [Function unknown]; Region: COG2835 583345002156 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 583345002157 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 583345002158 Ligand binding site; other site 583345002159 oligomer interface; other site 583345002160 PilZ domain; Region: PilZ; pfam07238 583345002161 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 583345002162 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 583345002163 dimer interface [polypeptide binding]; other site 583345002164 TPP-binding site [chemical binding]; other site 583345002165 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 583345002166 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 583345002167 E3 interaction surface; other site 583345002168 lipoyl attachment site [posttranslational modification]; other site 583345002169 e3 binding domain; Region: E3_binding; pfam02817 583345002170 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 583345002171 PAS domain; Region: PAS; smart00091 583345002172 PAS fold; Region: PAS_4; pfam08448 583345002173 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 583345002174 PAS domain; Region: PAS_9; pfam13426 583345002175 putative active site [active] 583345002176 heme pocket [chemical binding]; other site 583345002177 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345002178 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345002179 metal binding site [ion binding]; metal-binding site 583345002180 active site 583345002181 I-site; other site 583345002182 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 583345002183 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 583345002184 E3 interaction surface; other site 583345002185 lipoyl attachment site [posttranslational modification]; other site 583345002186 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 583345002187 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 583345002188 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 583345002189 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 583345002190 FAD binding domain; Region: FAD_binding_4; pfam01565 583345002191 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 583345002192 Type III pantothenate kinase; Region: Pan_kinase; cl17198 583345002193 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 583345002194 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 583345002195 DNA-binding site [nucleotide binding]; DNA binding site 583345002196 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 583345002197 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 583345002198 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 583345002199 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 583345002200 active site 583345002201 HIGH motif; other site 583345002202 nucleotide binding site [chemical binding]; other site 583345002203 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 583345002204 active site 583345002205 KMSKS motif; other site 583345002206 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 583345002207 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 583345002208 Catalytic domain of Protein Kinases; Region: PKc; cd00180 583345002209 active site 583345002210 ATP binding site [chemical binding]; other site 583345002211 substrate binding site [chemical binding]; other site 583345002212 activation loop (A-loop); other site 583345002213 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 583345002214 active site 583345002215 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 583345002216 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 583345002217 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 583345002218 oligomer interface [polypeptide binding]; other site 583345002219 metal binding site [ion binding]; metal-binding site 583345002220 metal binding site [ion binding]; metal-binding site 583345002221 Cl binding site [ion binding]; other site 583345002222 aspartate ring; other site 583345002223 basic sphincter; other site 583345002224 putative hydrophobic gate; other site 583345002225 periplasmic entrance; other site 583345002226 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 583345002227 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 583345002228 dimerization interface [polypeptide binding]; other site 583345002229 ATP binding site [chemical binding]; other site 583345002230 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 583345002231 dimerization interface [polypeptide binding]; other site 583345002232 ATP binding site [chemical binding]; other site 583345002233 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 583345002234 putative active site [active] 583345002235 catalytic triad [active] 583345002236 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 583345002237 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 583345002238 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 583345002239 Cytochrome c; Region: Cytochrom_C; cl11414 583345002240 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 583345002241 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 583345002242 putative membrane-bound dehydrogenase domain; Region: Piru_Ver_Nterm; TIGR02604 583345002243 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 583345002244 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 583345002245 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 583345002246 dinuclear metal binding motif [ion binding]; other site 583345002247 phosphoserine phosphatase SerB; Region: serB; TIGR00338 583345002248 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 583345002249 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 583345002250 motif II; other site 583345002251 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 583345002252 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 583345002253 CoA-ligase; Region: Ligase_CoA; pfam00549 583345002254 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 583345002255 CoA binding domain; Region: CoA_binding; smart00881 583345002256 CoA-ligase; Region: Ligase_CoA; pfam00549 583345002257 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 583345002258 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 583345002259 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 583345002260 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 583345002261 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 583345002262 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 583345002263 NAD synthetase; Provisional; Region: PRK13981 583345002264 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 583345002265 multimer interface [polypeptide binding]; other site 583345002266 active site 583345002267 catalytic triad [active] 583345002268 protein interface 1 [polypeptide binding]; other site 583345002269 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 583345002270 homodimer interface [polypeptide binding]; other site 583345002271 NAD binding pocket [chemical binding]; other site 583345002272 ATP binding pocket [chemical binding]; other site 583345002273 Mg binding site [ion binding]; other site 583345002274 active-site loop [active] 583345002275 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 583345002276 Nitrogen regulatory protein P-II; Region: P-II; smart00938 583345002277 Protein of unknown function, DUF486; Region: DUF486; cl01236 583345002278 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 583345002279 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 583345002280 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 583345002281 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 583345002282 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 583345002283 G1 box; other site 583345002284 GTP/Mg2+ binding site [chemical binding]; other site 583345002285 Switch I region; other site 583345002286 G2 box; other site 583345002287 G3 box; other site 583345002288 Switch II region; other site 583345002289 G4 box; other site 583345002290 G5 box; other site 583345002291 Nucleoside recognition; Region: Gate; pfam07670 583345002292 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 583345002293 Nucleoside recognition; Region: Gate; pfam07670 583345002294 FeoA domain; Region: FeoA; pfam04023 583345002295 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 583345002296 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 583345002297 BolA-like protein; Region: BolA; pfam01722 583345002298 YciI-like protein; Reviewed; Region: PRK11370 583345002299 intracellular septation protein A; Reviewed; Region: PRK00259 583345002300 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 583345002301 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 583345002302 active site 583345002303 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 583345002304 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 583345002305 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 583345002306 Peptidase family M50; Region: Peptidase_M50; pfam02163 583345002307 active site 583345002308 putative substrate binding region [chemical binding]; other site 583345002309 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 583345002310 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 583345002311 active site 583345002312 HIGH motif; other site 583345002313 dimer interface [polypeptide binding]; other site 583345002314 KMSKS motif; other site 583345002315 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 583345002316 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 583345002317 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 583345002318 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 583345002319 RNA binding surface [nucleotide binding]; other site 583345002320 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 583345002321 probable active site [active] 583345002322 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 583345002323 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 583345002324 S-adenosylmethionine binding site [chemical binding]; other site 583345002325 HemK family putative methylases; Region: hemK_fam; TIGR00536 583345002326 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 583345002327 S-adenosylmethionine binding site [chemical binding]; other site 583345002328 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 583345002329 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 583345002330 metal binding site [ion binding]; metal-binding site 583345002331 dimer interface [polypeptide binding]; other site 583345002332 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 583345002333 ArsC family; Region: ArsC; pfam03960 583345002334 putative catalytic residues [active] 583345002335 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 583345002336 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 583345002337 trimer interface [polypeptide binding]; other site 583345002338 active site 583345002339 substrate binding site [chemical binding]; other site 583345002340 CoA binding site [chemical binding]; other site 583345002341 Peptidase family M48; Region: Peptidase_M48; pfam01435 583345002342 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 583345002343 potassium uptake protein; Region: kup; TIGR00794 583345002344 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 583345002345 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 583345002346 generic binding surface II; other site 583345002347 generic binding surface I; other site 583345002348 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 583345002349 cysteine synthase B; Region: cysM; TIGR01138 583345002350 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 583345002351 dimer interface [polypeptide binding]; other site 583345002352 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345002353 catalytic residue [active] 583345002354 Dicarboxylate transport; Region: DctA-YdbH; cl14674 583345002355 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 583345002356 active site 583345002357 catalytic site [active] 583345002358 substrate binding site [chemical binding]; other site 583345002359 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 583345002360 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 583345002361 Peptidase family M48; Region: Peptidase_M48; cl12018 583345002362 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 583345002363 TRAM domain; Region: TRAM; cl01282 583345002364 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 583345002365 S-adenosylmethionine binding site [chemical binding]; other site 583345002366 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 583345002367 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 583345002368 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 583345002369 FeS/SAM binding site; other site 583345002370 HemN C-terminal domain; Region: HemN_C; pfam06969 583345002371 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 583345002372 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 583345002373 ligand binding site [chemical binding]; other site 583345002374 flexible hinge region; other site 583345002375 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 583345002376 non-specific DNA interactions [nucleotide binding]; other site 583345002377 DNA binding site [nucleotide binding] 583345002378 sequence specific DNA binding site [nucleotide binding]; other site 583345002379 putative cAMP binding site [chemical binding]; other site 583345002380 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 583345002381 FeS/SAM binding site; other site 583345002382 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 583345002383 Ligand Binding Site [chemical binding]; other site 583345002384 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 583345002385 Ligand Binding Site [chemical binding]; other site 583345002386 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 583345002387 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 583345002388 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 583345002389 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 583345002390 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 583345002391 Cytochrome c; Region: Cytochrom_C; pfam00034 583345002392 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 583345002393 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 583345002394 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 583345002395 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 583345002396 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 583345002397 Low-spin heme binding site [chemical binding]; other site 583345002398 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 583345002399 Putative water exit pathway; other site 583345002400 Binuclear center (active site) [active] 583345002401 Putative proton exit pathway; other site 583345002402 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 583345002403 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 583345002404 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 583345002405 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 583345002406 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 583345002407 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 583345002408 dimer interface [polypeptide binding]; other site 583345002409 conserved gate region; other site 583345002410 putative PBP binding loops; other site 583345002411 ABC-ATPase subunit interface; other site 583345002412 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 583345002413 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 583345002414 dimer interface [polypeptide binding]; other site 583345002415 conserved gate region; other site 583345002416 putative PBP binding loops; other site 583345002417 ABC-ATPase subunit interface; other site 583345002418 beta-hexosaminidase; Provisional; Region: PRK05337 583345002419 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 583345002420 YccA-like proteins; Region: YccA_like; cd10433 583345002421 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 583345002422 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 583345002423 nucleoside/Zn binding site; other site 583345002424 dimer interface [polypeptide binding]; other site 583345002425 catalytic motif [active] 583345002426 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 583345002427 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345002428 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 583345002429 dimerization interface [polypeptide binding]; other site 583345002430 YceI-like domain; Region: YceI; cl01001 583345002431 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 583345002432 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 583345002433 FMN binding site [chemical binding]; other site 583345002434 active site 583345002435 substrate binding site [chemical binding]; other site 583345002436 catalytic residue [active] 583345002437 Nitroreductase-like family 2. 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_2; cd02138 583345002438 putative FMN binding site [chemical binding]; other site 583345002439 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 583345002440 catalytic residues [active] 583345002441 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 583345002442 Peptidase family M23; Region: Peptidase_M23; pfam01551 583345002443 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 583345002444 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 583345002445 S-adenosylmethionine binding site [chemical binding]; other site 583345002446 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 583345002447 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 583345002448 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 583345002449 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 583345002450 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 583345002451 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 583345002452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 583345002453 Family of unknown function (DUF490); Region: DUF490; pfam04357 583345002454 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 583345002455 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 583345002456 Surface antigen; Region: Bac_surface_Ag; pfam01103 583345002457 adenylosuccinate lyase; Provisional; Region: PRK09285 583345002458 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 583345002459 tetramer interface [polypeptide binding]; other site 583345002460 active site 583345002461 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 583345002462 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 583345002463 ligand binding site [chemical binding]; other site 583345002464 active site 583345002465 UGI interface [polypeptide binding]; other site 583345002466 catalytic site [active] 583345002467 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 583345002468 2-methylcitrate dehydratase; Region: prpD; TIGR02330 583345002469 methylcitrate synthase; Provisional; Region: PRK12351 583345002470 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 583345002471 oxalacetate binding site [chemical binding]; other site 583345002472 citrylCoA binding site [chemical binding]; other site 583345002473 coenzyme A binding site [chemical binding]; other site 583345002474 catalytic triad [active] 583345002475 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 583345002476 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 583345002477 tetramer interface [polypeptide binding]; other site 583345002478 active site 583345002479 Mg2+/Mn2+ binding site [ion binding]; other site 583345002480 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 583345002481 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 583345002482 putative active site [active] 583345002483 putative catalytic site [active] 583345002484 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 583345002485 putative active site [active] 583345002486 putative catalytic site [active] 583345002487 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 583345002488 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 583345002489 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 583345002490 DNA-binding site [nucleotide binding]; DNA binding site 583345002491 UTRA domain; Region: UTRA; pfam07702 583345002492 Malic enzyme, N-terminal domain; Region: malic; pfam00390 583345002493 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 583345002494 putative NAD(P) binding site [chemical binding]; other site 583345002495 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 583345002496 Iron-sulfur protein interface; other site 583345002497 proximal quinone binding site [chemical binding]; other site 583345002498 SdhD (CybS) interface [polypeptide binding]; other site 583345002499 proximal heme binding site [chemical binding]; other site 583345002500 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 583345002501 SdhC subunit interface [polypeptide binding]; other site 583345002502 proximal heme binding site [chemical binding]; other site 583345002503 cardiolipin binding site; other site 583345002504 Iron-sulfur protein interface; other site 583345002505 proximal quinone binding site [chemical binding]; other site 583345002506 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 583345002507 L-aspartate oxidase; Provisional; Region: PRK06175 583345002508 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 583345002509 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 583345002510 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 583345002511 Somatotropin/prolactin hormone family; Region: growth_hormone_like; cl07831 583345002512 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 583345002513 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 583345002514 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 583345002515 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 583345002516 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 583345002517 acyl-activating enzyme (AAE) consensus motif; other site 583345002518 AMP binding site [chemical binding]; other site 583345002519 active site 583345002520 CoA binding site [chemical binding]; other site 583345002521 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 583345002522 Fumarase C-terminus; Region: Fumerase_C; pfam05683 583345002523 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 583345002524 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 583345002525 substrate binding site [chemical binding]; other site 583345002526 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 583345002527 substrate binding site [chemical binding]; other site 583345002528 ligand binding site [chemical binding]; other site 583345002529 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 583345002530 hypothetical protein; Provisional; Region: PRK05208 583345002531 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 583345002532 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 583345002533 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 583345002534 active site 1 [active] 583345002535 dimer interface [polypeptide binding]; other site 583345002536 hexamer interface [polypeptide binding]; other site 583345002537 active site 2 [active] 583345002538 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 583345002539 putative hydrophobic ligand binding site [chemical binding]; other site 583345002540 protein interface [polypeptide binding]; other site 583345002541 gate; other site 583345002542 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 583345002543 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 583345002544 GIY-YIG motif/motif A; other site 583345002545 active site 583345002546 catalytic site [active] 583345002547 putative DNA binding site [nucleotide binding]; other site 583345002548 metal binding site [ion binding]; metal-binding site 583345002549 UvrB/uvrC motif; Region: UVR; pfam02151 583345002550 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 583345002551 Helix-hairpin-helix motif; Region: HHH; pfam00633 583345002552 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 583345002553 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 583345002554 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 583345002555 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 583345002556 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 583345002557 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 583345002558 Walker A/P-loop; other site 583345002559 ATP binding site [chemical binding]; other site 583345002560 Q-loop/lid; other site 583345002561 ABC transporter signature motif; other site 583345002562 Walker B; other site 583345002563 D-loop; other site 583345002564 H-loop/switch region; other site 583345002565 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 583345002566 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 583345002567 E3 interaction surface; other site 583345002568 lipoyl attachment site [posttranslational modification]; other site 583345002569 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345002570 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 583345002571 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 583345002572 DNA binding residues [nucleotide binding] 583345002573 dimerization interface [polypeptide binding]; other site 583345002574 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 583345002575 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345002576 metal binding site [ion binding]; metal-binding site 583345002577 active site 583345002578 I-site; other site 583345002579 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 583345002580 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 583345002581 CshA-type fibril repeat; Region: CshA_fibril_rpt; TIGR04225 583345002582 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 583345002583 metal ion-dependent adhesion site (MIDAS); other site 583345002584 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 583345002585 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 583345002586 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 583345002587 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345002588 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345002589 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345002590 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 583345002591 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 583345002592 Walker A/P-loop; other site 583345002593 ATP binding site [chemical binding]; other site 583345002594 Q-loop/lid; other site 583345002595 ABC transporter signature motif; other site 583345002596 Walker B; other site 583345002597 D-loop; other site 583345002598 H-loop/switch region; other site 583345002599 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 583345002600 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 583345002601 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 583345002602 FtsX-like permease family; Region: FtsX; pfam02687 583345002603 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345002604 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345002605 metal binding site [ion binding]; metal-binding site 583345002606 active site 583345002607 I-site; other site 583345002608 Protein of unknown function (DUF779); Region: DUF779; cl01432 583345002609 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 583345002610 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 583345002611 NAD(P) binding site [chemical binding]; other site 583345002612 catalytic residues [active] 583345002613 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 583345002614 cyclase homology domain; Region: CHD; cd07302 583345002615 nucleotidyl binding site; other site 583345002616 metal binding site [ion binding]; metal-binding site 583345002617 dimer interface [polypeptide binding]; other site 583345002618 PqqA family; Region: PqqA; cl15372 583345002619 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 583345002620 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 583345002621 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 583345002622 dimer interface [polypeptide binding]; other site 583345002623 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345002624 catalytic residue [active] 583345002625 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 583345002626 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 583345002627 serine O-acetyltransferase; Region: cysE; TIGR01172 583345002628 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 583345002629 trimer interface [polypeptide binding]; other site 583345002630 active site 583345002631 substrate binding site [chemical binding]; other site 583345002632 CoA binding site [chemical binding]; other site 583345002633 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 583345002634 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 583345002635 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 583345002636 catalytic residue [active] 583345002637 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 583345002638 Uncharacterized small protein (DUF2292); Region: DUF2292; pfam10055 583345002639 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 583345002640 Protein of unknown function (DUF815); Region: DUF815; pfam05673 583345002641 Walker A motif; other site 583345002642 ATP binding site [chemical binding]; other site 583345002643 Walker B motif; other site 583345002644 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 583345002645 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 583345002646 ATP binding site [chemical binding]; other site 583345002647 Mg2+ binding site [ion binding]; other site 583345002648 G-X-G motif; other site 583345002649 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 583345002650 anchoring element; other site 583345002651 dimer interface [polypeptide binding]; other site 583345002652 ATP binding site [chemical binding]; other site 583345002653 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 583345002654 active site 583345002655 putative metal-binding site [ion binding]; other site 583345002656 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 583345002657 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 583345002658 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 583345002659 CAP-like domain; other site 583345002660 active site 583345002661 primary dimer interface [polypeptide binding]; other site 583345002662 Predicted transporter component [General function prediction only]; Region: COG2391 583345002663 Sulphur transport; Region: Sulf_transp; pfam04143 583345002664 Predicted transporter component [General function prediction only]; Region: COG2391 583345002665 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 583345002666 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 583345002667 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 583345002668 dimerization interface [polypeptide binding]; other site 583345002669 putative DNA binding site [nucleotide binding]; other site 583345002670 putative Zn2+ binding site [ion binding]; other site 583345002671 Putative phosphatase (DUF442); Region: DUF442; cl17385 583345002672 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 583345002673 Response regulator receiver domain; Region: Response_reg; pfam00072 583345002674 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 583345002675 active site 583345002676 phosphorylation site [posttranslational modification] 583345002677 intermolecular recognition site; other site 583345002678 dimerization interface [polypeptide binding]; other site 583345002679 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 583345002680 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 583345002681 dimer interface [polypeptide binding]; other site 583345002682 phosphorylation site [posttranslational modification] 583345002683 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 583345002684 ATP binding site [chemical binding]; other site 583345002685 Mg2+ binding site [ion binding]; other site 583345002686 G-X-G motif; other site 583345002687 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 583345002688 DNA binding residues [nucleotide binding] 583345002689 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 583345002690 active site 583345002691 phosphorylation site [posttranslational modification] 583345002692 intermolecular recognition site; other site 583345002693 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 583345002694 putative CheA interaction surface; other site 583345002695 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 583345002696 PAS fold; Region: PAS_3; pfam08447 583345002697 putative active site [active] 583345002698 heme pocket [chemical binding]; other site 583345002699 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 583345002700 Tar ligand binding domain homologue; Region: TarH; pfam02203 583345002701 HAMP domain; Region: HAMP; pfam00672 583345002702 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 583345002703 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345002704 putative active site [active] 583345002705 heme pocket [chemical binding]; other site 583345002706 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 583345002707 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345002708 putative active site [active] 583345002709 heme pocket [chemical binding]; other site 583345002710 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 583345002711 putative active site [active] 583345002712 heme pocket [chemical binding]; other site 583345002713 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345002714 dimer interface [polypeptide binding]; other site 583345002715 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 583345002716 putative CheW interface [polypeptide binding]; other site 583345002717 Response regulator receiver domain; Region: Response_reg; pfam00072 583345002718 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 583345002719 active site 583345002720 phosphorylation site [posttranslational modification] 583345002721 intermolecular recognition site; other site 583345002722 dimerization interface [polypeptide binding]; other site 583345002723 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 583345002724 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 583345002725 active site 583345002726 phosphorylation site [posttranslational modification] 583345002727 intermolecular recognition site; other site 583345002728 dimerization interface [polypeptide binding]; other site 583345002729 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 583345002730 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 583345002731 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 583345002732 homodimer interface [polypeptide binding]; other site 583345002733 oligonucleotide binding site [chemical binding]; other site 583345002734 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 583345002735 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 583345002736 RNA binding surface [nucleotide binding]; other site 583345002737 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 583345002738 active site 583345002739 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 583345002740 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 583345002741 motif II; other site 583345002742 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 583345002743 iron-sulfur cluster [ion binding]; other site 583345002744 [2Fe-2S] cluster binding site [ion binding]; other site 583345002745 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 583345002746 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 583345002747 tandem repeat interface [polypeptide binding]; other site 583345002748 oligomer interface [polypeptide binding]; other site 583345002749 active site residues [active] 583345002750 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 583345002751 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 583345002752 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 583345002753 active site 583345002754 dimer interface [polypeptide binding]; other site 583345002755 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 583345002756 dimer interface [polypeptide binding]; other site 583345002757 active site 583345002758 glycogen branching enzyme; Provisional; Region: PRK05402 583345002759 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 583345002760 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 583345002761 active site 583345002762 catalytic site [active] 583345002763 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 583345002764 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 583345002765 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 583345002766 ligand binding site; other site 583345002767 oligomer interface; other site 583345002768 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 583345002769 dimer interface [polypeptide binding]; other site 583345002770 N-terminal domain interface [polypeptide binding]; other site 583345002771 sulfate 1 binding site; other site 583345002772 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 583345002773 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 583345002774 putative active site [active] 583345002775 catalytic site [active] 583345002776 4-alpha-glucanotransferase; Provisional; Region: PRK14508 583345002777 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 583345002778 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 583345002779 nucleotide binding site [chemical binding]; other site 583345002780 PAS fold; Region: PAS_4; pfam08448 583345002781 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 583345002782 putative active site [active] 583345002783 heme pocket [chemical binding]; other site 583345002784 PAS fold; Region: PAS_4; pfam08448 583345002785 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345002786 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345002787 metal binding site [ion binding]; metal-binding site 583345002788 active site 583345002789 I-site; other site 583345002790 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 583345002791 epoxyqueuosine reductase; Region: TIGR00276 583345002792 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 583345002793 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 583345002794 AMIN domain; Region: AMIN; pfam11741 583345002795 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 583345002796 active site 583345002797 metal binding site [ion binding]; metal-binding site 583345002798 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 583345002799 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 583345002800 Beta-Casp domain; Region: Beta-Casp; smart01027 583345002801 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 583345002802 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 583345002803 ATP binding site [chemical binding]; other site 583345002804 putative Mg++ binding site [ion binding]; other site 583345002805 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 583345002806 nucleotide binding region [chemical binding]; other site 583345002807 ATP-binding site [chemical binding]; other site 583345002808 Mitochondrial degradasome RNA helicase subunit C terminal; Region: SUV3_C; pfam12513 583345002809 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 583345002810 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345002811 putative CheW interface [polypeptide binding]; other site 583345002812 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 583345002813 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 583345002814 ATP binding site [chemical binding]; other site 583345002815 Mg2+ binding site [ion binding]; other site 583345002816 G-X-G motif; other site 583345002817 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 583345002818 ATP binding site [chemical binding]; other site 583345002819 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 583345002820 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 583345002821 TrkA-N domain; Region: TrkA_N; pfam02254 583345002822 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 583345002823 TrkA-N domain; Region: TrkA_N; pfam02254 583345002824 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 583345002825 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 583345002826 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 583345002827 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 583345002828 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345002829 homodimer interface [polypeptide binding]; other site 583345002830 catalytic residue [active] 583345002831 EamA-like transporter family; Region: EamA; pfam00892 583345002832 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 583345002833 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345002834 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 583345002835 putative active site [active] 583345002836 heme pocket [chemical binding]; other site 583345002837 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 583345002838 putative active site [active] 583345002839 heme pocket [chemical binding]; other site 583345002840 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345002841 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345002842 metal binding site [ion binding]; metal-binding site 583345002843 active site 583345002844 I-site; other site 583345002845 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 583345002846 CheW-like domain; Region: CheW; pfam01584 583345002847 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 583345002848 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 583345002849 Walker A motif; other site 583345002850 ATP binding site [chemical binding]; other site 583345002851 Walker B motif; other site 583345002852 Tetratricopeptide repeat; Region: TPR_12; pfam13424 583345002853 TPR repeat; Region: TPR_11; pfam13414 583345002854 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 583345002855 TPR motif; other site 583345002856 binding surface 583345002857 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 583345002858 binding surface 583345002859 TPR motif; other site 583345002860 TPR repeat; Region: TPR_11; pfam13414 583345002861 cardiolipin synthase 2; Provisional; Region: PRK11263 583345002862 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 583345002863 putative active site [active] 583345002864 catalytic site [active] 583345002865 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 583345002866 putative active site [active] 583345002867 catalytic site [active] 583345002868 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 583345002869 putative catalytic site [active] 583345002870 putative metal binding site [ion binding]; other site 583345002871 putative phosphate binding site [ion binding]; other site 583345002872 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 583345002873 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 583345002874 active site residue [active] 583345002875 FwdC/FmdC. This domain of unknown function is found in the subunit C of formylmethanofuran dehydrogenase, an enzyme that catalyzes the first step in methane formation from CO2 in methanogenic archaea, hyperthermophiles and bacteria. There are two...; Region: FwdC/FmdC; cd00980 583345002876 putative subunit interface; other site 583345002877 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional; Region: PRK02114 583345002878 Formylmethanofuran-tetrahydromethanopterin formyltransferase; Region: FTR; pfam01913 583345002879 FTR, proximal lobe; Region: FTR_C; pfam02741 583345002880 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 583345002881 formylmethanofuran dehydrogenase subunit A; Region: one_C_dehyd_A; TIGR03121 583345002882 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 583345002883 active site 583345002884 The MopB_FmdB-FwdB CD contains the molybdenum/tungsten formylmethanofuran dehydrogenases, subunit B (FmdB/FwdB), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea...; Region: MopB_FmdB-FwdB; cd02761 583345002885 formylmethanofuran dehydrogenase subunit B; Region: one_C_dehyd_B; TIGR03129 583345002886 putative [4Fe-4S] binding site [ion binding]; other site 583345002887 putative molybdopterin cofactor binding site [chemical binding]; other site 583345002888 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 583345002889 active site 583345002890 multimer interface [polypeptide binding]; other site 583345002891 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 583345002892 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 583345002893 FeS/SAM binding site; other site 583345002894 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 583345002895 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 583345002896 TPR motif; other site 583345002897 binding surface 583345002898 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 583345002899 binding surface 583345002900 TPR motif; other site 583345002901 Helix-turn-helix domain; Region: HTH_25; pfam13413 583345002902 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 583345002903 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 583345002904 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 583345002905 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 583345002906 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 583345002907 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 583345002908 dimer interface [polypeptide binding]; other site 583345002909 motif 1; other site 583345002910 active site 583345002911 motif 2; other site 583345002912 motif 3; other site 583345002913 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 583345002914 anticodon binding site; other site 583345002915 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 583345002916 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 583345002917 Walker A/P-loop; other site 583345002918 ATP binding site [chemical binding]; other site 583345002919 Q-loop/lid; other site 583345002920 ABC transporter signature motif; other site 583345002921 Walker B; other site 583345002922 D-loop; other site 583345002923 H-loop/switch region; other site 583345002924 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 583345002925 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 583345002926 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 583345002927 Walker A/P-loop; other site 583345002928 ATP binding site [chemical binding]; other site 583345002929 Q-loop/lid; other site 583345002930 ABC transporter signature motif; other site 583345002931 Walker B; other site 583345002932 D-loop; other site 583345002933 H-loop/switch region; other site 583345002934 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 583345002935 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 583345002936 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 583345002937 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 583345002938 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 583345002939 Trp docking motif [polypeptide binding]; other site 583345002940 active site 583345002941 GTP-binding protein Der; Reviewed; Region: PRK00093 583345002942 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 583345002943 G1 box; other site 583345002944 GTP/Mg2+ binding site [chemical binding]; other site 583345002945 Switch I region; other site 583345002946 G2 box; other site 583345002947 Switch II region; other site 583345002948 G3 box; other site 583345002949 G4 box; other site 583345002950 G5 box; other site 583345002951 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 583345002952 G1 box; other site 583345002953 GTP/Mg2+ binding site [chemical binding]; other site 583345002954 Switch I region; other site 583345002955 G2 box; other site 583345002956 G3 box; other site 583345002957 Switch II region; other site 583345002958 G4 box; other site 583345002959 G5 box; other site 583345002960 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345002961 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345002962 dimer interface [polypeptide binding]; other site 583345002963 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 583345002964 putative CheW interface [polypeptide binding]; other site 583345002965 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 583345002966 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 583345002967 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 583345002968 binding surface 583345002969 TPR motif; other site 583345002970 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 583345002971 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 583345002972 RNA binding surface [nucleotide binding]; other site 583345002973 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 583345002974 active site 583345002975 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 583345002976 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 583345002977 ZIP Zinc transporter; Region: Zip; pfam02535 583345002978 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 583345002979 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 583345002980 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 583345002981 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 583345002982 FeS/SAM binding site; other site 583345002983 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 583345002984 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345002985 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 583345002986 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345002987 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345002988 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345002989 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 583345002990 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 583345002991 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 583345002992 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 583345002993 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 583345002994 active site 583345002995 HIGH motif; other site 583345002996 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 583345002997 active site 583345002998 KMSKS motif; other site 583345002999 bacterial Hfq-like; Region: Hfq; cd01716 583345003000 hexamer interface [polypeptide binding]; other site 583345003001 Sm1 motif; other site 583345003002 RNA binding site [nucleotide binding]; other site 583345003003 Sm2 motif; other site 583345003004 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 583345003005 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 583345003006 HflX GTPase family; Region: HflX; cd01878 583345003007 G1 box; other site 583345003008 GTP/Mg2+ binding site [chemical binding]; other site 583345003009 Switch I region; other site 583345003010 G2 box; other site 583345003011 G3 box; other site 583345003012 Switch II region; other site 583345003013 G4 box; other site 583345003014 G5 box; other site 583345003015 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 583345003016 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 583345003017 HflK protein; Region: hflK; TIGR01933 583345003018 HflC protein; Region: hflC; TIGR01932 583345003019 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 583345003020 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 583345003021 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 583345003022 dimer interface [polypeptide binding]; other site 583345003023 motif 1; other site 583345003024 active site 583345003025 motif 2; other site 583345003026 motif 3; other site 583345003027 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 583345003028 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 583345003029 GDP-binding site [chemical binding]; other site 583345003030 ACT binding site; other site 583345003031 IMP binding site; other site 583345003032 Archaeal flavoproteins [Energy production and conversion]; Region: COG1036 583345003033 Flavoprotein; Region: Flavoprotein; pfam02441 583345003034 dihydropteroate synthase-related protein; Region: TIGR00284 583345003035 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 583345003036 substrate binding pocket [chemical binding]; other site 583345003037 dimer interface [polypeptide binding]; other site 583345003038 inhibitor binding site; inhibition site 583345003039 Protein of unknown function (DUF447); Region: DUF447; pfam04289 583345003040 hypothetical protein; Provisional; Region: PRK02227 583345003041 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 583345003042 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 583345003043 ligand binding site [chemical binding]; other site 583345003044 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 583345003045 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 583345003046 active site 583345003047 putative substrate binding pocket [chemical binding]; other site 583345003048 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 583345003049 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 583345003050 S-adenosylmethionine binding site [chemical binding]; other site 583345003051 phosphoglycolate phosphatase; Provisional; Region: PRK13222 583345003052 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 583345003053 motif II; other site 583345003054 recombination protein RecR; Reviewed; Region: recR; PRK00076 583345003055 RecR protein; Region: RecR; pfam02132 583345003056 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 583345003057 putative active site [active] 583345003058 putative metal-binding site [ion binding]; other site 583345003059 tetramer interface [polypeptide binding]; other site 583345003060 hypothetical protein; Validated; Region: PRK00153 583345003061 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 583345003062 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 583345003063 Walker A motif; other site 583345003064 ATP binding site [chemical binding]; other site 583345003065 Walker B motif; other site 583345003066 arginine finger; other site 583345003067 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 583345003068 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 583345003069 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 583345003070 active site 583345003071 phosphorylation site [posttranslational modification] 583345003072 intermolecular recognition site; other site 583345003073 dimerization interface [polypeptide binding]; other site 583345003074 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345003075 Zn2+ binding site [ion binding]; other site 583345003076 Mg2+ binding site [ion binding]; other site 583345003077 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345003078 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 583345003079 Histidine kinase; Region: HisKA_3; pfam07730 583345003080 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 583345003081 ATP binding site [chemical binding]; other site 583345003082 Mg2+ binding site [ion binding]; other site 583345003083 G-X-G motif; other site 583345003084 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 583345003085 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 583345003086 active site 583345003087 phosphorylation site [posttranslational modification] 583345003088 intermolecular recognition site; other site 583345003089 dimerization interface [polypeptide binding]; other site 583345003090 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 583345003091 DNA binding residues [nucleotide binding] 583345003092 dimerization interface [polypeptide binding]; other site 583345003093 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 583345003094 binding surface 583345003095 TPR motif; other site 583345003096 TPR repeat; Region: TPR_11; pfam13414 583345003097 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 583345003098 binding surface 583345003099 TPR motif; other site 583345003100 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 583345003101 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 583345003102 binding surface 583345003103 TPR motif; other site 583345003104 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 583345003105 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 583345003106 binding surface 583345003107 TPR motif; other site 583345003108 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 583345003109 binding surface 583345003110 TPR motif; other site 583345003111 Glycosyltransferase like family; Region: Glyco_tranf_2_5; pfam13712 583345003112 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345003113 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345003114 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 583345003115 TPR motif; other site 583345003116 binding surface 583345003117 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 583345003118 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 583345003119 putative trimer interface [polypeptide binding]; other site 583345003120 putative active site [active] 583345003121 putative substrate binding site [chemical binding]; other site 583345003122 putative CoA binding site [chemical binding]; other site 583345003123 Protein of unknown function (DUF563); Region: DUF563; pfam04577 583345003124 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 583345003125 active site 583345003126 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 583345003127 dimer interface [polypeptide binding]; other site 583345003128 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 583345003129 Ligand Binding Site [chemical binding]; other site 583345003130 Molecular Tunnel; other site 583345003131 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 583345003132 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 583345003133 active site 583345003134 nucleotide binding site [chemical binding]; other site 583345003135 HIGH motif; other site 583345003136 KMSKS motif; other site 583345003137 WxcM-like, C-terminal; Region: FdtA; pfam05523 583345003138 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 583345003139 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 583345003140 inhibitor-cofactor binding pocket; inhibition site 583345003141 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003142 catalytic residue [active] 583345003143 Methyltransferase domain; Region: Methyltransf_23; pfam13489 583345003144 Methyltransferase domain; Region: Methyltransf_11; pfam08241 583345003145 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345003146 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 583345003147 TPR motif; other site 583345003148 binding surface 583345003149 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 583345003150 binding surface 583345003151 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345003152 TPR motif; other site 583345003153 TPR repeat; Region: TPR_11; pfam13414 583345003154 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 583345003155 binding surface 583345003156 TPR motif; other site 583345003157 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 583345003158 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 583345003159 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 583345003160 FlaG protein; Region: FlaG; pfam03646 583345003161 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 583345003162 flagellar capping protein; Provisional; Region: PRK12765 583345003163 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 583345003164 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 583345003165 Flagellar protein FliS; Region: FliS; cl00654 583345003166 Flagellar protein FliT; Region: FliT; pfam05400 583345003167 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 583345003168 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 583345003169 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 583345003170 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 583345003171 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 583345003172 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 583345003173 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 583345003174 FliG C-terminal domain; Region: FliG_C; pfam01706 583345003175 flagellar assembly protein H; Validated; Region: fliH; PRK05687 583345003176 Flagellar assembly protein FliH; Region: FliH; pfam02108 583345003177 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 583345003178 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 583345003179 Walker A motif/ATP binding site; other site 583345003180 Walker B motif; other site 583345003181 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 583345003182 Flagellar FliJ protein; Region: FliJ; pfam02050 583345003183 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 583345003184 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07021 583345003185 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 583345003186 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 583345003187 flagellar motor switch protein; Validated; Region: fliN; PRK05698 583345003188 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 583345003189 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 583345003190 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 583345003191 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 583345003192 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 583345003193 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 583345003194 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 583345003195 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 583345003196 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 583345003197 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 583345003198 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 583345003199 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 583345003200 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 583345003201 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 583345003202 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 583345003203 Flagellar L-ring protein; Region: FlgH; pfam02107 583345003204 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 583345003205 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 583345003206 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 583345003207 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 583345003208 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 583345003209 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 583345003210 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 583345003211 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 583345003212 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 583345003213 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 583345003214 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 583345003215 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 583345003216 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 583345003217 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 583345003218 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 583345003219 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 583345003220 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 583345003221 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 583345003222 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 583345003223 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 583345003224 FlgN protein; Region: FlgN; pfam05130 583345003225 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 583345003226 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 583345003227 ATP binding site [chemical binding]; other site 583345003228 putative Mg++ binding site [ion binding]; other site 583345003229 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 583345003230 nucleotide binding region [chemical binding]; other site 583345003231 ATP-binding site [chemical binding]; other site 583345003232 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 583345003233 HRDC domain; Region: HRDC; pfam00570 583345003234 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 583345003235 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345003236 Walker A/P-loop; other site 583345003237 ATP binding site [chemical binding]; other site 583345003238 Q-loop/lid; other site 583345003239 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345003240 ABC transporter signature motif; other site 583345003241 Walker B; other site 583345003242 D-loop; other site 583345003243 ABC transporter; Region: ABC_tran_2; pfam12848 583345003244 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345003245 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 583345003246 dimer interface [polypeptide binding]; other site 583345003247 FMN binding site [chemical binding]; other site 583345003248 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 583345003249 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 583345003250 GMP synthase; Reviewed; Region: guaA; PRK00074 583345003251 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 583345003252 AMP/PPi binding site [chemical binding]; other site 583345003253 candidate oxyanion hole; other site 583345003254 catalytic triad [active] 583345003255 potential glutamine specificity residues [chemical binding]; other site 583345003256 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 583345003257 ATP Binding subdomain [chemical binding]; other site 583345003258 Ligand Binding sites [chemical binding]; other site 583345003259 Dimerization subdomain; other site 583345003260 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 583345003261 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 583345003262 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 583345003263 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 583345003264 active site 583345003265 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 583345003266 RnfH family Ubiquitin; Region: Ub-RnfH; pfam03658 583345003267 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 583345003268 putative coenzyme Q binding site [chemical binding]; other site 583345003269 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 583345003270 SmpB-tmRNA interface; other site 583345003271 GAF domain; Region: GAF; pfam01590 583345003272 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 583345003273 PAS domain; Region: PAS_9; pfam13426 583345003274 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 583345003275 putative active site [active] 583345003276 heme pocket [chemical binding]; other site 583345003277 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345003278 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345003279 metal binding site [ion binding]; metal-binding site 583345003280 active site 583345003281 I-site; other site 583345003282 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 583345003283 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 583345003284 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345003285 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 583345003286 putative dimerization interface [polypeptide binding]; other site 583345003287 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 583345003288 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 583345003289 THF binding site; other site 583345003290 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 583345003291 substrate binding site [chemical binding]; other site 583345003292 THF binding site; other site 583345003293 zinc-binding site [ion binding]; other site 583345003294 GAF domain; Region: GAF; pfam01590 583345003295 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 583345003296 PAS domain S-box; Region: sensory_box; TIGR00229 583345003297 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 583345003298 putative active site [active] 583345003299 heme pocket [chemical binding]; other site 583345003300 PAS domain; Region: PAS_9; pfam13426 583345003301 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 583345003302 putative active site [active] 583345003303 heme pocket [chemical binding]; other site 583345003304 PAS domain S-box; Region: sensory_box; TIGR00229 583345003305 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 583345003306 putative active site [active] 583345003307 heme pocket [chemical binding]; other site 583345003308 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345003309 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345003310 metal binding site [ion binding]; metal-binding site 583345003311 active site 583345003312 I-site; other site 583345003313 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 583345003314 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 583345003315 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 583345003316 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 583345003317 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 583345003318 substrate binding site [chemical binding]; other site 583345003319 ligand binding site [chemical binding]; other site 583345003320 Predicted small secreted protein [Function unknown]; Region: COG5510 583345003321 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 583345003322 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 583345003323 substrate binding site [chemical binding]; other site 583345003324 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 583345003325 tartrate dehydrogenase; Region: TTC; TIGR02089 583345003326 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 583345003327 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 583345003328 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 583345003329 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 583345003330 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 583345003331 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 583345003332 dimerization interface 3.5A [polypeptide binding]; other site 583345003333 active site 583345003334 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 583345003335 active site 583345003336 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 583345003337 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 583345003338 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003339 catalytic residue [active] 583345003340 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 583345003341 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 583345003342 substrate binding site [chemical binding]; other site 583345003343 active site 583345003344 catalytic residues [active] 583345003345 heterodimer interface [polypeptide binding]; other site 583345003346 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 583345003347 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 583345003348 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 583345003349 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 583345003350 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 583345003351 Sporulation related domain; Region: SPOR; pfam05036 583345003352 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 583345003353 Colicin V production protein; Region: Colicin_V; pfam02674 583345003354 amidophosphoribosyltransferase; Provisional; Region: PRK09246 583345003355 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 583345003356 active site 583345003357 tetramer interface [polypeptide binding]; other site 583345003358 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345003359 active site 583345003360 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 583345003361 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 583345003362 homodimer interface [polypeptide binding]; other site 583345003363 substrate-cofactor binding pocket; other site 583345003364 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003365 catalytic residue [active] 583345003366 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 583345003367 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 583345003368 DNA gyrase subunit A; Validated; Region: PRK05560 583345003369 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 583345003370 CAP-like domain; other site 583345003371 active site 583345003372 primary dimer interface [polypeptide binding]; other site 583345003373 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 583345003374 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 583345003375 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 583345003376 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 583345003377 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 583345003378 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 583345003379 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 583345003380 homodimer interface [polypeptide binding]; other site 583345003381 substrate-cofactor binding pocket; other site 583345003382 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003383 catalytic residue [active] 583345003384 Chorismate mutase type II; Region: CM_2; cl00693 583345003385 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 583345003386 Prephenate dehydratase; Region: PDT; pfam00800 583345003387 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 583345003388 putative L-Phe binding site [chemical binding]; other site 583345003389 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 583345003390 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 583345003391 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003392 homodimer interface [polypeptide binding]; other site 583345003393 catalytic residue [active] 583345003394 PqqA family; Region: PqqA; cl15372 583345003395 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 583345003396 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 583345003397 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 583345003398 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 583345003399 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 583345003400 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 583345003401 FeS/SAM binding site; other site 583345003402 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 583345003403 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 583345003404 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 583345003405 putative substrate translocation pore; other site 583345003406 Predicted membrane protein [Function unknown]; Region: COG2259 583345003407 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 583345003408 Ferredoxin [Energy production and conversion]; Region: COG1146 583345003409 4Fe-4S binding domain; Region: Fer4; cl02805 583345003410 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 583345003411 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 583345003412 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 583345003413 CysD dimerization site [polypeptide binding]; other site 583345003414 G1 box; other site 583345003415 putative GEF interaction site [polypeptide binding]; other site 583345003416 GTP/Mg2+ binding site [chemical binding]; other site 583345003417 Switch I region; other site 583345003418 G2 box; other site 583345003419 G3 box; other site 583345003420 Switch II region; other site 583345003421 G4 box; other site 583345003422 G5 box; other site 583345003423 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 583345003424 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 583345003425 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 583345003426 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 583345003427 Active Sites [active] 583345003428 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 583345003429 Active Sites [active] 583345003430 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 583345003431 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 583345003432 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 583345003433 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 583345003434 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 583345003435 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 583345003436 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345003437 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 583345003438 substrate binding site [chemical binding]; other site 583345003439 dimerization interface [polypeptide binding]; other site 583345003440 Domain of unknown function DUF302; Region: DUF302; cl01364 583345003441 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 583345003442 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 583345003443 Uncharacterized conserved protein [Function unknown]; Region: COG1739 583345003444 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 583345003445 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 583345003446 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 583345003447 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 583345003448 Peptidase family M48; Region: Peptidase_M48; pfam01435 583345003449 Bacterial SH3 domain; Region: SH3_3; cl17532 583345003450 CHASE2 domain; Region: CHASE2; pfam05226 583345003451 RmuC family; Region: RmuC; pfam02646 583345003452 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 583345003453 MoaE interaction surface [polypeptide binding]; other site 583345003454 MoeB interaction surface [polypeptide binding]; other site 583345003455 thiocarboxylated glycine; other site 583345003456 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 583345003457 MoaE homodimer interface [polypeptide binding]; other site 583345003458 MoaD interaction [polypeptide binding]; other site 583345003459 active site residues [active] 583345003460 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 583345003461 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 583345003462 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 583345003463 RNA binding surface [nucleotide binding]; other site 583345003464 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 583345003465 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 583345003466 active site 583345003467 substrate binding site [chemical binding]; other site 583345003468 metal binding site [ion binding]; metal-binding site 583345003469 EPS-associated transcriptional regulator, MarR family; Region: MarR_EPS; TIGR04176 583345003470 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 583345003471 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 583345003472 Substrate binding site; other site 583345003473 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 583345003474 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 583345003475 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 583345003476 NADP-binding site; other site 583345003477 homotetramer interface [polypeptide binding]; other site 583345003478 substrate binding site [chemical binding]; other site 583345003479 homodimer interface [polypeptide binding]; other site 583345003480 active site 583345003481 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 583345003482 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 583345003483 NADP binding site [chemical binding]; other site 583345003484 active site 583345003485 putative substrate binding site [chemical binding]; other site 583345003486 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 583345003487 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 583345003488 inhibitor-cofactor binding pocket; inhibition site 583345003489 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003490 catalytic residue [active] 583345003491 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 583345003492 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 583345003493 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 583345003494 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 583345003495 Walker A/P-loop; other site 583345003496 ATP binding site [chemical binding]; other site 583345003497 Q-loop/lid; other site 583345003498 ABC transporter signature motif; other site 583345003499 Walker B; other site 583345003500 D-loop; other site 583345003501 H-loop/switch region; other site 583345003502 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 583345003503 putative carbohydrate binding site [chemical binding]; other site 583345003504 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 583345003505 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 583345003506 GDP-Fucose binding site [chemical binding]; other site 583345003507 Methyltransferase domain; Region: Methyltransf_23; pfam13489 583345003508 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 583345003509 S-adenosylmethionine binding site [chemical binding]; other site 583345003510 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 583345003511 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 583345003512 active site 583345003513 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 583345003514 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 583345003515 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345003516 active site 583345003517 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345003518 RfbF is a putative dTDP-rhamnosyl transferase; Region: GT2_RfbF_like; cd02526 583345003519 L-rhamnosyltransferase; Region: rhamnosyltran; TIGR01556 583345003520 Ligand binding site; other site 583345003521 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 583345003522 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345003523 active site 583345003524 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 583345003525 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 583345003526 putative NAD(P) binding site [chemical binding]; other site 583345003527 active site 583345003528 putative substrate binding site [chemical binding]; other site 583345003529 Bacterial sugar transferase; Region: Bac_transf; pfam02397 583345003530 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 583345003531 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 583345003532 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 583345003533 NAD(P) binding site [chemical binding]; other site 583345003534 homodimer interface [polypeptide binding]; other site 583345003535 substrate binding site [chemical binding]; other site 583345003536 active site 583345003537 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345003538 active site 583345003539 transcriptional regulator EpsA; Region: EpsA; TIGR03020 583345003540 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 583345003541 DNA binding residues [nucleotide binding] 583345003542 dimerization interface [polypeptide binding]; other site 583345003543 ribonuclease R; Region: RNase_R; TIGR02063 583345003544 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 583345003545 RNB domain; Region: RNB; pfam00773 583345003546 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 583345003547 RNA binding site [nucleotide binding]; other site 583345003548 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 583345003549 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 583345003550 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 583345003551 malate:quinone oxidoreductase; Validated; Region: PRK05257 583345003552 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 583345003553 FHA domain; Region: FHA; pfam00498 583345003554 phosphopeptide binding site; other site 583345003555 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 583345003556 heme-binding residues [chemical binding]; other site 583345003557 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 583345003558 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 583345003559 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 583345003560 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 583345003561 ligand binding site [chemical binding]; other site 583345003562 flexible hinge region; other site 583345003563 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 583345003564 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 583345003565 ligand binding site [chemical binding]; other site 583345003566 flexible hinge region; other site 583345003567 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 583345003568 4Fe-4S binding domain; Region: Fer4; pfam00037 583345003569 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 583345003570 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 583345003571 CHASE domain; Region: CHASE; pfam03924 583345003572 PAS domain S-box; Region: sensory_box; TIGR00229 583345003573 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 583345003574 putative active site [active] 583345003575 heme pocket [chemical binding]; other site 583345003576 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 583345003577 GAF domain; Region: GAF; pfam01590 583345003578 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 583345003579 PAS fold; Region: PAS_3; pfam08447 583345003580 putative active site [active] 583345003581 heme pocket [chemical binding]; other site 583345003582 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 583345003583 PAS domain; Region: PAS_9; pfam13426 583345003584 putative active site [active] 583345003585 heme pocket [chemical binding]; other site 583345003586 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345003587 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345003588 metal binding site [ion binding]; metal-binding site 583345003589 active site 583345003590 I-site; other site 583345003591 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 583345003592 Cytochrome c; Region: Cytochrom_C; pfam00034 583345003593 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 583345003594 D-pathway; other site 583345003595 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 583345003596 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 583345003597 Binuclear center (active site) [active] 583345003598 K-pathway; other site 583345003599 Putative proton exit pathway; other site 583345003600 Putative water exit pathway; other site 583345003601 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 583345003602 Subunit I/III interface [polypeptide binding]; other site 583345003603 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; pfam03626 583345003604 MoxR-like ATPases [General function prediction only]; Region: COG0714 583345003605 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 583345003606 Walker A motif; other site 583345003607 ATP binding site [chemical binding]; other site 583345003608 Walker B motif; other site 583345003609 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 583345003610 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 583345003611 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 583345003612 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 583345003613 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 583345003614 ligand binding site [chemical binding]; other site 583345003615 flexible hinge region; other site 583345003616 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 583345003617 putative switch regulator; other site 583345003618 non-specific DNA interactions [nucleotide binding]; other site 583345003619 DNA binding site [nucleotide binding] 583345003620 sequence specific DNA binding site [nucleotide binding]; other site 583345003621 putative cAMP binding site [chemical binding]; other site 583345003622 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 583345003623 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 583345003624 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 583345003625 Cu(I) binding site [ion binding]; other site 583345003626 Uncharacterized conserved protein [Function unknown]; Region: COG1262 583345003627 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 583345003628 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 583345003629 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 583345003630 Multicopper oxidase; Region: Cu-oxidase; pfam00394 583345003631 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 583345003632 Cytochrome c; Region: Cytochrom_C; pfam00034 583345003633 Predicted transcriptional regulator [Transcription]; Region: COG1959 583345003634 Transcriptional regulator; Region: Rrf2; cl17282 583345003635 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 583345003636 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 583345003637 heme-binding site [chemical binding]; other site 583345003638 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 583345003639 FAD binding pocket [chemical binding]; other site 583345003640 FAD binding motif [chemical binding]; other site 583345003641 phosphate binding motif [ion binding]; other site 583345003642 beta-alpha-beta structure motif; other site 583345003643 NAD binding pocket [chemical binding]; other site 583345003644 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 583345003645 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 583345003646 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345003647 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345003648 metal binding site [ion binding]; metal-binding site 583345003649 active site 583345003650 I-site; other site 583345003651 HAMP domain; Region: HAMP; pfam00672 583345003652 dimerization interface [polypeptide binding]; other site 583345003653 Histidine kinase; Region: HisKA_3; pfam07730 583345003654 Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]; Region: RsbW; COG2172 583345003655 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 583345003656 ATP binding site [chemical binding]; other site 583345003657 Mg2+ binding site [ion binding]; other site 583345003658 G-X-G motif; other site 583345003659 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 583345003660 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 583345003661 active site 583345003662 phosphorylation site [posttranslational modification] 583345003663 intermolecular recognition site; other site 583345003664 dimerization interface [polypeptide binding]; other site 583345003665 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 583345003666 DNA binding residues [nucleotide binding] 583345003667 dimerization interface [polypeptide binding]; other site 583345003668 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 583345003669 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 583345003670 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 583345003671 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 583345003672 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 583345003673 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 583345003674 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 583345003675 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345003676 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345003677 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 583345003678 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 583345003679 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 583345003680 Walker A motif; other site 583345003681 ATP binding site [chemical binding]; other site 583345003682 Walker B motif; other site 583345003683 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 583345003684 Pilus assembly protein, PilO; Region: PilO; cl01234 583345003685 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 583345003686 binding surface 583345003687 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345003688 TPR motif; other site 583345003689 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 583345003690 Secretin and TonB N terminus short domain; Region: STN; smart00965 583345003691 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 583345003692 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 583345003693 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 583345003694 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 583345003695 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 583345003696 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 583345003697 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 583345003698 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 583345003699 Walker A/P-loop; other site 583345003700 ATP binding site [chemical binding]; other site 583345003701 Q-loop/lid; other site 583345003702 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 583345003703 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 583345003704 ABC transporter signature motif; other site 583345003705 Walker B; other site 583345003706 D-loop; other site 583345003707 H-loop/switch region; other site 583345003708 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 583345003709 FtsZ protein binding site [polypeptide binding]; other site 583345003710 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 583345003711 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 583345003712 nucleotide binding pocket [chemical binding]; other site 583345003713 K-X-D-G motif; other site 583345003714 catalytic site [active] 583345003715 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 583345003716 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 583345003717 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 583345003718 Dimer interface [polypeptide binding]; other site 583345003719 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 583345003720 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 583345003721 active site 583345003722 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 583345003723 binding surface 583345003724 TPR motif; other site 583345003725 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 583345003726 binding surface 583345003727 TPR motif; other site 583345003728 Tetratricopeptide repeat; Region: TPR_12; pfam13424 583345003729 TMAO/DMSO reductase; Reviewed; Region: PRK05363 583345003730 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 583345003731 Moco binding site; other site 583345003732 metal coordination site [ion binding]; other site 583345003733 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 583345003734 Predicted membrane protein [Function unknown]; Region: COG2259 583345003735 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 583345003736 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 583345003737 heme-binding site [chemical binding]; other site 583345003738 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 583345003739 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 583345003740 dimerization interface [polypeptide binding]; other site 583345003741 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345003742 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345003743 metal binding site [ion binding]; metal-binding site 583345003744 active site 583345003745 I-site; other site 583345003746 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 583345003747 PAS domain S-box; Region: sensory_box; TIGR00229 583345003748 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 583345003749 putative active site [active] 583345003750 heme pocket [chemical binding]; other site 583345003751 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345003752 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345003753 metal binding site [ion binding]; metal-binding site 583345003754 active site 583345003755 I-site; other site 583345003756 GAF domain; Region: GAF; pfam01590 583345003757 GAF domain; Region: GAF_2; pfam13185 583345003758 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345003759 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345003760 short chain dehydrogenase; Provisional; Region: PRK06179 583345003761 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 583345003762 NADP binding site [chemical binding]; other site 583345003763 active site 583345003764 steroid binding site; other site 583345003765 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 583345003766 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 583345003767 putative NAD(P) binding site [chemical binding]; other site 583345003768 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345003769 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345003770 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 583345003771 metal ion-dependent adhesion site (MIDAS); other site 583345003772 TPR repeat; Region: TPR_11; pfam13414 583345003773 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 583345003774 metal ion-dependent adhesion site (MIDAS); other site 583345003775 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 583345003776 Protein of unknown function DUF58; Region: DUF58; pfam01882 583345003777 MoxR-like ATPases [General function prediction only]; Region: COG0714 583345003778 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 583345003779 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345003780 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345003781 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 583345003782 IHF dimer interface [polypeptide binding]; other site 583345003783 IHF - DNA interface [nucleotide binding]; other site 583345003784 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 583345003785 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 583345003786 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 583345003787 active site residue [active] 583345003788 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 583345003789 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 583345003790 putative substrate translocation pore; other site 583345003791 Pirin-related protein [General function prediction only]; Region: COG1741 583345003792 Pirin; Region: Pirin; pfam02678 583345003793 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 583345003794 Uncharacterized conserved protein [Function unknown]; Region: COG2353 583345003795 YceI-like domain; Region: YceI; smart00867 583345003796 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 583345003797 Transcriptional regulator [Transcription]; Region: LysR; COG0583 583345003798 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345003799 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 583345003800 dimerization interface [polypeptide binding]; other site 583345003801 recombination associated protein; Reviewed; Region: rdgC; PRK00321 583345003802 Yip1 domain; Region: Yip1; cl17815 583345003803 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 583345003804 [2Fe-2S] cluster binding site [ion binding]; other site 583345003805 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 583345003806 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 583345003807 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 583345003808 trimerization site [polypeptide binding]; other site 583345003809 active site 583345003810 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 583345003811 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 583345003812 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 583345003813 catalytic residue [active] 583345003814 FeS assembly protein SufD; Region: sufD; TIGR01981 583345003815 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 583345003816 FeS assembly ATPase SufC; Region: sufC; TIGR01978 583345003817 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 583345003818 Walker A/P-loop; other site 583345003819 ATP binding site [chemical binding]; other site 583345003820 Q-loop/lid; other site 583345003821 ABC transporter signature motif; other site 583345003822 Walker B; other site 583345003823 D-loop; other site 583345003824 H-loop/switch region; other site 583345003825 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 583345003826 putative ABC transporter; Region: ycf24; CHL00085 583345003827 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 583345003828 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 583345003829 active site 583345003830 motif I; other site 583345003831 motif II; other site 583345003832 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 583345003833 putative hydrolase; Provisional; Region: PRK02113 583345003834 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 583345003835 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 583345003836 active site 583345003837 PilZ domain; Region: PilZ; cl01260 583345003838 DNA polymerase III subunit delta'; Validated; Region: PRK06964 583345003839 DNA polymerase III subunit delta'; Validated; Region: PRK08485 583345003840 thymidylate kinase; Validated; Region: tmk; PRK00698 583345003841 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 583345003842 TMP-binding site; other site 583345003843 ATP-binding site [chemical binding]; other site 583345003844 YceG-like family; Region: YceG; pfam02618 583345003845 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 583345003846 dimerization interface [polypeptide binding]; other site 583345003847 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 583345003848 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 583345003849 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345003850 catalytic residue [active] 583345003851 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 583345003852 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 583345003853 dimer interface [polypeptide binding]; other site 583345003854 active site 583345003855 acyl carrier protein; Provisional; Region: acpP; PRK00982 583345003856 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 583345003857 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 583345003858 NAD(P) binding site [chemical binding]; other site 583345003859 homotetramer interface [polypeptide binding]; other site 583345003860 homodimer interface [polypeptide binding]; other site 583345003861 active site 583345003862 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 583345003863 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 583345003864 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 583345003865 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 583345003866 dimer interface [polypeptide binding]; other site 583345003867 active site 583345003868 CoA binding pocket [chemical binding]; other site 583345003869 putative phosphate acyltransferase; Provisional; Region: PRK05331 583345003870 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 583345003871 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 583345003872 pyruvate carboxylase subunit A; Validated; Region: PRK07178 583345003873 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 583345003874 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 583345003875 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 583345003876 pyruvate carboxylase subunit B; Validated; Region: PRK09282 583345003877 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 583345003878 active site 583345003879 catalytic residues [active] 583345003880 metal binding site [ion binding]; metal-binding site 583345003881 homodimer binding site [polypeptide binding]; other site 583345003882 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 583345003883 carboxyltransferase (CT) interaction site; other site 583345003884 biotinylation site [posttranslational modification]; other site 583345003885 Maf-like protein; Region: Maf; pfam02545 583345003886 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 583345003887 active site 583345003888 dimer interface [polypeptide binding]; other site 583345003889 Uncharacterized conserved protein [Function unknown]; Region: COG5316 583345003890 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 583345003891 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 583345003892 putative SAM binding site [chemical binding]; other site 583345003893 homodimer interface [polypeptide binding]; other site 583345003894 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 583345003895 RNA/DNA hybrid binding site [nucleotide binding]; other site 583345003896 active site 583345003897 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 583345003898 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 583345003899 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 583345003900 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 583345003901 active site 583345003902 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 583345003903 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 583345003904 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 583345003905 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 583345003906 trimer interface [polypeptide binding]; other site 583345003907 active site 583345003908 UDP-GlcNAc binding site [chemical binding]; other site 583345003909 lipid binding site [chemical binding]; lipid-binding site 583345003910 periplasmic chaperone; Provisional; Region: PRK10780 583345003911 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 583345003912 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 583345003913 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 583345003914 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 583345003915 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 583345003916 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 583345003917 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 583345003918 Surface antigen; Region: Bac_surface_Ag; pfam01103 583345003919 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 583345003920 zinc metallopeptidase RseP; Provisional; Region: PRK10779 583345003921 active site 583345003922 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 583345003923 protein binding site [polypeptide binding]; other site 583345003924 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 583345003925 protein binding site [polypeptide binding]; other site 583345003926 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 583345003927 putative substrate binding region [chemical binding]; other site 583345003928 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 583345003929 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 583345003930 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 583345003931 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 583345003932 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 583345003933 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 583345003934 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 583345003935 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 583345003936 catalytic residue [active] 583345003937 putative FPP diphosphate binding site; other site 583345003938 putative FPP binding hydrophobic cleft; other site 583345003939 dimer interface [polypeptide binding]; other site 583345003940 putative IPP diphosphate binding site; other site 583345003941 ribosome recycling factor; Reviewed; Region: frr; PRK00083 583345003942 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 583345003943 hinge region; other site 583345003944 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 583345003945 putative nucleotide binding site [chemical binding]; other site 583345003946 uridine monophosphate binding site [chemical binding]; other site 583345003947 homohexameric interface [polypeptide binding]; other site 583345003948 elongation factor Ts; Provisional; Region: tsf; PRK09377 583345003949 UBA/TS-N domain; Region: UBA; pfam00627 583345003950 Elongation factor TS; Region: EF_TS; pfam00889 583345003951 Elongation factor TS; Region: EF_TS; pfam00889 583345003952 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 583345003953 rRNA interaction site [nucleotide binding]; other site 583345003954 S8 interaction site; other site 583345003955 putative laminin-1 binding site; other site 583345003956 HDOD domain; Region: HDOD; pfam08668 583345003957 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 583345003958 active site 583345003959 PII uridylyl-transferase; Provisional; Region: PRK03059 583345003960 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 583345003961 metal binding triad; other site 583345003962 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 583345003963 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; smart00471 583345003964 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 583345003965 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 583345003966 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 583345003967 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 583345003968 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 583345003969 active site 583345003970 catalytic residues [active] 583345003971 metal binding site [ion binding]; metal-binding site 583345003972 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 583345003973 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 583345003974 active site lid residues [active] 583345003975 substrate binding pocket [chemical binding]; other site 583345003976 catalytic residues [active] 583345003977 substrate-Mg2+ binding site; other site 583345003978 aspartate-rich region 1; other site 583345003979 aspartate-rich region 2; other site 583345003980 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 583345003981 active site lid residues [active] 583345003982 substrate binding pocket [chemical binding]; other site 583345003983 catalytic residues [active] 583345003984 substrate-Mg2+ binding site; other site 583345003985 aspartate-rich region 1; other site 583345003986 aspartate-rich region 2; other site 583345003987 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 583345003988 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 583345003989 hydroxyglutarate oxidase; Provisional; Region: PRK11728 583345003990 DNA repair protein RadA; Provisional; Region: PRK11823 583345003991 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 583345003992 Walker A motif/ATP binding site; other site 583345003993 ATP binding site [chemical binding]; other site 583345003994 Walker B motif; other site 583345003995 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 583345003996 alanine racemase; Reviewed; Region: dadX; PRK03646 583345003997 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 583345003998 active site 583345003999 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 583345004000 substrate binding site [chemical binding]; other site 583345004001 catalytic residues [active] 583345004002 dimer interface [polypeptide binding]; other site 583345004003 replicative DNA helicase; Region: DnaB; TIGR00665 583345004004 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 583345004005 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 583345004006 Walker A motif; other site 583345004007 ATP binding site [chemical binding]; other site 583345004008 Walker B motif; other site 583345004009 DNA binding loops [nucleotide binding] 583345004010 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 583345004011 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 583345004012 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 583345004013 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 583345004014 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 583345004015 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 583345004016 excinuclease ABC subunit B; Provisional; Region: PRK05298 583345004017 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 583345004018 ATP binding site [chemical binding]; other site 583345004019 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 583345004020 nucleotide binding region [chemical binding]; other site 583345004021 ATP-binding site [chemical binding]; other site 583345004022 Ultra-violet resistance protein B; Region: UvrB; pfam12344 583345004023 UvrB/uvrC motif; Region: UVR; pfam02151 583345004024 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 583345004025 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 583345004026 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 583345004027 TPR repeat; Region: TPR_11; pfam13414 583345004028 binding surface 583345004029 aspartate aminotransferase; Provisional; Region: PRK05764 583345004030 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 583345004031 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345004032 homodimer interface [polypeptide binding]; other site 583345004033 catalytic residue [active] 583345004034 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 583345004035 Leucine rich repeat; Region: LRR_8; pfam13855 583345004036 Leucine rich repeat; Region: LRR_8; pfam13855 583345004037 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 583345004038 active site 583345004039 ATP binding site [chemical binding]; other site 583345004040 substrate binding site [chemical binding]; other site 583345004041 activation loop (A-loop); other site 583345004042 Domain of unknown function (DUF386); Region: DUF386; cl01047 583345004043 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 583345004044 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 583345004045 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 583345004046 Walker A motif; other site 583345004047 ATP binding site [chemical binding]; other site 583345004048 Walker B motif; other site 583345004049 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 583345004050 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345004051 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345004052 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 583345004053 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 583345004054 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 583345004055 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 583345004056 Secretin and TonB N terminus short domain; Region: STN; pfam07660 583345004057 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 583345004058 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 583345004059 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 583345004060 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 583345004061 AAA ATPase domain; Region: AAA_16; pfam13191 583345004062 Walker A motif; other site 583345004063 ATP binding site [chemical binding]; other site 583345004064 Walker B motif; other site 583345004065 arginine finger; other site 583345004066 TPR repeat; Region: TPR_11; pfam13414 583345004067 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 583345004068 binding surface 583345004069 TPR motif; other site 583345004070 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 583345004071 binding surface 583345004072 TPR motif; other site 583345004073 TPR repeat; Region: TPR_11; pfam13414 583345004074 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 583345004075 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 583345004076 metal-binding site [ion binding] 583345004077 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 583345004078 Soluble P-type ATPase [General function prediction only]; Region: COG4087 583345004079 Protein of unknown function (DUF808); Region: DUF808; pfam05661 583345004080 Uncharacterized conserved protein [Function unknown]; Region: COG4095 583345004081 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 583345004082 active site 583345004083 catalytic triad [active] 583345004084 oxyanion hole [active] 583345004085 switch loop; other site 583345004086 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 583345004087 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 583345004088 Trp docking motif [polypeptide binding]; other site 583345004089 active site 583345004090 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 583345004091 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 583345004092 ATP binding site [chemical binding]; other site 583345004093 putative Mg++ binding site [ion binding]; other site 583345004094 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 583345004095 nucleotide binding region [chemical binding]; other site 583345004096 ATP-binding site [chemical binding]; other site 583345004097 Helicase associated domain (HA2); Region: HA2; pfam04408 583345004098 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 583345004099 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 583345004100 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 583345004101 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345004102 putative active site [active] 583345004103 heme pocket [chemical binding]; other site 583345004104 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 583345004105 putative active site [active] 583345004106 heme pocket [chemical binding]; other site 583345004107 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 583345004108 putative active site [active] 583345004109 heme pocket [chemical binding]; other site 583345004110 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345004111 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345004112 metal binding site [ion binding]; metal-binding site 583345004113 active site 583345004114 I-site; other site 583345004115 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 583345004116 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 583345004117 Transcriptional regulator [Transcription]; Region: LysR; COG0583 583345004118 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345004119 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 583345004120 putative effector binding pocket; other site 583345004121 dimerization interface [polypeptide binding]; other site 583345004122 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 583345004123 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 583345004124 TrkA-N domain; Region: TrkA_N; pfam02254 583345004125 CHASE3 domain; Region: CHASE3; pfam05227 583345004126 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345004127 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345004128 metal binding site [ion binding]; metal-binding site 583345004129 active site 583345004130 I-site; other site 583345004131 PAS domain S-box; Region: sensory_box; TIGR00229 583345004132 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 583345004133 putative active site [active] 583345004134 heme pocket [chemical binding]; other site 583345004135 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 583345004136 GAF domain; Region: GAF; pfam01590 583345004137 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 583345004138 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345004139 putative active site [active] 583345004140 heme pocket [chemical binding]; other site 583345004141 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 583345004142 putative active site [active] 583345004143 heme pocket [chemical binding]; other site 583345004144 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 583345004145 dimer interface [polypeptide binding]; other site 583345004146 phosphorylation site [posttranslational modification] 583345004147 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 583345004148 ATP binding site [chemical binding]; other site 583345004149 Mg2+ binding site [ion binding]; other site 583345004150 G-X-G motif; other site 583345004151 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 583345004152 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 583345004153 active site 583345004154 phosphorylation site [posttranslational modification] 583345004155 intermolecular recognition site; other site 583345004156 dimerization interface [polypeptide binding]; other site 583345004157 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 583345004158 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 583345004159 active site 583345004160 phosphorylation site [posttranslational modification] 583345004161 intermolecular recognition site; other site 583345004162 dimerization interface [polypeptide binding]; other site 583345004163 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345004164 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345004165 metal binding site [ion binding]; metal-binding site 583345004166 active site 583345004167 I-site; other site 583345004168 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 583345004169 Methyltransferase domain; Region: Methyltransf_32; pfam13679 583345004170 Methyltransferase domain; Region: Methyltransf_31; pfam13847 583345004171 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345004172 RNA polymerase factor sigma-70; Validated; Region: PRK09047 583345004173 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 583345004174 DNA binding residues [nucleotide binding] 583345004175 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 583345004176 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 583345004177 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 583345004178 GTP/Mg2+ binding site [chemical binding]; other site 583345004179 G4 box; other site 583345004180 G5 box; other site 583345004181 G1 box; other site 583345004182 Switch I region; other site 583345004183 G2 box; other site 583345004184 G3 box; other site 583345004185 Switch II region; other site 583345004186 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 583345004187 Part of AAA domain; Region: AAA_19; pfam13245 583345004188 Family description; Region: UvrD_C_2; pfam13538 583345004189 ABC transporter ATPase component; Reviewed; Region: PRK11147 583345004190 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345004191 Walker A/P-loop; other site 583345004192 ATP binding site [chemical binding]; other site 583345004193 Q-loop/lid; other site 583345004194 ABC transporter signature motif; other site 583345004195 Walker B; other site 583345004196 D-loop; other site 583345004197 H-loop/switch region; other site 583345004198 ABC transporter; Region: ABC_tran_2; pfam12848 583345004199 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345004200 Sulfatase; Region: Sulfatase; cl17466 583345004201 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 583345004202 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 583345004203 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345004204 active site 583345004205 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 583345004206 Vitamin K epoxide reductase (VKOR) family; Region: VKOR; cl01729 583345004207 redox center [active] 583345004208 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 583345004209 putative active site [active] 583345004210 YdjC motif; other site 583345004211 Mg binding site [ion binding]; other site 583345004212 putative homodimer interface [polypeptide binding]; other site 583345004213 Predicted membrane protein [Function unknown]; Region: COG2246 583345004214 GtrA-like protein; Region: GtrA; pfam04138 583345004215 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 583345004216 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 583345004217 Ligand binding site; other site 583345004218 Putative Catalytic site; other site 583345004219 DXD motif; other site 583345004220 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 583345004221 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 583345004222 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 583345004223 catalytic triad [active] 583345004224 chemotaxis regulator CheZ; Provisional; Region: PRK11166 583345004225 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 583345004226 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 583345004227 active site 583345004228 phosphorylation site [posttranslational modification] 583345004229 intermolecular recognition site; other site 583345004230 dimerization interface [polypeptide binding]; other site 583345004231 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 583345004232 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 583345004233 active site 583345004234 phosphorylation site [posttranslational modification] 583345004235 intermolecular recognition site; other site 583345004236 dimerization interface [polypeptide binding]; other site 583345004237 CheB methylesterase; Region: CheB_methylest; pfam01339 583345004238 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 583345004239 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 583345004240 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 583345004241 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 583345004242 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 583345004243 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 583345004244 PAS domain; Region: PAS_9; pfam13426 583345004245 putative active site [active] 583345004246 heme pocket [chemical binding]; other site 583345004247 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 583345004248 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 583345004249 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345004250 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 583345004251 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345004252 dimer interface [polypeptide binding]; other site 583345004253 putative CheW interface [polypeptide binding]; other site 583345004254 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 583345004255 Tar ligand binding domain homologue; Region: TarH; pfam02203 583345004256 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 583345004257 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345004258 dimer interface [polypeptide binding]; other site 583345004259 putative CheW interface [polypeptide binding]; other site 583345004260 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 583345004261 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345004262 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345004263 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 583345004264 putative active site [active] 583345004265 heme pocket [chemical binding]; other site 583345004266 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 583345004267 putative active site [active] 583345004268 heme pocket [chemical binding]; other site 583345004269 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345004270 dimer interface [polypeptide binding]; other site 583345004271 putative CheW interface [polypeptide binding]; other site 583345004272 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 583345004273 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 583345004274 putative binding surface; other site 583345004275 active site 583345004276 CheY binding; Region: CheY-binding; pfam09078 583345004277 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 583345004278 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 583345004279 ATP binding site [chemical binding]; other site 583345004280 Mg2+ binding site [ion binding]; other site 583345004281 G-X-G motif; other site 583345004282 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 583345004283 Response regulator receiver domain; Region: Response_reg; pfam00072 583345004284 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 583345004285 active site 583345004286 phosphorylation site [posttranslational modification] 583345004287 intermolecular recognition site; other site 583345004288 dimerization interface [polypeptide binding]; other site 583345004289 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 583345004290 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 583345004291 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 583345004292 ligand binding site [chemical binding]; other site 583345004293 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 583345004294 flagellar motor protein MotA; Validated; Region: PRK09110 583345004295 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 583345004296 S-adenosylmethionine binding site [chemical binding]; other site 583345004297 transcriptional activator FlhC; Provisional; Region: PRK12722 583345004298 transcriptional activator FlhD; Provisional; Region: PRK02909 583345004299 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 583345004300 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 583345004301 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 583345004302 FHIPEP family; Region: FHIPEP; pfam00771 583345004303 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 583345004304 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 583345004305 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 583345004306 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 583345004307 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345004308 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 583345004309 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 583345004310 DNA binding residues [nucleotide binding] 583345004311 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 583345004312 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 583345004313 flagellar motor protein MotD; Reviewed; Region: PRK09038 583345004314 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 583345004315 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 583345004316 ligand binding site [chemical binding]; other site 583345004317 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 583345004318 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 583345004319 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 583345004320 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 583345004321 G1 box; other site 583345004322 putative GEF interaction site [polypeptide binding]; other site 583345004323 GTP/Mg2+ binding site [chemical binding]; other site 583345004324 Switch I region; other site 583345004325 G2 box; other site 583345004326 G3 box; other site 583345004327 Switch II region; other site 583345004328 G4 box; other site 583345004329 G5 box; other site 583345004330 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 583345004331 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 583345004332 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 583345004333 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 583345004334 ATP binding site [chemical binding]; other site 583345004335 Mg++ binding site [ion binding]; other site 583345004336 motif III; other site 583345004337 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 583345004338 nucleotide binding region [chemical binding]; other site 583345004339 ATP-binding site [chemical binding]; other site 583345004340 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 583345004341 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 583345004342 ATP binding site [chemical binding]; other site 583345004343 Mg++ binding site [ion binding]; other site 583345004344 motif III; other site 583345004345 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 583345004346 nucleotide binding region [chemical binding]; other site 583345004347 ATP-binding site [chemical binding]; other site 583345004348 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 583345004349 apolar tunnel; other site 583345004350 heme binding site [chemical binding]; other site 583345004351 dimerization interface [polypeptide binding]; other site 583345004352 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 583345004353 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 583345004354 ATP-grasp domain; Region: ATP-grasp; pfam02222 583345004355 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 583345004356 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 583345004357 active site 583345004358 phosphorylation site [posttranslational modification] 583345004359 intermolecular recognition site; other site 583345004360 dimerization interface [polypeptide binding]; other site 583345004361 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 583345004362 Walker A motif; other site 583345004363 ATP binding site [chemical binding]; other site 583345004364 Walker B motif; other site 583345004365 arginine finger; other site 583345004366 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345004367 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 583345004368 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 583345004369 N-terminal plug; other site 583345004370 ligand-binding site [chemical binding]; other site 583345004371 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 583345004372 FtsX-like permease family; Region: FtsX; pfam02687 583345004373 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 583345004374 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 583345004375 Walker A/P-loop; other site 583345004376 ATP binding site [chemical binding]; other site 583345004377 Q-loop/lid; other site 583345004378 ABC transporter signature motif; other site 583345004379 Walker B; other site 583345004380 D-loop; other site 583345004381 H-loop/switch region; other site 583345004382 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 583345004383 active site 583345004384 catalytic triad [active] 583345004385 oxyanion hole [active] 583345004386 switch loop; other site 583345004387 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 583345004388 TilS substrate binding domain; Region: TilS; pfam09179 583345004389 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 583345004390 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 583345004391 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 583345004392 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 583345004393 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 583345004394 putative active site [active] 583345004395 putative PHP Thumb interface [polypeptide binding]; other site 583345004396 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 583345004397 generic binding surface II; other site 583345004398 generic binding surface I; other site 583345004399 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 583345004400 putative binding surface; other site 583345004401 active site 583345004402 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 583345004403 putative binding surface; other site 583345004404 active site 583345004405 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 583345004406 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 583345004407 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 583345004408 ATP binding site [chemical binding]; other site 583345004409 Mg2+ binding site [ion binding]; other site 583345004410 G-X-G motif; other site 583345004411 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 583345004412 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 583345004413 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 583345004414 active site 583345004415 phosphorylation site [posttranslational modification] 583345004416 intermolecular recognition site; other site 583345004417 dimerization interface [polypeptide binding]; other site 583345004418 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345004419 dimer interface [polypeptide binding]; other site 583345004420 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 583345004421 putative CheW interface [polypeptide binding]; other site 583345004422 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 583345004423 Response regulator receiver domain; Region: Response_reg; pfam00072 583345004424 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 583345004425 active site 583345004426 phosphorylation site [posttranslational modification] 583345004427 intermolecular recognition site; other site 583345004428 dimerization interface [polypeptide binding]; other site 583345004429 Response regulator receiver domain; Region: Response_reg; pfam00072 583345004430 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 583345004431 active site 583345004432 phosphorylation site [posttranslational modification] 583345004433 intermolecular recognition site; other site 583345004434 dimerization interface [polypeptide binding]; other site 583345004435 Uncharacterized conserved protein [Function unknown]; Region: COG3287 583345004436 FIST N domain; Region: FIST; pfam08495 583345004437 FIST C domain; Region: FIST_C; pfam10442 583345004438 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 583345004439 dimer interface [polypeptide binding]; other site 583345004440 catalytic triad [active] 583345004441 peroxidatic and resolving cysteines [active] 583345004442 RDD family; Region: RDD; pfam06271 583345004443 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 583345004444 putative deacylase active site [active] 583345004445 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 583345004446 homodimer interface [polypeptide binding]; other site 583345004447 chemical substrate binding site [chemical binding]; other site 583345004448 oligomer interface [polypeptide binding]; other site 583345004449 metal binding site [ion binding]; metal-binding site 583345004450 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 583345004451 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 583345004452 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 583345004453 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 583345004454 S-adenosylmethionine binding site [chemical binding]; other site 583345004455 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 583345004456 RNB domain; Region: RNB; pfam00773 583345004457 hypothetical protein; Validated; Region: PRK00029 583345004458 Uncharacterized conserved protein [Function unknown]; Region: COG0397 583345004459 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 583345004460 metal binding site 2 [ion binding]; metal-binding site 583345004461 putative DNA binding helix; other site 583345004462 metal binding site 1 [ion binding]; metal-binding site 583345004463 dimer interface [polypeptide binding]; other site 583345004464 structural Zn2+ binding site [ion binding]; other site 583345004465 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 583345004466 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 583345004467 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 583345004468 Methyltransferase domain; Region: Methyltransf_11; pfam08241 583345004469 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 583345004470 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 583345004471 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 583345004472 N-acetyl-D-glucosamine binding site [chemical binding]; other site 583345004473 catalytic residue [active] 583345004474 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 583345004475 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 583345004476 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 583345004477 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 583345004478 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 583345004479 The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold; Region: PBP2_AppA_like; cd08514 583345004480 peptide binding site [polypeptide binding]; other site 583345004481 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 583345004482 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 583345004483 dimer interface [polypeptide binding]; other site 583345004484 conserved gate region; other site 583345004485 putative PBP binding loops; other site 583345004486 ABC-ATPase subunit interface; other site 583345004487 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 583345004488 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 583345004489 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 583345004490 dimer interface [polypeptide binding]; other site 583345004491 conserved gate region; other site 583345004492 putative PBP binding loops; other site 583345004493 ABC-ATPase subunit interface; other site 583345004494 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 583345004495 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 583345004496 NAD binding site [chemical binding]; other site 583345004497 homotetramer interface [polypeptide binding]; other site 583345004498 homodimer interface [polypeptide binding]; other site 583345004499 substrate binding site [chemical binding]; other site 583345004500 active site 583345004501 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 583345004502 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 583345004503 putative substrate translocation pore; other site 583345004504 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 583345004505 TAP-like protein; Region: Abhydrolase_4; pfam08386 583345004506 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 583345004507 classical (c) SDRs; Region: SDR_c; cd05233 583345004508 NAD(P) binding site [chemical binding]; other site 583345004509 active site 583345004510 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 583345004511 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345004512 periplasmic folding chaperone; Provisional; Region: PRK10788 583345004513 SurA N-terminal domain; Region: SurA_N_3; cl07813 583345004514 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 583345004515 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 583345004516 IHF dimer interface [polypeptide binding]; other site 583345004517 IHF - DNA interface [nucleotide binding]; other site 583345004518 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 583345004519 Found in ATP-dependent protease La (LON); Region: LON; smart00464 583345004520 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 583345004521 Walker A motif; other site 583345004522 ATP binding site [chemical binding]; other site 583345004523 Walker B motif; other site 583345004524 arginine finger; other site 583345004525 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 583345004526 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 583345004527 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 583345004528 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 583345004529 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 583345004530 Walker A motif; other site 583345004531 ATP binding site [chemical binding]; other site 583345004532 Walker B motif; other site 583345004533 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 583345004534 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 583345004535 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 583345004536 oligomer interface [polypeptide binding]; other site 583345004537 active site residues [active] 583345004538 trigger factor; Provisional; Region: tig; PRK01490 583345004539 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 583345004540 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 583345004541 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 583345004542 dimer interface [polypeptide binding]; other site 583345004543 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 583345004544 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 583345004545 active site 583345004546 phosphorylation site [posttranslational modification] 583345004547 intermolecular recognition site; other site 583345004548 dimerization interface [polypeptide binding]; other site 583345004549 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 583345004550 DNA binding site [nucleotide binding] 583345004551 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 583345004552 dimerization interface [polypeptide binding]; other site 583345004553 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 583345004554 dimer interface [polypeptide binding]; other site 583345004555 phosphorylation site [posttranslational modification] 583345004556 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 583345004557 ATP binding site [chemical binding]; other site 583345004558 Mg2+ binding site [ion binding]; other site 583345004559 G-X-G motif; other site 583345004560 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 583345004561 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345004562 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 583345004563 Protein export membrane protein; Region: SecD_SecF; cl14618 583345004564 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; cd00488 583345004565 aromatic arch; other site 583345004566 DCoH dimer interaction site [polypeptide binding]; other site 583345004567 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 583345004568 DCoH tetramer interaction site [polypeptide binding]; other site 583345004569 substrate binding site [chemical binding]; other site 583345004570 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 583345004571 substrate binding site [chemical binding]; other site 583345004572 nucleotide binding site [chemical binding]; other site 583345004573 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 583345004574 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 583345004575 chorismate binding enzyme; Region: Chorismate_bind; cl10555 583345004576 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: COG1548; cl00668 583345004577 ATP-grasp domain; Region: ATP-grasp_4; cl17255 583345004578 hisA/hisF family protein; Region: hisAF_rel; TIGR00734 583345004579 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an...; Region: HisA_HisF; cd04723 583345004580 active site 583345004581 Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with...; Region: SIS_PHI; cd05005 583345004582 tetramer interface [polypeptide binding]; other site 583345004583 active site 583345004584 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 583345004585 phosphate binding site [ion binding]; other site 583345004586 transaldolase-like protein; Provisional; Region: PTZ00411 583345004587 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 583345004588 active site 583345004589 dimer interface [polypeptide binding]; other site 583345004590 catalytic residue [active] 583345004591 CHASE2 domain; Region: CHASE2; pfam05226 583345004592 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 583345004593 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345004594 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 583345004595 ATP binding site [chemical binding]; other site 583345004596 Mg2+ binding site [ion binding]; other site 583345004597 G-X-G motif; other site 583345004598 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 583345004599 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 583345004600 active site 583345004601 phosphorylation site [posttranslational modification] 583345004602 intermolecular recognition site; other site 583345004603 dimerization interface [polypeptide binding]; other site 583345004604 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 583345004605 DNA binding site [nucleotide binding] 583345004606 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; pfam01874 583345004607 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 583345004608 ATP-grasp domain; Region: ATP-grasp_4; cl17255 583345004609 Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5), N...; Region: MCH; cd00545 583345004610 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional; Region: PRK02264 583345004611 trimer interface I [polypeptide binding]; other site 583345004612 putative substrate binding pocket [chemical binding]; other site 583345004613 trimer interface II [polypeptide binding]; other site 583345004614 Predicted ATP-dependent carboligase related to biotin carboxylase [General function prediction only]; Region: COG2232 583345004615 ATP-grasp domain; Region: ATP-grasp_4; cl17255 583345004616 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; Region: Mpt_N; pfam09176 583345004617 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 583345004618 NAD(P) binding pocket [chemical binding]; other site 583345004619 Predicted archaeal sugar kinases [General function prediction only]; Region: COG1907 583345004620 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 583345004621 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 583345004622 phosphoenolpyruvate synthase; Validated; Region: PRK06464 583345004623 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 583345004624 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 583345004625 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 583345004626 PEP synthetase regulatory protein; Provisional; Region: PRK05339 583345004627 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 583345004628 catalytic residues [active] 583345004629 dimer interface [polypeptide binding]; other site 583345004630 CrcB-like protein; Region: CRCB; cl09114 583345004631 glycogen synthase; Provisional; Region: glgA; PRK00654 583345004632 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 583345004633 ADP-binding pocket [chemical binding]; other site 583345004634 homodimer interface [polypeptide binding]; other site 583345004635 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 583345004636 catalytic site [active] 583345004637 putative active site [active] 583345004638 putative substrate binding site [chemical binding]; other site 583345004639 dimer interface [polypeptide binding]; other site 583345004640 Peptidase family M48; Region: Peptidase_M48; pfam01435 583345004641 Cytochrome c; Region: Cytochrom_C; cl11414 583345004642 Cytochrome c; Region: Cytochrom_C; cl11414 583345004643 GTPase RsgA; Reviewed; Region: PRK00098 583345004644 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 583345004645 RNA binding site [nucleotide binding]; other site 583345004646 homodimer interface [polypeptide binding]; other site 583345004647 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 583345004648 GTPase/Zn-binding domain interface [polypeptide binding]; other site 583345004649 GTP/Mg2+ binding site [chemical binding]; other site 583345004650 G4 box; other site 583345004651 G5 box; other site 583345004652 G1 box; other site 583345004653 Switch I region; other site 583345004654 G2 box; other site 583345004655 G3 box; other site 583345004656 Switch II region; other site 583345004657 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 583345004658 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 583345004659 putative active site [active] 583345004660 Zn binding site [ion binding]; other site 583345004661 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 583345004662 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 583345004663 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345004664 Zn2+ binding site [ion binding]; other site 583345004665 Mg2+ binding site [ion binding]; other site 583345004666 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345004667 I-site; other site 583345004668 active site 583345004669 metal binding site [ion binding]; metal-binding site 583345004670 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 583345004671 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 583345004672 active site 583345004673 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 583345004674 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 583345004675 NADP binding site [chemical binding]; other site 583345004676 active site 583345004677 putative substrate binding site [chemical binding]; other site 583345004678 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 583345004679 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 583345004680 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 583345004681 substrate binding site; other site 583345004682 tetramer interface; other site 583345004683 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 583345004684 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 583345004685 NAD binding site [chemical binding]; other site 583345004686 substrate binding site [chemical binding]; other site 583345004687 homodimer interface [polypeptide binding]; other site 583345004688 active site 583345004689 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 583345004690 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 583345004691 active site 583345004692 catalytic site [active] 583345004693 substrate binding site [chemical binding]; other site 583345004694 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 583345004695 RNA/DNA hybrid binding site [nucleotide binding]; other site 583345004696 active site 583345004697 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 583345004698 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 583345004699 active site 583345004700 zinc binding site [ion binding]; other site 583345004701 argininosuccinate synthase; Provisional; Region: PRK13820 583345004702 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 583345004703 ANP binding site [chemical binding]; other site 583345004704 Substrate Binding Site II [chemical binding]; other site 583345004705 Substrate Binding Site I [chemical binding]; other site 583345004706 ornithine carbamoyltransferase; Provisional; Region: PRK00779 583345004707 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 583345004708 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 583345004709 acetylornithine aminotransferase; Provisional; Region: PRK02627 583345004710 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 583345004711 inhibitor-cofactor binding pocket; inhibition site 583345004712 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345004713 catalytic residue [active] 583345004714 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 583345004715 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 583345004716 [2Fe-2S] cluster binding site [ion binding]; other site 583345004717 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 583345004718 alpha subunit interface [polypeptide binding]; other site 583345004719 active site 583345004720 substrate binding site [chemical binding]; other site 583345004721 Fe binding site [ion binding]; other site 583345004722 EamA-like transporter family; Region: EamA; pfam00892 583345004723 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 583345004724 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 583345004725 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 583345004726 active site 583345004727 phosphorylation site [posttranslational modification] 583345004728 intermolecular recognition site; other site 583345004729 dimerization interface [polypeptide binding]; other site 583345004730 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 583345004731 DNA binding residues [nucleotide binding] 583345004732 dimerization interface [polypeptide binding]; other site 583345004733 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 583345004734 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 583345004735 dimerization interface [polypeptide binding]; other site 583345004736 Histidine kinase; Region: HisKA_3; pfam07730 583345004737 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 583345004738 ATP binding site [chemical binding]; other site 583345004739 Mg2+ binding site [ion binding]; other site 583345004740 G-X-G motif; other site 583345004741 DAK2 domain; Region: Dak2; cl03685 583345004742 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481 583345004743 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 583345004744 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345004745 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345004746 metal binding site [ion binding]; metal-binding site 583345004747 active site 583345004748 I-site; other site 583345004749 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 583345004750 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 583345004751 metal binding triad; other site 583345004752 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 583345004753 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 583345004754 metal binding triad; other site 583345004755 acetyl-CoA synthetase; Provisional; Region: PRK00174 583345004756 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 583345004757 active site 583345004758 CoA binding site [chemical binding]; other site 583345004759 acyl-activating enzyme (AAE) consensus motif; other site 583345004760 AMP binding site [chemical binding]; other site 583345004761 acetate binding site [chemical binding]; other site 583345004762 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 583345004763 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 583345004764 TPR repeat; Region: TPR_11; pfam13414 583345004765 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 583345004766 binding surface 583345004767 TPR motif; other site 583345004768 TPR repeat; Region: TPR_11; pfam13414 583345004769 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 583345004770 binding surface 583345004771 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345004772 TPR motif; other site 583345004773 LytR cell envelope-related transcriptional attenuator; Region: LytR_C; pfam13399 583345004774 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 583345004775 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345004776 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 583345004777 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 583345004778 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 583345004779 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 583345004780 ATP binding site [chemical binding]; other site 583345004781 Walker A motif; other site 583345004782 hexamer interface [polypeptide binding]; other site 583345004783 Walker B motif; other site 583345004784 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 583345004785 active site 583345004786 phosphorylation site [posttranslational modification] 583345004787 intermolecular recognition site; other site 583345004788 dimerization interface [polypeptide binding]; other site 583345004789 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 583345004790 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 583345004791 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 583345004792 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 583345004793 TadE-like protein; Region: TadE; pfam07811 583345004794 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 583345004795 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 583345004796 BON domain; Region: BON; pfam04972 583345004797 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 583345004798 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 583345004799 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 583345004800 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 583345004801 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 583345004802 Walker A motif; other site 583345004803 ATP binding site [chemical binding]; other site 583345004804 Walker B motif; other site 583345004805 arginine finger; other site 583345004806 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 583345004807 Flp/Fap pilin component; Region: Flp_Fap; cl01585 583345004808 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 583345004809 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 583345004810 putative active site [active] 583345004811 heme pocket [chemical binding]; other site 583345004812 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 583345004813 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 583345004814 dimer interface [polypeptide binding]; other site 583345004815 phosphorylation site [posttranslational modification] 583345004816 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 583345004817 ATP binding site [chemical binding]; other site 583345004818 Mg2+ binding site [ion binding]; other site 583345004819 G-X-G motif; other site 583345004820 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 583345004821 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 583345004822 active site 583345004823 phosphorylation site [posttranslational modification] 583345004824 intermolecular recognition site; other site 583345004825 dimerization interface [polypeptide binding]; other site 583345004826 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 583345004827 DNA binding residues [nucleotide binding] 583345004828 dimerization interface [polypeptide binding]; other site 583345004829 NAD(P)H:flavin oxidoreductase-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; Region: NADPH_oxidoreductase_1; cd02150 583345004830 putative FMN binding site [chemical binding]; other site 583345004831 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 583345004832 Ligand Binding Site [chemical binding]; other site 583345004833 FOG: CBS domain [General function prediction only]; Region: COG0517 583345004834 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 583345004835 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 583345004836 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 583345004837 G1 box; other site 583345004838 putative GEF interaction site [polypeptide binding]; other site 583345004839 GTP/Mg2+ binding site [chemical binding]; other site 583345004840 Switch I region; other site 583345004841 G2 box; other site 583345004842 G3 box; other site 583345004843 Switch II region; other site 583345004844 G4 box; other site 583345004845 G5 box; other site 583345004846 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 583345004847 SEC-C motif; Region: SEC-C; pfam02810 583345004848 hypothetical protein; Provisional; Region: PRK04233 583345004849 ATP-dependent protease, Lon family; Region: spore_lon_C; TIGR02903 583345004850 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345004851 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 583345004852 Walker A/P-loop; other site 583345004853 ATP binding site [chemical binding]; other site 583345004854 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345004855 ABC transporter signature motif; other site 583345004856 Walker B; other site 583345004857 D-loop; other site 583345004858 ABC transporter; Region: ABC_tran_2; pfam12848 583345004859 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345004860 TIGR02099 family protein; Region: TIGR02099 583345004861 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 583345004862 nitrilase; Region: PLN02798 583345004863 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 583345004864 putative active site [active] 583345004865 catalytic triad [active] 583345004866 dimer interface [polypeptide binding]; other site 583345004867 protease TldD; Provisional; Region: tldD; PRK10735 583345004868 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 583345004869 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 583345004870 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 583345004871 ATP binding site [chemical binding]; other site 583345004872 putative Mg++ binding site [ion binding]; other site 583345004873 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 583345004874 nucleotide binding region [chemical binding]; other site 583345004875 ATP-binding site [chemical binding]; other site 583345004876 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 583345004877 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 583345004878 PAS fold; Region: PAS_3; pfam08447 583345004879 putative active site [active] 583345004880 heme pocket [chemical binding]; other site 583345004881 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345004882 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345004883 metal binding site [ion binding]; metal-binding site 583345004884 active site 583345004885 I-site; other site 583345004886 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 583345004887 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 583345004888 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 583345004889 HflX GTPase family; Region: HflX; cd01878 583345004890 G1 box; other site 583345004891 GTP/Mg2+ binding site [chemical binding]; other site 583345004892 Switch I region; other site 583345004893 G2 box; other site 583345004894 G3 box; other site 583345004895 Switch II region; other site 583345004896 G4 box; other site 583345004897 G5 box; other site 583345004898 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 583345004899 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 583345004900 hexamer interface [polypeptide binding]; other site 583345004901 ligand binding site [chemical binding]; other site 583345004902 putative active site [active] 583345004903 NAD(P) binding site [chemical binding]; other site 583345004904 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 583345004905 Part of AAA domain; Region: AAA_19; pfam13245 583345004906 probable DNA repair protein; Region: TIGR03623 583345004907 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 583345004908 Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]; Region: ThiH; COG1060 583345004909 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 583345004910 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 583345004911 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 583345004912 hypothetical protein; Provisional; Region: PRK09272 583345004913 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 583345004914 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 583345004915 elongation factor P; Validated; Region: PRK00529 583345004916 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 583345004917 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 583345004918 RNA binding site [nucleotide binding]; other site 583345004919 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 583345004920 RNA binding site [nucleotide binding]; other site 583345004921 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 583345004922 tetramer (dimer of dimers) interface [polypeptide binding]; other site 583345004923 active site 583345004924 dimer interface [polypeptide binding]; other site 583345004925 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 583345004926 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 583345004927 substrate binding pocket [chemical binding]; other site 583345004928 membrane-bound complex binding site; other site 583345004929 hinge residues; other site 583345004930 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 583345004931 N-acetyl-D-glucosamine binding site [chemical binding]; other site 583345004932 catalytic residue [active] 583345004933 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 583345004934 EamA-like transporter family; Region: EamA; cl17759 583345004935 seryl-tRNA synthetase; Provisional; Region: PRK05431 583345004936 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 583345004937 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 583345004938 dimer interface [polypeptide binding]; other site 583345004939 active site 583345004940 motif 1; other site 583345004941 motif 2; other site 583345004942 motif 3; other site 583345004943 recombination factor protein RarA; Reviewed; Region: PRK13342 583345004944 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 583345004945 Walker A motif; other site 583345004946 ATP binding site [chemical binding]; other site 583345004947 Walker B motif; other site 583345004948 arginine finger; other site 583345004949 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 583345004950 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 583345004951 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 583345004952 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 583345004953 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 583345004954 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 583345004955 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 583345004956 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 583345004957 dimerization interface [polypeptide binding]; other site 583345004958 DPS ferroxidase diiron center [ion binding]; other site 583345004959 ion pore; other site 583345004960 thioredoxin reductase; Provisional; Region: PRK10262 583345004961 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 583345004962 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 583345004963 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 583345004964 Smr domain; Region: Smr; pfam01713 583345004965 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 583345004966 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 583345004967 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 583345004968 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 583345004969 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 583345004970 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 583345004971 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 583345004972 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 583345004973 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 583345004974 DNA-binding site [nucleotide binding]; DNA binding site 583345004975 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 583345004976 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345004977 homodimer interface [polypeptide binding]; other site 583345004978 catalytic residue [active] 583345004979 FlaG protein; Region: FlaG; pfam03646 583345004980 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 583345004981 SnoaL-like domain; Region: SnoaL_2; pfam12680 583345004982 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 583345004983 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 583345004984 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 583345004985 Walker A/P-loop; other site 583345004986 ATP binding site [chemical binding]; other site 583345004987 Q-loop/lid; other site 583345004988 ABC transporter signature motif; other site 583345004989 Walker B; other site 583345004990 D-loop; other site 583345004991 H-loop/switch region; other site 583345004992 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 583345004993 homotrimer interaction site [polypeptide binding]; other site 583345004994 zinc binding site [ion binding]; other site 583345004995 CDP-binding sites; other site 583345004996 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 583345004997 substrate binding site; other site 583345004998 dimer interface; other site 583345004999 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 583345005000 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 583345005001 DNA-binding site [nucleotide binding]; DNA binding site 583345005002 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 583345005003 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345005004 homodimer interface [polypeptide binding]; other site 583345005005 catalytic residue [active] 583345005006 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 583345005007 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 583345005008 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 583345005009 active site 583345005010 phosphorylation site [posttranslational modification] 583345005011 intermolecular recognition site; other site 583345005012 dimerization interface [polypeptide binding]; other site 583345005013 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 583345005014 DNA binding site [nucleotide binding] 583345005015 sensor protein KdpD; Provisional; Region: PRK10490 583345005016 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 583345005017 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 583345005018 Ligand Binding Site [chemical binding]; other site 583345005019 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 583345005020 GAF domain; Region: GAF_3; pfam13492 583345005021 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 583345005022 dimer interface [polypeptide binding]; other site 583345005023 phosphorylation site [posttranslational modification] 583345005024 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 583345005025 ATP binding site [chemical binding]; other site 583345005026 Mg2+ binding site [ion binding]; other site 583345005027 G-X-G motif; other site 583345005028 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 583345005029 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 583345005030 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 583345005031 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 583345005032 RES domain; Region: RES; pfam08808 583345005033 hypothetical protein; Provisional; Region: PRK06153 583345005034 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 583345005035 ATP binding site [chemical binding]; other site 583345005036 substrate interface [chemical binding]; other site 583345005037 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 583345005038 Domain of unknown function (DUF955); Region: DUF955; pfam06114 583345005039 phage-associated protein, BcepMu gp16 family; Region: BcepMu_gp16; TIGR04111 583345005040 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 583345005041 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 583345005042 non-specific DNA binding site [nucleotide binding]; other site 583345005043 salt bridge; other site 583345005044 sequence-specific DNA binding site [nucleotide binding]; other site 583345005045 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 583345005046 non-specific DNA binding site [nucleotide binding]; other site 583345005047 salt bridge; other site 583345005048 sequence-specific DNA binding site [nucleotide binding]; other site 583345005049 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 583345005050 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 583345005051 non-specific DNA binding site [nucleotide binding]; other site 583345005052 salt bridge; other site 583345005053 sequence-specific DNA binding site [nucleotide binding]; other site 583345005054 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 583345005055 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 583345005056 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 583345005057 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345005058 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 583345005059 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 583345005060 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 583345005061 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345005062 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 583345005063 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 583345005064 Outer membrane efflux protein; Region: OEP; pfam02321 583345005065 Outer membrane efflux protein; Region: OEP; pfam02321 583345005066 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 583345005067 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 583345005068 DNA binding residues [nucleotide binding] 583345005069 dimer interface [polypeptide binding]; other site 583345005070 copper binding site [ion binding]; other site 583345005071 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 583345005072 metal-binding site [ion binding] 583345005073 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 583345005074 YHS domain; Region: YHS; pfam04945 583345005075 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 583345005076 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 583345005077 Soluble P-type ATPase [General function prediction only]; Region: COG4087 583345005078 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 583345005079 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 583345005080 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 583345005081 Walker A motif; other site 583345005082 ATP binding site [chemical binding]; other site 583345005083 Walker B motif; other site 583345005084 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 583345005085 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 583345005086 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 583345005087 active site 583345005088 HIGH motif; other site 583345005089 nucleotide binding site [chemical binding]; other site 583345005090 active site 583345005091 KMSKS motif; other site 583345005092 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 583345005093 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 583345005094 dimerization interface [polypeptide binding]; other site 583345005095 domain crossover interface; other site 583345005096 redox-dependent activation switch; other site 583345005097 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 583345005098 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 583345005099 Pilin (bacterial filament); Region: Pilin; pfam00114 583345005100 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 583345005101 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 583345005102 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 583345005103 amphipathic channel; other site 583345005104 Asn-Pro-Ala signature motifs; other site 583345005105 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 583345005106 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 583345005107 active site 583345005108 uracil binding [chemical binding]; other site 583345005109 Protein of unknown function (DUF502); Region: DUF502; cl01107 583345005110 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 583345005111 TraB family; Region: TraB; pfam01963 583345005112 hypothetical protein; Provisional; Region: PRK01254 583345005113 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 583345005114 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 583345005115 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 583345005116 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 583345005117 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 583345005118 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 583345005119 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 583345005120 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 583345005121 PAS domain; Region: PAS; smart00091 583345005122 PAS domain S-box; Region: sensory_box; TIGR00229 583345005123 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345005124 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345005125 metal binding site [ion binding]; metal-binding site 583345005126 active site 583345005127 I-site; other site 583345005128 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 583345005129 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 583345005130 prephenate dehydrogenase; Validated; Region: PRK08507 583345005131 3-phosphoshikimate 1-carboxyvinyltransferase; Region: PLN02338 583345005132 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 583345005133 hinge; other site 583345005134 active site 583345005135 cytidylate kinase; Provisional; Region: cmk; PRK00023 583345005136 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 583345005137 CMP-binding site; other site 583345005138 The sites determining sugar specificity; other site 583345005139 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06676 583345005140 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 583345005141 RNA binding site [nucleotide binding]; other site 583345005142 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 583345005143 RNA binding site [nucleotide binding]; other site 583345005144 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 583345005145 RNA binding site [nucleotide binding]; other site 583345005146 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 583345005147 RNA binding site [nucleotide binding]; other site 583345005148 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 583345005149 RNA binding site [nucleotide binding]; other site 583345005150 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 583345005151 IHF dimer interface [polypeptide binding]; other site 583345005152 IHF - DNA interface [nucleotide binding]; other site 583345005153 tetratricopeptide repeat protein; Provisional; Region: PRK11788 583345005154 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 583345005155 binding surface 583345005156 TPR motif; other site 583345005157 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 583345005158 active site 583345005159 dimer interface [polypeptide binding]; other site 583345005160 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 583345005161 Helix-hairpin-helix motif; Region: HHH; pfam00633 583345005162 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 583345005163 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 583345005164 active site 583345005165 HIGH motif; other site 583345005166 KMSKS motif; other site 583345005167 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 583345005168 tRNA binding surface [nucleotide binding]; other site 583345005169 anticodon binding site; other site 583345005170 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 583345005171 dimer interface [polypeptide binding]; other site 583345005172 putative tRNA-binding site [nucleotide binding]; other site 583345005173 Domain of unknown function DUF59; Region: DUF59; pfam01883 583345005174 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 583345005175 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 583345005176 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 583345005177 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 583345005178 putative active site [active] 583345005179 glucose-6-phosphate 1-dehydrogenase; Provisional; Region: PRK12853 583345005180 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 583345005181 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 583345005182 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 583345005183 trimer interface [polypeptide binding]; other site 583345005184 active site 583345005185 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 583345005186 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 583345005187 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 583345005188 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 583345005189 catalytic residue [active] 583345005190 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 583345005191 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 583345005192 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 583345005193 folate binding site [chemical binding]; other site 583345005194 NADP+ binding site [chemical binding]; other site 583345005195 thymidylate synthase; Reviewed; Region: thyA; PRK01827 583345005196 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 583345005197 dimerization interface [polypeptide binding]; other site 583345005198 active site 583345005199 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 583345005200 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 583345005201 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345005202 catalytic residue [active] 583345005203 homoserine dehydrogenase; Provisional; Region: PRK06349 583345005204 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 583345005205 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 583345005206 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 583345005207 aminotransferase AlaT; Validated; Region: PRK09265 583345005208 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 583345005209 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345005210 homodimer interface [polypeptide binding]; other site 583345005211 catalytic residue [active] 583345005212 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 583345005213 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 583345005214 putative DNA binding site [nucleotide binding]; other site 583345005215 putative Zn2+ binding site [ion binding]; other site 583345005216 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 583345005217 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 583345005218 active site 583345005219 FMN binding site [chemical binding]; other site 583345005220 substrate binding site [chemical binding]; other site 583345005221 homotetramer interface [polypeptide binding]; other site 583345005222 catalytic residue [active] 583345005223 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 583345005224 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 583345005225 dimer interface [polypeptide binding]; other site 583345005226 active site 583345005227 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 583345005228 active site 1 [active] 583345005229 dimer interface [polypeptide binding]; other site 583345005230 active site 2 [active] 583345005231 MoxR-like ATPases [General function prediction only]; Region: COG0714 583345005232 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 583345005233 Walker A motif; other site 583345005234 ATP binding site [chemical binding]; other site 583345005235 Walker B motif; other site 583345005236 arginine finger; other site 583345005237 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 583345005238 Protein of unknown function DUF58; Region: DUF58; pfam01882 583345005239 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 583345005240 metal ion-dependent adhesion site (MIDAS); other site 583345005241 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 583345005242 Tetratricopeptide repeat; Region: TPR_12; pfam13424 583345005243 von Willebrand factor type A domain; Region: VWA_2; pfam13519 583345005244 metal ion-dependent adhesion site (MIDAS); other site 583345005245 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 583345005246 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 583345005247 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 583345005248 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 583345005249 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 583345005250 enolase; Provisional; Region: eno; PRK00077 583345005251 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 583345005252 dimer interface [polypeptide binding]; other site 583345005253 metal binding site [ion binding]; metal-binding site 583345005254 substrate binding pocket [chemical binding]; other site 583345005255 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 583345005256 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 583345005257 CTP synthetase; Validated; Region: pyrG; PRK05380 583345005258 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 583345005259 Catalytic site [active] 583345005260 active site 583345005261 UTP binding site [chemical binding]; other site 583345005262 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 583345005263 active site 583345005264 putative oxyanion hole; other site 583345005265 catalytic triad [active] 583345005266 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 583345005267 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 583345005268 intersubunit interface [polypeptide binding]; other site 583345005269 active site 583345005270 Zn2+ binding site [ion binding]; other site 583345005271 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 583345005272 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 583345005273 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 583345005274 active site 583345005275 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 583345005276 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 583345005277 catalytic motif [active] 583345005278 Zn binding site [ion binding]; other site 583345005279 RibD C-terminal domain; Region: RibD_C; cl17279 583345005280 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 583345005281 ATP cone domain; Region: ATP-cone; pfam03477 583345005282 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 583345005283 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 583345005284 dimer interface [polypeptide binding]; other site 583345005285 active site 583345005286 glycine-pyridoxal phosphate binding site [chemical binding]; other site 583345005287 folate binding site [chemical binding]; other site 583345005288 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 583345005289 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 583345005290 catalytic motif [active] 583345005291 Catalytic residue [active] 583345005292 phosphoglucomutase; Region: PLN02307 583345005293 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction; Region: PGM1; cd03085 583345005294 substrate binding site [chemical binding]; other site 583345005295 dimer interface [polypeptide binding]; other site 583345005296 active site 583345005297 metal binding site [ion binding]; metal-binding site 583345005298 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 583345005299 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 583345005300 Flagellar regulator YcgR; Region: YcgR; pfam07317 583345005301 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 583345005302 PilZ domain; Region: PilZ; pfam07238 583345005303 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 583345005304 Cytochrome c; Region: Cytochrom_C; cl11414 583345005305 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 583345005306 4Fe-4S binding domain; Region: Fer4_5; pfam12801 583345005307 4Fe-4S binding domain; Region: Fer4_5; pfam12801 583345005308 MauM/NapG family ferredoxin-type protein; Region: mauM_napG; TIGR00397 583345005309 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 583345005310 tryptophan tryptophylquinone biosynthesis enzyme MauG; Region: TTQ_mauG; TIGR03791 583345005311 Methylamine dehydrogenase, L chain; Region: Me-amine-dh_L; cl03812 583345005312 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 583345005313 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 583345005314 Methylamine utilisation protein MauE; Region: MauE; pfam07291 583345005315 methylamine dehydrogenase (amicyanin) heavy chain; Region: TTQ_MADH_Hv; TIGR02658 583345005316 transcriptional regulator EutR; Provisional; Region: PRK10130 583345005317 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 583345005318 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 583345005319 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 583345005320 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 583345005321 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 583345005322 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 583345005323 DNA binding residues [nucleotide binding] 583345005324 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 583345005325 IHF dimer interface [polypeptide binding]; other site 583345005326 IHF - DNA interface [nucleotide binding]; other site 583345005327 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 583345005328 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 583345005329 putative tRNA-binding site [nucleotide binding]; other site 583345005330 B3/4 domain; Region: B3_4; pfam03483 583345005331 tRNA synthetase B5 domain; Region: B5; smart00874 583345005332 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 583345005333 dimer interface [polypeptide binding]; other site 583345005334 motif 1; other site 583345005335 motif 3; other site 583345005336 motif 2; other site 583345005337 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 583345005338 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 583345005339 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 583345005340 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 583345005341 dimer interface [polypeptide binding]; other site 583345005342 motif 1; other site 583345005343 active site 583345005344 motif 2; other site 583345005345 motif 3; other site 583345005346 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 583345005347 23S rRNA binding site [nucleotide binding]; other site 583345005348 L21 binding site [polypeptide binding]; other site 583345005349 L13 binding site [polypeptide binding]; other site 583345005350 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 583345005351 translation initiation factor IF-3; Region: infC; TIGR00168 583345005352 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 583345005353 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 583345005354 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 583345005355 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 583345005356 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 583345005357 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 583345005358 active site 583345005359 dimer interface [polypeptide binding]; other site 583345005360 motif 1; other site 583345005361 motif 2; other site 583345005362 motif 3; other site 583345005363 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 583345005364 anticodon binding site; other site 583345005365 Transglycosylase SLT domain; Region: SLT_2; pfam13406 583345005366 murein hydrolase B; Provisional; Region: PRK10760; cl17906 583345005367 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 583345005368 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 583345005369 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 583345005370 putative NAD(P) binding site [chemical binding]; other site 583345005371 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 583345005372 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 583345005373 dimer interface [polypeptide binding]; other site 583345005374 ADP-ribose binding site [chemical binding]; other site 583345005375 active site 583345005376 nudix motif; other site 583345005377 metal binding site [ion binding]; metal-binding site 583345005378 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 583345005379 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 583345005380 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 583345005381 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 583345005382 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 583345005383 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 583345005384 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 583345005385 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 583345005386 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 583345005387 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 583345005388 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 583345005389 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 583345005390 4Fe-4S binding domain; Region: Fer4; pfam00037 583345005391 4Fe-4S binding domain; Region: Fer4; pfam00037 583345005392 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 583345005393 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 583345005394 NADH dehydrogenase subunit G; Validated; Region: PRK09129 583345005395 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 583345005396 catalytic loop [active] 583345005397 iron binding site [ion binding]; other site 583345005398 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 583345005399 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 583345005400 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 583345005401 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 583345005402 SLBB domain; Region: SLBB; pfam10531 583345005403 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 583345005404 NADH dehydrogenase subunit E; Validated; Region: PRK07539 583345005405 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 583345005406 putative dimer interface [polypeptide binding]; other site 583345005407 [2Fe-2S] cluster binding site [ion binding]; other site 583345005408 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 583345005409 NADH dehydrogenase subunit D; Validated; Region: PRK06075 583345005410 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 583345005411 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 583345005412 NADH dehydrogenase subunit B; Validated; Region: PRK06411 583345005413 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 583345005414 preprotein translocase subunit SecG; Reviewed; Region: secG; PRK06870 583345005415 triosephosphate isomerase; Provisional; Region: PRK14567 583345005416 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 583345005417 substrate binding site [chemical binding]; other site 583345005418 dimer interface [polypeptide binding]; other site 583345005419 catalytic triad [active] 583345005420 phospholipid:lipid A palmitoyltransferase; Provisional; Region: pagP; PRK11045 583345005421 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 583345005422 putative substrate binding site [chemical binding]; other site 583345005423 putative ATP binding site [chemical binding]; other site 583345005424 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 583345005425 DHH family; Region: DHH; pfam01368 583345005426 DHHA1 domain; Region: DHHA1; pfam02272 583345005427 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 583345005428 DNA polymerase IV; Reviewed; Region: PRK03103 583345005429 Y-family of DNA polymerases; Region: PolY; cd00424 583345005430 active site 583345005431 DNA binding site [nucleotide binding] 583345005432 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 583345005433 methionine sulfoxide reductase A; Provisional; Region: PRK14054 583345005434 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 583345005435 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 583345005436 homodimer interface [polypeptide binding]; other site 583345005437 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 583345005438 active site pocket [active] 583345005439 heat shock protein 90; Provisional; Region: PRK05218 583345005440 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 583345005441 ATP binding site [chemical binding]; other site 583345005442 Mg2+ binding site [ion binding]; other site 583345005443 G-X-G motif; other site 583345005444 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 583345005445 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 583345005446 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39A; cd02549 583345005447 putative active site [active] 583345005448 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 583345005449 catalytic core [active] 583345005450 polyphosphate kinase; Provisional; Region: PRK05443 583345005451 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 583345005452 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 583345005453 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 583345005454 putative active site [active] 583345005455 catalytic site [active] 583345005456 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 583345005457 putative domain interface [polypeptide binding]; other site 583345005458 putative active site [active] 583345005459 catalytic site [active] 583345005460 triosephosphate isomerase; Provisional; Region: PRK14567 583345005461 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 583345005462 substrate binding site [chemical binding]; other site 583345005463 dimer interface [polypeptide binding]; other site 583345005464 catalytic triad [active] 583345005465 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 583345005466 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 583345005467 putative ATP binding site [chemical binding]; other site 583345005468 putative substrate interface [chemical binding]; other site 583345005469 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 583345005470 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 583345005471 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 583345005472 active site 583345005473 hydrophilic channel; other site 583345005474 dimerization interface [polypeptide binding]; other site 583345005475 catalytic residues [active] 583345005476 active site lid [active] 583345005477 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 583345005478 Recombination protein O N terminal; Region: RecO_N; pfam11967 583345005479 Recombination protein O C terminal; Region: RecO_C; pfam02565 583345005480 GTPase Era; Reviewed; Region: era; PRK00089 583345005481 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 583345005482 G1 box; other site 583345005483 GTP/Mg2+ binding site [chemical binding]; other site 583345005484 Switch I region; other site 583345005485 G2 box; other site 583345005486 Switch II region; other site 583345005487 G3 box; other site 583345005488 G4 box; other site 583345005489 G5 box; other site 583345005490 KH domain; Region: KH_2; pfam07650 583345005491 ribonuclease III; Reviewed; Region: rnc; PRK00102 583345005492 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 583345005493 dimerization interface [polypeptide binding]; other site 583345005494 active site 583345005495 metal binding site [ion binding]; metal-binding site 583345005496 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 583345005497 dsRNA binding site [nucleotide binding]; other site 583345005498 signal peptidase I; Provisional; Region: PRK10861 583345005499 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 583345005500 Catalytic site [active] 583345005501 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 583345005502 GTP-binding protein LepA; Provisional; Region: PRK05433 583345005503 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 583345005504 G1 box; other site 583345005505 putative GEF interaction site [polypeptide binding]; other site 583345005506 GTP/Mg2+ binding site [chemical binding]; other site 583345005507 Switch I region; other site 583345005508 G2 box; other site 583345005509 G3 box; other site 583345005510 Switch II region; other site 583345005511 G4 box; other site 583345005512 G5 box; other site 583345005513 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 583345005514 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 583345005515 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 583345005516 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 583345005517 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 583345005518 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 583345005519 protein binding site [polypeptide binding]; other site 583345005520 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 583345005521 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 583345005522 anti-sigma E factor; Provisional; Region: rseB; PRK09455 583345005523 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 583345005524 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 583345005525 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 583345005526 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345005527 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 583345005528 DNA binding residues [nucleotide binding] 583345005529 L-aspartate oxidase; Provisional; Region: PRK09077 583345005530 L-aspartate oxidase; Provisional; Region: PRK06175 583345005531 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 583345005532 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 583345005533 DEAD-like helicases superfamily; Region: DEXDc; smart00487 583345005534 ATP binding site [chemical binding]; other site 583345005535 Mg++ binding site [ion binding]; other site 583345005536 motif III; other site 583345005537 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 583345005538 nucleotide binding region [chemical binding]; other site 583345005539 ATP-binding site [chemical binding]; other site 583345005540 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 583345005541 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 583345005542 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 583345005543 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 583345005544 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 583345005545 [4Fe-4S] binding site [ion binding]; other site 583345005546 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 583345005547 molybdopterin cofactor binding site; other site 583345005548 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 583345005549 molybdopterin cofactor binding site; other site 583345005550 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 583345005551 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 583345005552 [2Fe-2S] cluster binding site [ion binding]; other site 583345005553 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 583345005554 active site 583345005555 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 583345005556 Catalytic domain of Protein Kinases; Region: PKc; cd00180 583345005557 active site 583345005558 ATP binding site [chemical binding]; other site 583345005559 substrate binding site [chemical binding]; other site 583345005560 activation loop (A-loop); other site 583345005561 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 583345005562 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 583345005563 putative substrate translocation pore; other site 583345005564 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 583345005565 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 583345005566 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 583345005567 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 583345005568 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 583345005569 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 583345005570 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 583345005571 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 583345005572 Walker A/P-loop; other site 583345005573 ATP binding site [chemical binding]; other site 583345005574 Q-loop/lid; other site 583345005575 ABC transporter signature motif; other site 583345005576 Walker B; other site 583345005577 D-loop; other site 583345005578 H-loop/switch region; other site 583345005579 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 583345005580 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 583345005581 dimer interface [polypeptide binding]; other site 583345005582 conserved gate region; other site 583345005583 putative PBP binding loops; other site 583345005584 ABC-ATPase subunit interface; other site 583345005585 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 583345005586 NMT1-like family; Region: NMT1_2; pfam13379 583345005587 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 583345005588 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 583345005589 active site 583345005590 phosphorylation site [posttranslational modification] 583345005591 intermolecular recognition site; other site 583345005592 dimerization interface [polypeptide binding]; other site 583345005593 ANTAR domain; Region: ANTAR; pfam03861 583345005594 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 583345005595 MutS domain I; Region: MutS_I; pfam01624 583345005596 MutS domain II; Region: MutS_II; pfam05188 583345005597 MutS domain III; Region: MutS_III; pfam05192 583345005598 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 583345005599 Walker A/P-loop; other site 583345005600 ATP binding site [chemical binding]; other site 583345005601 Q-loop/lid; other site 583345005602 ABC transporter signature motif; other site 583345005603 Walker B; other site 583345005604 D-loop; other site 583345005605 H-loop/switch region; other site 583345005606 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 583345005607 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 583345005608 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345005609 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345005610 metal binding site [ion binding]; metal-binding site 583345005611 active site 583345005612 I-site; other site 583345005613 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 583345005614 PAS domain; Region: PAS_9; pfam13426 583345005615 putative active site [active] 583345005616 heme pocket [chemical binding]; other site 583345005617 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 583345005618 Tar ligand binding domain homologue; Region: TarH; pfam02203 583345005619 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 583345005620 dimer interface [polypeptide binding]; other site 583345005621 putative CheW interface [polypeptide binding]; other site 583345005622 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 583345005623 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345005624 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345005625 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 583345005626 Fusaric acid resistance protein family; Region: FUSC; pfam04632 583345005627 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 583345005628 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 583345005629 MarR family; Region: MarR_2; cl17246 583345005630 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 583345005631 Site-specific recombinase; Region: SpecificRecomb; pfam10136 583345005632 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 583345005633 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 583345005634 active site 583345005635 dimerization interface [polypeptide binding]; other site 583345005636 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 583345005637 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 583345005638 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 583345005639 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 583345005640 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 583345005641 binding surface 583345005642 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345005643 TPR motif; other site 583345005644 serine O-acetyltransferase; Region: cysE; TIGR01172 583345005645 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 583345005646 trimer interface [polypeptide binding]; other site 583345005647 active site 583345005648 substrate binding site [chemical binding]; other site 583345005649 CoA binding site [chemical binding]; other site 583345005650 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 583345005651 Rrf2 family protein; Region: rrf2_super; TIGR00738 583345005652 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 583345005653 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 583345005654 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 583345005655 catalytic residue [active] 583345005656 cysteine desulfurase; Provisional; Region: PRK14012 583345005657 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 583345005658 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 583345005659 catalytic residue [active] 583345005660 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 583345005661 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 583345005662 trimerization site [polypeptide binding]; other site 583345005663 active site 583345005664 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 583345005665 co-chaperone HscB; Provisional; Region: hscB; PRK03578 583345005666 DnaJ domain; Region: DnaJ; pfam00226 583345005667 HSP70 interaction site [polypeptide binding]; other site 583345005668 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 583345005669 chaperone protein HscA; Provisional; Region: hscA; PRK05183 583345005670 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 583345005671 nucleotide binding site [chemical binding]; other site 583345005672 putative NEF/HSP70 interaction site [polypeptide binding]; other site 583345005673 SBD interface [polypeptide binding]; other site 583345005674 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 583345005675 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 583345005676 catalytic loop [active] 583345005677 iron binding site [ion binding]; other site 583345005678 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_cladeC; cd03378 583345005679 active site clefts [active] 583345005680 zinc binding site [ion binding]; other site 583345005681 dimer interface [polypeptide binding]; other site 583345005682 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 583345005683 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 583345005684 Sulfate transporter family; Region: Sulfate_transp; pfam00916 583345005685 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 583345005686 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 583345005687 DNA binding residues [nucleotide binding] 583345005688 dimerization interface [polypeptide binding]; other site 583345005689 CHASE3 domain; Region: CHASE3; pfam05227 583345005690 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 583345005691 HAMP domain; Region: HAMP; pfam00672 583345005692 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 583345005693 dimer interface [polypeptide binding]; other site 583345005694 phosphorylation site [posttranslational modification] 583345005695 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 583345005696 ATP binding site [chemical binding]; other site 583345005697 Mg2+ binding site [ion binding]; other site 583345005698 G-X-G motif; other site 583345005699 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 583345005700 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 583345005701 active site 583345005702 phosphorylation site [posttranslational modification] 583345005703 intermolecular recognition site; other site 583345005704 dimerization interface [polypeptide binding]; other site 583345005705 Response regulator receiver domain; Region: Response_reg; pfam00072 583345005706 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 583345005707 active site 583345005708 phosphorylation site [posttranslational modification] 583345005709 intermolecular recognition site; other site 583345005710 dimerization interface [polypeptide binding]; other site 583345005711 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 583345005712 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 583345005713 dimer interface [polypeptide binding]; other site 583345005714 putative anticodon binding site; other site 583345005715 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 583345005716 motif 1; other site 583345005717 active site 583345005718 motif 2; other site 583345005719 motif 3; other site 583345005720 peptide chain release factor 2; Validated; Region: prfB; PRK00578 583345005721 This domain is found in peptide chain release factors; Region: PCRF; smart00937 583345005722 RF-1 domain; Region: RF-1; pfam00472 583345005723 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 583345005724 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 583345005725 PBP superfamily domain; Region: PBP_like_2; cl17296 583345005726 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 583345005727 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 583345005728 dimer interface [polypeptide binding]; other site 583345005729 conserved gate region; other site 583345005730 putative PBP binding loops; other site 583345005731 ABC-ATPase subunit interface; other site 583345005732 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 583345005733 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 583345005734 dimer interface [polypeptide binding]; other site 583345005735 conserved gate region; other site 583345005736 putative PBP binding loops; other site 583345005737 ABC-ATPase subunit interface; other site 583345005738 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 583345005739 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 583345005740 Walker A/P-loop; other site 583345005741 ATP binding site [chemical binding]; other site 583345005742 Q-loop/lid; other site 583345005743 ABC transporter signature motif; other site 583345005744 Walker B; other site 583345005745 D-loop; other site 583345005746 H-loop/switch region; other site 583345005747 aminopeptidase N; Provisional; Region: pepN; PRK14015 583345005748 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 583345005749 active site 583345005750 Zn binding site [ion binding]; other site 583345005751 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 583345005752 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 583345005753 putative ADP-binding pocket [chemical binding]; other site 583345005754 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; pfam00882 583345005755 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 583345005756 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 583345005757 active site 583345005758 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 583345005759 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 583345005760 active site 583345005761 substrate binding site [chemical binding]; other site 583345005762 metal binding site [ion binding]; metal-binding site 583345005763 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 583345005764 dihydropteroate synthase; Region: DHPS; TIGR01496 583345005765 substrate binding pocket [chemical binding]; other site 583345005766 dimer interface [polypeptide binding]; other site 583345005767 inhibitor binding site; inhibition site 583345005768 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 583345005769 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 583345005770 Walker A motif; other site 583345005771 ATP binding site [chemical binding]; other site 583345005772 Walker B motif; other site 583345005773 arginine finger; other site 583345005774 Peptidase family M41; Region: Peptidase_M41; pfam01434 583345005775 FtsJ-like methyltransferase; Region: FtsJ; cl17430 583345005776 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 583345005777 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; pfam01985 583345005778 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 583345005779 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 583345005780 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 583345005781 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 583345005782 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 583345005783 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 583345005784 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 583345005785 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 583345005786 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 583345005787 ATP-grasp domain; Region: ATP-grasp_4; cl17255 583345005788 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 583345005789 IMP binding site; other site 583345005790 dimer interface [polypeptide binding]; other site 583345005791 interdomain contacts; other site 583345005792 partial ornithine binding site; other site 583345005793 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 583345005794 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 583345005795 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 583345005796 catalytic site [active] 583345005797 subunit interface [polypeptide binding]; other site 583345005798 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 583345005799 dihydrodipicolinate reductase; Provisional; Region: PRK00048 583345005800 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 583345005801 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 583345005802 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 583345005803 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 583345005804 ferric uptake regulator; Provisional; Region: fur; PRK09462 583345005805 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 583345005806 metal binding site 2 [ion binding]; metal-binding site 583345005807 putative DNA binding helix; other site 583345005808 metal binding site 1 [ion binding]; metal-binding site 583345005809 dimer interface [polypeptide binding]; other site 583345005810 structural Zn2+ binding site [ion binding]; other site 583345005811 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 583345005812 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 583345005813 Walker A/P-loop; other site 583345005814 ATP binding site [chemical binding]; other site 583345005815 Q-loop/lid; other site 583345005816 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 583345005817 ABC transporter signature motif; other site 583345005818 Walker B; other site 583345005819 D-loop; other site 583345005820 H-loop/switch region; other site 583345005821 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 583345005822 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 583345005823 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 583345005824 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 583345005825 Sulfatase; Region: Sulfatase; pfam00884 583345005826 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 583345005827 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 583345005828 ferrochelatase; Reviewed; Region: hemH; PRK00035 583345005829 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 583345005830 C-terminal domain interface [polypeptide binding]; other site 583345005831 active site 583345005832 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 583345005833 active site 583345005834 N-terminal domain interface [polypeptide binding]; other site 583345005835 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 583345005836 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 583345005837 NADP binding site [chemical binding]; other site 583345005838 homopentamer interface [polypeptide binding]; other site 583345005839 substrate binding site [chemical binding]; other site 583345005840 active site 583345005841 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 583345005842 dimer interface [polypeptide binding]; other site 583345005843 active site 583345005844 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 583345005845 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 583345005846 putative ribose interaction site [chemical binding]; other site 583345005847 putative ADP binding site [chemical binding]; other site 583345005848 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 583345005849 active site 583345005850 nucleotide binding site [chemical binding]; other site 583345005851 HIGH motif; other site 583345005852 KMSKS motif; other site 583345005853 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 583345005854 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 583345005855 putative active site [active] 583345005856 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 583345005857 lipopolysaccharide core biosynthesis protein; Provisional; Region: PRK09822 583345005858 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345005859 active site 583345005860 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 583345005861 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 583345005862 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 583345005863 NAD binding site [chemical binding]; other site 583345005864 homodimer interface [polypeptide binding]; other site 583345005865 active site 583345005866 substrate binding site [chemical binding]; other site 583345005867 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 583345005868 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 583345005869 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 583345005870 active site 583345005871 intersubunit interface [polypeptide binding]; other site 583345005872 catalytic residue [active] 583345005873 phosphogluconate dehydratase; Validated; Region: PRK09054 583345005874 6-phosphogluconate dehydratase; Region: edd; TIGR01196 583345005875 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 583345005876 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 583345005877 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 583345005878 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 583345005879 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 583345005880 active site 583345005881 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 583345005882 active site 583345005883 ATP binding site [chemical binding]; other site 583345005884 substrate binding site [chemical binding]; other site 583345005885 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 583345005886 putative acyl-acceptor binding pocket; other site 583345005887 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 583345005888 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 583345005889 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 583345005890 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 583345005891 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 583345005892 putative active site [active] 583345005893 GrpE; Region: GrpE; pfam01025 583345005894 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 583345005895 dimer interface [polypeptide binding]; other site 583345005896 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 583345005897 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 583345005898 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 583345005899 nucleotide binding site [chemical binding]; other site 583345005900 chaperone protein DnaJ; Provisional; Region: PRK10767 583345005901 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 583345005902 HSP70 interaction site [polypeptide binding]; other site 583345005903 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 583345005904 substrate binding site [polypeptide binding]; other site 583345005905 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 583345005906 Zn binding sites [ion binding]; other site 583345005907 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 583345005908 dimer interface [polypeptide binding]; other site 583345005909 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 583345005910 Response regulator receiver domain; Region: Response_reg; pfam00072 583345005911 active site 583345005912 phosphorylation site [posttranslational modification] 583345005913 intermolecular recognition site; other site 583345005914 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345005915 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345005916 metal binding site [ion binding]; metal-binding site 583345005917 active site 583345005918 I-site; other site 583345005919 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 583345005920 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 583345005921 active site 583345005922 phosphorylation site [posttranslational modification] 583345005923 intermolecular recognition site; other site 583345005924 dimerization interface [polypeptide binding]; other site 583345005925 PAS domain S-box; Region: sensory_box; TIGR00229 583345005926 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 583345005927 putative active site [active] 583345005928 heme pocket [chemical binding]; other site 583345005929 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 583345005930 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 583345005931 putative active site [active] 583345005932 heme pocket [chemical binding]; other site 583345005933 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 583345005934 dimer interface [polypeptide binding]; other site 583345005935 phosphorylation site [posttranslational modification] 583345005936 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 583345005937 ATP binding site [chemical binding]; other site 583345005938 Mg2+ binding site [ion binding]; other site 583345005939 G-X-G motif; other site 583345005940 putative cation:proton antiport protein; Provisional; Region: PRK10669 583345005941 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 583345005942 TrkA-N domain; Region: TrkA_N; pfam02254 583345005943 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 583345005944 GIY-YIG motif/motif A; other site 583345005945 putative active site [active] 583345005946 putative metal binding site [ion binding]; other site 583345005947 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 583345005948 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 583345005949 dimer interface [polypeptide binding]; other site 583345005950 active site 583345005951 metal binding site [ion binding]; metal-binding site 583345005952 glutathione binding site [chemical binding]; other site 583345005953 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 583345005954 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 583345005955 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 583345005956 active site 583345005957 (T/H)XGH motif; other site 583345005958 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 583345005959 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 583345005960 S-adenosylmethionine binding site [chemical binding]; other site 583345005961 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 583345005962 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 583345005963 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 583345005964 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 583345005965 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 583345005966 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 583345005967 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 583345005968 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 583345005969 P loop; other site 583345005970 GTP binding site [chemical binding]; other site 583345005971 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 583345005972 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345005973 Walker A/P-loop; other site 583345005974 ATP binding site [chemical binding]; other site 583345005975 Q-loop/lid; other site 583345005976 ABC transporter signature motif; other site 583345005977 Walker B; other site 583345005978 D-loop; other site 583345005979 H-loop/switch region; other site 583345005980 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 583345005981 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 583345005982 Predicted membrane protein [Function unknown]; Region: COG3212 583345005983 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 583345005984 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 583345005985 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 583345005986 active site 583345005987 phosphorylation site [posttranslational modification] 583345005988 intermolecular recognition site; other site 583345005989 dimerization interface [polypeptide binding]; other site 583345005990 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 583345005991 DNA binding site [nucleotide binding] 583345005992 sensor protein PhoQ; Provisional; Region: PRK10815 583345005993 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 583345005994 ATP binding site [chemical binding]; other site 583345005995 Mg2+ binding site [ion binding]; other site 583345005996 G-X-G motif; other site 583345005997 Predicted membrane protein [Function unknown]; Region: COG3212 583345005998 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 583345005999 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 583345006000 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 583345006001 PAS fold; Region: PAS_3; pfam08447 583345006002 putative active site [active] 583345006003 heme pocket [chemical binding]; other site 583345006004 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345006005 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345006006 metal binding site [ion binding]; metal-binding site 583345006007 active site 583345006008 I-site; other site 583345006009 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 583345006010 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 583345006011 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345006012 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 583345006013 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345006014 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 583345006015 rRNA binding site [nucleotide binding]; other site 583345006016 predicted 30S ribosome binding site; other site 583345006017 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 583345006018 DNA-binding site [nucleotide binding]; DNA binding site 583345006019 RNA-binding motif; other site 583345006020 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345006021 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345006022 metal binding site [ion binding]; metal-binding site 583345006023 active site 583345006024 I-site; other site 583345006025 Cytochrome c; Region: Cytochrom_C; cl11414 583345006026 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 583345006027 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 583345006028 Trp docking motif [polypeptide binding]; other site 583345006029 dimer interface [polypeptide binding]; other site 583345006030 active site 583345006031 small subunit binding site [polypeptide binding]; other site 583345006032 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 583345006033 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 583345006034 Walker A motif; other site 583345006035 ATP binding site [chemical binding]; other site 583345006036 Walker B motif; other site 583345006037 arginine finger; other site 583345006038 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345006039 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 583345006040 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 583345006041 Ligand binding site; other site 583345006042 metal-binding site 583345006043 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 583345006044 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 583345006045 XdhC Rossmann domain; Region: XdhC_C; pfam13478 583345006046 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 583345006047 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 583345006048 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 583345006049 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 583345006050 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 583345006051 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 583345006052 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 583345006053 catalytic loop [active] 583345006054 iron binding site [ion binding]; other site 583345006055 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 583345006056 Transcriptional regulator [Transcription]; Region: LysR; COG0583 583345006057 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345006058 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 583345006059 putative effector binding pocket; other site 583345006060 dimerization interface [polypeptide binding]; other site 583345006061 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 583345006062 putative NAD(P) binding site [chemical binding]; other site 583345006063 homodimer interface [polypeptide binding]; other site 583345006064 Transcriptional regulator [Transcription]; Region: LysR; COG0583 583345006065 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345006066 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_8; cd08477 583345006067 putative effector binding pocket; other site 583345006068 putative dimerization interface [polypeptide binding]; other site 583345006069 C factor cell-cell signaling protein; Provisional; Region: PRK09009 583345006070 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 583345006071 NADP binding site [chemical binding]; other site 583345006072 homodimer interface [polypeptide binding]; other site 583345006073 active site 583345006074 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 583345006075 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345006076 Zn2+ binding site [ion binding]; other site 583345006077 Mg2+ binding site [ion binding]; other site 583345006078 PEP-CTERM motif; Region: VPEP; pfam07589 583345006079 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 583345006080 active site 583345006081 tetramer interface; other site 583345006082 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 583345006083 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 583345006084 Substrate binding site; other site 583345006085 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 583345006086 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 583345006087 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 583345006088 active site 583345006089 substrate binding site [chemical binding]; other site 583345006090 metal binding site [ion binding]; metal-binding site 583345006091 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 583345006092 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 583345006093 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 583345006094 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 583345006095 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 583345006096 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 583345006097 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 583345006098 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 583345006099 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 583345006100 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 583345006101 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 583345006102 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 583345006103 active site 583345006104 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 583345006105 O-Antigen ligase; Region: Wzy_C; pfam04932 583345006106 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 583345006107 Protein of unknown function (DUF3485); Region: DUF3485; pfam11984 583345006108 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 583345006109 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 583345006110 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 583345006111 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 583345006112 chain length determinant protein EpsF; Region: EpsF; TIGR03017 583345006113 Chain length determinant protein; Region: Wzz; cl15801 583345006114 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 583345006115 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 583345006116 SLBB domain; Region: SLBB; pfam10531 583345006117 SLBB domain; Region: SLBB; pfam10531 583345006118 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 583345006119 exopolysaccharide biosynthesis operon protein EpsL; Region: EpsL; TIGR03014 583345006120 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 583345006121 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 583345006122 ligand binding site [chemical binding]; other site 583345006123 flexible hinge region; other site 583345006124 transcriptional regulator EpsA; Region: EpsA; TIGR03020 583345006125 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 583345006126 DNA binding residues [nucleotide binding] 583345006127 dimerization interface [polypeptide binding]; other site 583345006128 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 583345006129 Bacterial sugar transferase; Region: Bac_transf; pfam02397 583345006130 VanZ like family; Region: VanZ; cl01971 583345006131 choice-of-anchor C domain; Region: choice_anch_C; TIGR04362 583345006132 PEP-CTERM motif; Region: VPEP; pfam07589 583345006133 BNR repeat-like domain; Region: BNR_2; pfam13088 583345006134 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 583345006135 Low molecular weight phosphatase family; Region: LMWPc; cl00105 583345006136 active site 583345006137 Low molecular weight phosphatase family; Region: LMWPc; cd00115 583345006138 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 583345006139 active site 583345006140 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; cl00200 583345006141 amphipathic channel; other site 583345006142 Asn-Pro-Ala signature motifs; other site 583345006143 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 583345006144 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 583345006145 putative metal binding site [ion binding]; other site 583345006146 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 583345006147 dimerization interface [polypeptide binding]; other site 583345006148 putative DNA binding site [nucleotide binding]; other site 583345006149 putative Zn2+ binding site [ion binding]; other site 583345006150 YcaO domain protein; Region: TIGR03549 583345006151 OsmC-like protein; Region: OsmC; pfam02566 583345006152 YcaO-like family; Region: YcaO; pfam02624 583345006153 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 583345006154 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 583345006155 putative NAD(P) binding site [chemical binding]; other site 583345006156 putative substrate binding site [chemical binding]; other site 583345006157 catalytic Zn binding site [ion binding]; other site 583345006158 structural Zn binding site [ion binding]; other site 583345006159 dimer interface [polypeptide binding]; other site 583345006160 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 583345006161 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 583345006162 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345006163 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 583345006164 DNA binding residues [nucleotide binding] 583345006165 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 583345006166 Dynamin family; Region: Dynamin_N; pfam00350 583345006167 G1 box; other site 583345006168 GTP/Mg2+ binding site [chemical binding]; other site 583345006169 G2 box; other site 583345006170 Switch I region; other site 583345006171 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 583345006172 G3 box; other site 583345006173 Switch II region; other site 583345006174 GTP/Mg2+ binding site [chemical binding]; other site 583345006175 G4 box; other site 583345006176 G5 box; other site 583345006177 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 583345006178 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 583345006179 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 583345006180 S-adenosylmethionine binding site [chemical binding]; other site 583345006181 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 583345006182 SCP-2 sterol transfer family; Region: SCP2; pfam02036 583345006183 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 583345006184 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 583345006185 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 583345006186 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 583345006187 Na binding site [ion binding]; other site 583345006188 putative glycosylation site [posttranslational modification]; other site 583345006189 putative glycosylation site [posttranslational modification]; other site 583345006190 GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria; Region: GIY-YIG_HE_Tlr8p_PBC-V_like; cd10443 583345006191 GIY-YIG motif/motif A; other site 583345006192 putative active site [active] 583345006193 putative metal binding site [ion binding]; other site 583345006194 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 583345006195 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 583345006196 DNA binding site [nucleotide binding] 583345006197 catalytic residue [active] 583345006198 H2TH interface [polypeptide binding]; other site 583345006199 putative catalytic residues [active] 583345006200 turnover-facilitating residue; other site 583345006201 intercalation triad [nucleotide binding]; other site 583345006202 8OG recognition residue [nucleotide binding]; other site 583345006203 putative reading head residues; other site 583345006204 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 583345006205 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 583345006206 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 583345006207 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 583345006208 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 583345006209 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 583345006210 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345006211 Walker A/P-loop; other site 583345006212 ATP binding site [chemical binding]; other site 583345006213 Q-loop/lid; other site 583345006214 ABC transporter signature motif; other site 583345006215 Walker B; other site 583345006216 D-loop; other site 583345006217 H-loop/switch region; other site 583345006218 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 583345006219 binding surface 583345006220 TPR motif; other site 583345006221 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 583345006222 binding surface 583345006223 TPR motif; other site 583345006224 TPR repeat; Region: TPR_11; pfam13414 583345006225 TPR repeat; Region: TPR_11; pfam13414 583345006226 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 583345006227 binding surface 583345006228 TPR motif; other site 583345006229 TPR repeat; Region: TPR_11; pfam13414 583345006230 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 583345006231 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 583345006232 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 583345006233 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 583345006234 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 583345006235 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 583345006236 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 583345006237 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345006238 active site 583345006239 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 583345006240 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 583345006241 5S rRNA interface [nucleotide binding]; other site 583345006242 CTC domain interface [polypeptide binding]; other site 583345006243 L16 interface [polypeptide binding]; other site 583345006244 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 583345006245 putative active site [active] 583345006246 catalytic residue [active] 583345006247 GTP-binding protein YchF; Reviewed; Region: PRK09601 583345006248 YchF GTPase; Region: YchF; cd01900 583345006249 G1 box; other site 583345006250 GTP/Mg2+ binding site [chemical binding]; other site 583345006251 Switch I region; other site 583345006252 G2 box; other site 583345006253 Switch II region; other site 583345006254 G3 box; other site 583345006255 G4 box; other site 583345006256 G5 box; other site 583345006257 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 583345006258 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 583345006259 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 583345006260 putative binding surface; other site 583345006261 active site 583345006262 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 583345006263 ATP binding site [chemical binding]; other site 583345006264 Mg2+ binding site [ion binding]; other site 583345006265 G-X-G motif; other site 583345006266 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 583345006267 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 583345006268 active site 583345006269 phosphorylation site [posttranslational modification] 583345006270 intermolecular recognition site; other site 583345006271 dimerization interface [polypeptide binding]; other site 583345006272 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 583345006273 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 583345006274 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 583345006275 putative active site [active] 583345006276 putative NTP binding site [chemical binding]; other site 583345006277 putative nucleic acid binding site [nucleotide binding]; other site 583345006278 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 583345006279 putative transposase OrfB; Reviewed; Region: PHA02517 583345006280 HTH-like domain; Region: HTH_21; pfam13276 583345006281 Integrase core domain; Region: rve; pfam00665 583345006282 Integrase core domain; Region: rve_3; pfam13683 583345006283 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 583345006284 Transposase; Region: HTH_Tnp_1; pfam01527 583345006285 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 583345006286 Z1 domain; Region: Z1; pfam10593 583345006287 Domain of unknown function (DUF4420); Region: DUF4420; pfam14390 583345006288 AIPR protein; Region: AIPR; pfam10592 583345006289 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 583345006290 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 583345006291 cofactor binding site; other site 583345006292 DNA binding site [nucleotide binding] 583345006293 substrate interaction site [chemical binding]; other site 583345006294 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3183 583345006295 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 583345006296 active site 583345006297 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 583345006298 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 583345006299 metal-binding site [ion binding] 583345006300 transcriptional activator FlhD; Provisional; Region: PRK02909 583345006301 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 583345006302 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 583345006303 AAA domain; Region: AAA_31; pfam13614 583345006304 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 583345006305 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 583345006306 EF-hand domain pair; Region: EF_hand_5; pfam13499 583345006307 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 583345006308 Ca2+ binding site [ion binding]; other site 583345006309 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 583345006310 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 583345006311 Protein of unknown function, DUF482; Region: DUF482; pfam04339 583345006312 EF-hand domain pair; Region: EF_hand_5; pfam13499 583345006313 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 583345006314 Ca2+ binding site [ion binding]; other site 583345006315 osmolarity response regulator; Provisional; Region: ompR; PRK09468 583345006316 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 583345006317 active site 583345006318 phosphorylation site [posttranslational modification] 583345006319 intermolecular recognition site; other site 583345006320 dimerization interface [polypeptide binding]; other site 583345006321 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 583345006322 DNA binding site [nucleotide binding] 583345006323 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 583345006324 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 583345006325 dimerization interface [polypeptide binding]; other site 583345006326 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 583345006327 dimer interface [polypeptide binding]; other site 583345006328 phosphorylation site [posttranslational modification] 583345006329 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 583345006330 ATP binding site [chemical binding]; other site 583345006331 Mg2+ binding site [ion binding]; other site 583345006332 G-X-G motif; other site 583345006333 siroheme synthase; Provisional; Region: cysG; PRK10637 583345006334 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 583345006335 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 583345006336 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 583345006337 active site 583345006338 SAM binding site [chemical binding]; other site 583345006339 homodimer interface [polypeptide binding]; other site 583345006340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 583345006341 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 583345006342 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 583345006343 FeS/SAM binding site; other site 583345006344 TRAM domain; Region: TRAM; pfam01938 583345006345 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 583345006346 PhoH-like protein; Region: PhoH; pfam02562 583345006347 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 583345006348 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 583345006349 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 583345006350 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 583345006351 Transporter associated domain; Region: CorC_HlyC; smart01091 583345006352 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 583345006353 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 583345006354 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 583345006355 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 583345006356 putative active site [active] 583345006357 catalytic triad [active] 583345006358 putative dimer interface [polypeptide binding]; other site 583345006359 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 583345006360 dimer interface [polypeptide binding]; other site 583345006361 motif 1; other site 583345006362 active site 583345006363 motif 2; other site 583345006364 motif 3; other site 583345006365 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 583345006366 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 583345006367 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 583345006368 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 583345006369 active site 583345006370 motif I; other site 583345006371 motif II; other site 583345006372 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 583345006373 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 583345006374 putative acyl-acceptor binding pocket; other site 583345006375 Protein of unknown function DUF45; Region: DUF45; pfam01863 583345006376 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 583345006377 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 583345006378 Cu(I) binding site [ion binding]; other site 583345006379 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 583345006380 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 583345006381 homodimer interface [polypeptide binding]; other site 583345006382 substrate-cofactor binding pocket; other site 583345006383 catalytic residue [active] 583345006384 Zinc-finger domain; Region: zf-CHCC; cl01821 583345006385 glutamate racemase; Provisional; Region: PRK00865 583345006386 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 583345006387 poly(A) polymerase; Region: pcnB; TIGR01942 583345006388 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 583345006389 active site 583345006390 NTP binding site [chemical binding]; other site 583345006391 metal binding triad [ion binding]; metal-binding site 583345006392 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 583345006393 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 583345006394 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 583345006395 catalytic center binding site [active] 583345006396 ATP binding site [chemical binding]; other site 583345006397 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 583345006398 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 583345006399 Substrate-binding site [chemical binding]; other site 583345006400 Substrate specificity [chemical binding]; other site 583345006401 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 583345006402 oligomerization interface [polypeptide binding]; other site 583345006403 active site 583345006404 metal binding site [ion binding]; metal-binding site 583345006405 pantoate--beta-alanine ligase; Region: panC; TIGR00018 583345006406 Pantoate-beta-alanine ligase; Region: PanC; cd00560 583345006407 active site 583345006408 ATP-binding site [chemical binding]; other site 583345006409 pantoate-binding site; other site 583345006410 HXXH motif; other site 583345006411 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 583345006412 tetramerization interface [polypeptide binding]; other site 583345006413 active site 583345006414 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 583345006415 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 583345006416 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 583345006417 DNA photolyase; Region: DNA_photolyase; pfam00875 583345006418 VacJ like lipoprotein; Region: VacJ; cl01073 583345006419 peptidase PmbA; Provisional; Region: PRK11040 583345006420 hypothetical protein; Provisional; Region: PRK05255 583345006421 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 583345006422 CPxP motif; other site 583345006423 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 583345006424 protein binding site [polypeptide binding]; other site 583345006425 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 583345006426 MPT binding site; other site 583345006427 trimer interface [polypeptide binding]; other site 583345006428 thiamine monophosphate kinase; Provisional; Region: PRK05731 583345006429 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 583345006430 ATP binding site [chemical binding]; other site 583345006431 dimerization interface [polypeptide binding]; other site 583345006432 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 583345006433 tetramer interfaces [polypeptide binding]; other site 583345006434 binuclear metal-binding site [ion binding]; other site 583345006435 Competence-damaged protein; Region: CinA; cl00666 583345006436 recombinase A; Provisional; Region: recA; PRK09354 583345006437 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 583345006438 hexamer interface [polypeptide binding]; other site 583345006439 Walker A motif; other site 583345006440 ATP binding site [chemical binding]; other site 583345006441 Walker B motif; other site 583345006442 RecX family; Region: RecX; cl00936 583345006443 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 583345006444 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 583345006445 motif 1; other site 583345006446 active site 583345006447 motif 2; other site 583345006448 motif 3; other site 583345006449 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 583345006450 aspartate kinase; Reviewed; Region: PRK06635 583345006451 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 583345006452 putative nucleotide binding site [chemical binding]; other site 583345006453 putative catalytic residues [active] 583345006454 putative Mg ion binding site [ion binding]; other site 583345006455 putative aspartate binding site [chemical binding]; other site 583345006456 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 583345006457 putative allosteric regulatory site; other site 583345006458 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 583345006459 putative allosteric regulatory residue; other site 583345006460 T5orf172 domain; Region: T5orf172; pfam10544 583345006461 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 583345006462 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 583345006463 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 583345006464 putative metal binding site [ion binding]; other site 583345006465 putative homodimer interface [polypeptide binding]; other site 583345006466 putative homotetramer interface [polypeptide binding]; other site 583345006467 putative homodimer-homodimer interface [polypeptide binding]; other site 583345006468 putative allosteric switch controlling residues; other site 583345006469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 583345006470 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 583345006471 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 583345006472 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 583345006473 N-terminal plug; other site 583345006474 ligand-binding site [chemical binding]; other site 583345006475 multidrug efflux system protein; Provisional; Region: PRK11431 583345006476 putative metal dependent hydrolase; Provisional; Region: PRK11598 583345006477 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 583345006478 Sulfatase; Region: Sulfatase; pfam00884 583345006479 Predicted membrane protein [Function unknown]; Region: COG2510 583345006480 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 583345006481 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 583345006482 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 583345006483 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 583345006484 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 583345006485 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 583345006486 ATP cone domain; Region: ATP-cone; pfam03477 583345006487 Class I ribonucleotide reductase; Region: RNR_I; cd01679 583345006488 active site 583345006489 dimer interface [polypeptide binding]; other site 583345006490 catalytic residues [active] 583345006491 effector binding site; other site 583345006492 R2 peptide binding site; other site 583345006493 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 583345006494 dimer interface [polypeptide binding]; other site 583345006495 putative radical transfer pathway; other site 583345006496 diiron center [ion binding]; other site 583345006497 tyrosyl radical; other site 583345006498 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 583345006499 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 583345006500 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 583345006501 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 583345006502 GAF domain; Region: GAF; pfam01590 583345006503 PAS fold; Region: PAS_3; pfam08447 583345006504 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 583345006505 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345006506 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345006507 metal binding site [ion binding]; metal-binding site 583345006508 active site 583345006509 I-site; other site 583345006510 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 583345006511 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345006512 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345006513 metal binding site [ion binding]; metal-binding site 583345006514 active site 583345006515 I-site; other site 583345006516 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 583345006517 PAS fold; Region: PAS_3; pfam08447 583345006518 PAS fold; Region: PAS_4; pfam08448 583345006519 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 583345006520 PAS fold; Region: PAS_3; pfam08447 583345006521 putative active site [active] 583345006522 heme pocket [chemical binding]; other site 583345006523 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345006524 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345006525 metal binding site [ion binding]; metal-binding site 583345006526 active site 583345006527 I-site; other site 583345006528 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 583345006529 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 583345006530 S-adenosylmethionine binding site [chemical binding]; other site 583345006531 signal recognition particle protein; Provisional; Region: PRK10867 583345006532 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 583345006533 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 583345006534 P loop; other site 583345006535 GTP binding site [chemical binding]; other site 583345006536 Signal peptide binding domain; Region: SRP_SPB; pfam02978 583345006537 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 583345006538 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 583345006539 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 583345006540 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 583345006541 EamA-like transporter family; Region: EamA; pfam00892 583345006542 acyl-CoA synthetase; Validated; Region: PRK05850 583345006543 2-isopropylmalate synthase; Validated; Region: PRK00915 583345006544 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 583345006545 active site 583345006546 catalytic residues [active] 583345006547 metal binding site [ion binding]; metal-binding site 583345006548 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 583345006549 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 583345006550 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 583345006551 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 583345006552 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 583345006553 ligand binding site [chemical binding]; other site 583345006554 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 583345006555 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 583345006556 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 583345006557 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 583345006558 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 583345006559 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 583345006560 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 583345006561 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 583345006562 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 583345006563 Protein export membrane protein; Region: SecD_SecF; pfam02355 583345006564 Domain of unknown function DUF21; Region: DUF21; pfam01595 583345006565 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 583345006566 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 583345006567 Transporter associated domain; Region: CorC_HlyC; smart01091 583345006568 Uncharacterized conserved protein [Function unknown]; Region: COG2127 583345006569 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 583345006570 Clp amino terminal domain; Region: Clp_N; pfam02861 583345006571 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 583345006572 Walker A motif; other site 583345006573 ATP binding site [chemical binding]; other site 583345006574 Walker B motif; other site 583345006575 arginine finger; other site 583345006576 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 583345006577 Walker A motif; other site 583345006578 ATP binding site [chemical binding]; other site 583345006579 Walker B motif; other site 583345006580 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 583345006581 UPF0126 domain; Region: UPF0126; pfam03458 583345006582 Predicted membrane protein [Function unknown]; Region: COG2860 583345006583 UPF0126 domain; Region: UPF0126; pfam03458 583345006584 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 583345006585 GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega 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_Omega_like; cd03060 583345006586 putative GSH binding site (G-site) [chemical binding]; other site 583345006587 active site cysteine [active] 583345006588 putative C-terminal domain interface [polypeptide binding]; other site 583345006589 putative dimer interface [polypeptide binding]; other site 583345006590 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 583345006591 putative N-terminal domain interface [polypeptide binding]; other site 583345006592 putative dimer interface [polypeptide binding]; other site 583345006593 putative substrate binding pocket (H-site) [chemical binding]; other site 583345006594 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 583345006595 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 583345006596 quinone interaction residues [chemical binding]; other site 583345006597 active site 583345006598 catalytic residues [active] 583345006599 FMN binding site [chemical binding]; other site 583345006600 substrate binding site [chemical binding]; other site 583345006601 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 583345006602 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 583345006603 putative [4Fe-4S] binding site [ion binding]; other site 583345006604 putative molybdopterin cofactor binding site [chemical binding]; other site 583345006605 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 583345006606 putative molybdopterin cofactor binding site; other site 583345006607 Uncharacterized conserved protein [Function unknown]; Region: COG2850 583345006608 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 583345006609 catalytic site [active] 583345006610 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 583345006611 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 583345006612 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 583345006613 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 583345006614 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 583345006615 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 583345006616 dihydrodipicolinate synthase; Region: dapA; TIGR00674 583345006617 dimer interface [polypeptide binding]; other site 583345006618 active site 583345006619 catalytic residue [active] 583345006620 electron transport complex protein RsxA; Provisional; Region: PRK05151 583345006621 ferredoxin; Provisional; Region: PRK08764 583345006622 Putative Fe-S cluster; Region: FeS; pfam04060 583345006623 4Fe-4S binding domain; Region: Fer4; pfam00037 583345006624 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 583345006625 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 583345006626 E3 interaction surface; other site 583345006627 SLBB domain; Region: SLBB; pfam10531 583345006628 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 583345006629 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 583345006630 FMN-binding domain; Region: FMN_bind; cl01081 583345006631 electron transport complex RsxE subunit; Provisional; Region: PRK12405 583345006632 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 583345006633 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 583345006634 minor groove reading motif; other site 583345006635 helix-hairpin-helix signature motif; other site 583345006636 substrate binding pocket [chemical binding]; other site 583345006637 active site 583345006638 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 583345006639 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4398 583345006640 FIST C domain; Region: FIST_C; pfam10442 583345006641 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 583345006642 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345006643 RNA polymerase sigma factor; Provisional; Region: PRK12520 583345006644 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 583345006645 DNA binding residues [nucleotide binding] 583345006646 Putative zinc-finger; Region: zf-HC2; pfam13490 583345006647 hypothetical protein; Provisional; Region: PRK05409 583345006648 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 583345006649 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 583345006650 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 583345006651 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 583345006652 SEC-C motif; Region: SEC-C; pfam02810 583345006653 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 583345006654 Peptidase family M23; Region: Peptidase_M23; pfam01551 583345006655 Protein of unknown function (DUF721); Region: DUF721; pfam05258 583345006656 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 583345006657 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 583345006658 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 583345006659 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 583345006660 dimer interface [polypeptide binding]; other site 583345006661 substrate binding site [chemical binding]; other site 583345006662 metal binding sites [ion binding]; metal-binding site 583345006663 Protein of unknown function (DUF1232); Region: DUF1232; pfam06803 583345006664 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 583345006665 ATP binding site [chemical binding]; other site 583345006666 active site 583345006667 substrate binding site [chemical binding]; other site 583345006668 pyruvate kinase; Provisional; Region: PRK05826 583345006669 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 583345006670 domain interfaces; other site 583345006671 active site 583345006672 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 583345006673 Phosphoglycerate kinase; Region: PGK; pfam00162 583345006674 substrate binding site [chemical binding]; other site 583345006675 hinge regions; other site 583345006676 ADP binding site [chemical binding]; other site 583345006677 catalytic site [active] 583345006678 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 583345006679 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 583345006680 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 583345006681 transketolase; Reviewed; Region: PRK12753 583345006682 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 583345006683 TPP-binding site [chemical binding]; other site 583345006684 dimer interface [polypeptide binding]; other site 583345006685 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 583345006686 PYR/PP interface [polypeptide binding]; other site 583345006687 dimer interface [polypeptide binding]; other site 583345006688 TPP binding site [chemical binding]; other site 583345006689 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 583345006690 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 583345006691 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 583345006692 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 583345006693 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 583345006694 putative catalytic residue [active] 583345006695 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 583345006696 Methyltransferase domain; Region: Methyltransf_23; pfam13489 583345006697 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 583345006698 S-adenosylmethionine binding site [chemical binding]; other site 583345006699 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 583345006700 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 583345006701 non-specific DNA binding site [nucleotide binding]; other site 583345006702 salt bridge; other site 583345006703 sequence-specific DNA binding site [nucleotide binding]; other site 583345006704 N-acetylglutamate synthase; Validated; Region: PRK05279 583345006705 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 583345006706 putative feedback inhibition sensing region; other site 583345006707 putative nucleotide binding site [chemical binding]; other site 583345006708 putative substrate binding site [chemical binding]; other site 583345006709 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 583345006710 Coenzyme A binding pocket [chemical binding]; other site 583345006711 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 583345006712 homohexameric interface [polypeptide binding]; other site 583345006713 nucleotide binding site [chemical binding]; other site 583345006714 N-acetyl-L-glutamate binding site [chemical binding]; other site 583345006715 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 583345006716 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 583345006717 motif II; other site 583345006718 division inhibitor protein; Provisional; Region: slmA; PRK09480 583345006719 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 583345006720 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 583345006721 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 583345006722 active site 583345006723 NTP binding site [chemical binding]; other site 583345006724 metal binding triad [ion binding]; metal-binding site 583345006725 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 583345006726 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345006727 Zn2+ binding site [ion binding]; other site 583345006728 Mg2+ binding site [ion binding]; other site 583345006729 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 583345006730 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 583345006731 putative NAD(P) binding site [chemical binding]; other site 583345006732 active site 583345006733 lytic murein transglycosylase; Provisional; Region: PRK11619 583345006734 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 583345006735 N-acetyl-D-glucosamine binding site [chemical binding]; other site 583345006736 catalytic residue [active] 583345006737 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 583345006738 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 583345006739 cell division protein FtsZ; Validated; Region: PRK09330 583345006740 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 583345006741 nucleotide binding site [chemical binding]; other site 583345006742 SulA interaction site; other site 583345006743 cell division protein FtsA; Region: ftsA; TIGR01174 583345006744 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 583345006745 nucleotide binding site [chemical binding]; other site 583345006746 Cell division protein FtsA; Region: FtsA; pfam14450 583345006747 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 583345006748 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 583345006749 Cell division protein FtsQ; Region: FtsQ; pfam03799 583345006750 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 583345006751 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 583345006752 D-ala D-ala ligase C-terminus; Region: Dala_Dala_lig_C; pfam07478 583345006753 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 583345006754 FAD binding domain; Region: FAD_binding_4; pfam01565 583345006755 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 583345006756 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 583345006757 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 583345006758 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 583345006759 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 583345006760 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 583345006761 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 583345006762 active site 583345006763 homodimer interface [polypeptide binding]; other site 583345006764 cell division protein FtsW; Region: ftsW; TIGR02614 583345006765 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 583345006766 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 583345006767 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 583345006768 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 583345006769 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 583345006770 Mg++ binding site [ion binding]; other site 583345006771 putative catalytic motif [active] 583345006772 putative substrate binding site [chemical binding]; other site 583345006773 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 583345006774 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 583345006775 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 583345006776 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 583345006777 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 583345006778 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 583345006779 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 583345006780 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 583345006781 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 583345006782 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 583345006783 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 583345006784 Cell division protein FtsL; Region: FtsL; pfam04999 583345006785 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 583345006786 MraW methylase family; Region: Methyltransf_5; pfam01795 583345006787 cell division protein MraZ; Reviewed; Region: PRK00326 583345006788 MraZ protein; Region: MraZ; pfam02381 583345006789 MraZ protein; Region: MraZ; pfam02381 583345006790 Putative motility protein; Region: YjfB_motility; pfam14070 583345006791 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 583345006792 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 583345006793 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 583345006794 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 583345006795 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 583345006796 LysR family transcriptional regulator; Provisional; Region: PRK14997 583345006797 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 583345006798 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 583345006799 putative effector binding pocket; other site 583345006800 dimerization interface [polypeptide binding]; other site 583345006801 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 583345006802 active site 583345006803 substrate binding pocket [chemical binding]; other site 583345006804 dimer interface [polypeptide binding]; other site 583345006805 Predicted methyltransferases [General function prediction only]; Region: COG0313 583345006806 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 583345006807 putative SAM binding site [chemical binding]; other site 583345006808 putative homodimer interface [polypeptide binding]; other site 583345006809 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 583345006810 hypothetical protein; Reviewed; Region: PRK12497 583345006811 BON domain; Region: BON; pfam04972 583345006812 BON domain; Region: BON; pfam04972 583345006813 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 583345006814 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 583345006815 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 583345006816 catalytic residues [active] 583345006817 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 583345006818 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 583345006819 catalytic residues [active] 583345006820 transcription termination factor Rho; Provisional; Region: rho; PRK09376 583345006821 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 583345006822 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 583345006823 RNA binding site [nucleotide binding]; other site 583345006824 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 583345006825 multimer interface [polypeptide binding]; other site 583345006826 Walker A motif; other site 583345006827 ATP binding site [chemical binding]; other site 583345006828 Walker B motif; other site 583345006829 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 583345006830 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 583345006831 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 583345006832 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 583345006833 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 583345006834 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 583345006835 catalytic loop [active] 583345006836 iron binding site [ion binding]; other site 583345006837 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; smart00929 583345006838 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 583345006839 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 583345006840 [4Fe-4S] binding site [ion binding]; other site 583345006841 molybdopterin cofactor binding site; other site 583345006842 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 583345006843 molybdopterin cofactor binding site; other site 583345006844 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 583345006845 putative dimer interface [polypeptide binding]; other site 583345006846 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 583345006847 SLBB domain; Region: SLBB; pfam10531 583345006848 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 583345006849 formate dehydrogenase subunit gamma; Validated; Region: PRK05988 583345006850 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 583345006851 putative dimer interface [polypeptide binding]; other site 583345006852 [2Fe-2S] cluster binding site [ion binding]; other site 583345006853 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 583345006854 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 583345006855 FeS/SAM binding site; other site 583345006856 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 583345006857 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 583345006858 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 583345006859 GTP binding site; other site 583345006860 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 583345006861 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 583345006862 dimer interface [polypeptide binding]; other site 583345006863 putative functional site; other site 583345006864 putative MPT binding site; other site 583345006865 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 583345006866 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 583345006867 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 583345006868 dimerization interface [polypeptide binding]; other site 583345006869 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 583345006870 dimer interface [polypeptide binding]; other site 583345006871 phosphorylation site [posttranslational modification] 583345006872 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 583345006873 ATP binding site [chemical binding]; other site 583345006874 Mg2+ binding site [ion binding]; other site 583345006875 G-X-G motif; other site 583345006876 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 583345006877 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 583345006878 catalytic triad [active] 583345006879 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 583345006880 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 583345006881 putative active site [active] 583345006882 PhoH-like protein; Region: PhoH; pfam02562 583345006883 lysophospholipid transporter LplT; Provisional; Region: PRK11195 583345006884 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 583345006885 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 583345006886 Cytochrome c; Region: Cytochrom_C; cl11414 583345006887 Cytochrome c; Region: Cytochrom_C; cl11414 583345006888 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein; Region: ABC_peri_MoxJ_2; TIGR03871 583345006889 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 583345006890 substrate binding pocket [chemical binding]; other site 583345006891 membrane-bound complex binding site; other site 583345006892 hinge residues; other site 583345006893 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 583345006894 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 583345006895 Trp docking motif [polypeptide binding]; other site 583345006896 dimer interface [polypeptide binding]; other site 583345006897 active site 583345006898 small subunit binding site [polypeptide binding]; other site 583345006899 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 583345006900 TAP-like protein; Region: Abhydrolase_4; pfam08386 583345006901 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 583345006902 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 583345006903 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 583345006904 ligand binding site [chemical binding]; other site 583345006905 flexible hinge region; other site 583345006906 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345006907 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 583345006908 binding surface 583345006909 TPR motif; other site 583345006910 TPR repeat; Region: TPR_11; pfam13414 583345006911 TPR repeat; Region: TPR_11; pfam13414 583345006912 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 583345006913 binding surface 583345006914 TPR motif; other site 583345006915 Tetratricopeptide repeat; Region: TPR_16; pfam13432 583345006916 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; pfam13759 583345006917 CHASE domain; Region: CHASE; pfam03924 583345006918 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345006919 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345006920 metal binding site [ion binding]; metal-binding site 583345006921 active site 583345006922 I-site; other site 583345006923 GAF domain; Region: GAF; pfam01590 583345006924 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345006925 Zn2+ binding site [ion binding]; other site 583345006926 Mg2+ binding site [ion binding]; other site 583345006927 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 583345006928 HNH endonuclease; Region: HNH; pfam01844 583345006929 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 583345006930 Beta-Casp domain; Region: Beta-Casp; smart01027 583345006931 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 583345006932 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 583345006933 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 583345006934 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 583345006935 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 583345006936 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345006937 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 583345006938 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 583345006939 DNA binding residues [nucleotide binding] 583345006940 DNA primase; Validated; Region: dnaG; PRK05667 583345006941 CHC2 zinc finger; Region: zf-CHC2; pfam01807 583345006942 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 583345006943 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 583345006944 active site 583345006945 metal binding site [ion binding]; metal-binding site 583345006946 interdomain interaction site; other site 583345006947 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 583345006948 Yqey-like protein; Region: YqeY; pfam09424 583345006949 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 583345006950 UGMP family protein; Validated; Region: PRK09604 583345006951 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 583345006952 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 583345006953 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 583345006954 homooctamer interface [polypeptide binding]; other site 583345006955 active site 583345006956 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 583345006957 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 583345006958 active site 583345006959 Int/Topo IB signature motif; other site 583345006960 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 583345006961 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 583345006962 DNA binding site [nucleotide binding] 583345006963 active site 583345006964 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 583345006965 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 583345006966 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 583345006967 RimM N-terminal domain; Region: RimM; pfam01782 583345006968 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 583345006969 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 583345006970 Ligand Binding Site [chemical binding]; other site 583345006971 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 583345006972 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 583345006973 FeS/SAM binding site; other site 583345006974 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 583345006975 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 583345006976 binding surface 583345006977 TPR motif; other site 583345006978 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 583345006979 murein hydrolase B; Provisional; Region: PRK10760; cl17906 583345006980 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 583345006981 ligand binding site [chemical binding]; other site 583345006982 translocation protein TolB; Provisional; Region: tolB; PRK02889 583345006983 TolB amino-terminal domain; Region: TolB_N; pfam04052 583345006984 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 583345006985 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 583345006986 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 583345006987 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 583345006988 TolA protein; Region: tolA_full; TIGR02794 583345006989 TonB C terminal; Region: TonB_2; pfam13103 583345006990 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 583345006991 TolR protein; Region: tolR; TIGR02801 583345006992 TolQ protein; Region: tolQ; TIGR02796 583345006993 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 583345006994 active site 583345006995 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 583345006996 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 583345006997 Walker A motif; other site 583345006998 ATP binding site [chemical binding]; other site 583345006999 Walker B motif; other site 583345007000 arginine finger; other site 583345007001 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 583345007002 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 583345007003 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 583345007004 RuvA N terminal domain; Region: RuvA_N; pfam01330 583345007005 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 583345007006 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 583345007007 active site 583345007008 putative DNA-binding cleft [nucleotide binding]; other site 583345007009 dimer interface [polypeptide binding]; other site 583345007010 hypothetical protein; Validated; Region: PRK00110 583345007011 EamA-like transporter family; Region: EamA; pfam00892 583345007012 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 583345007013 EamA-like transporter family; Region: EamA; pfam00892 583345007014 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 583345007015 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 583345007016 MarR family; Region: MarR_2; cl17246 583345007017 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 583345007018 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 583345007019 Chromate transporter; Region: Chromate_transp; pfam02417 583345007020 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 583345007021 FOG: CBS domain [General function prediction only]; Region: COG0517 583345007022 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 583345007023 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 583345007024 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 583345007025 active site 583345007026 substrate binding site [chemical binding]; other site 583345007027 FMN binding site [chemical binding]; other site 583345007028 putative catalytic residues [active] 583345007029 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 583345007030 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 583345007031 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 583345007032 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 583345007033 N-terminal plug; other site 583345007034 ligand-binding site [chemical binding]; other site 583345007035 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 583345007036 macrolide transporter subunit MacA; Provisional; Region: PRK11578 583345007037 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345007038 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345007039 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 583345007040 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 583345007041 Walker A/P-loop; other site 583345007042 ATP binding site [chemical binding]; other site 583345007043 Q-loop/lid; other site 583345007044 ABC transporter signature motif; other site 583345007045 Walker B; other site 583345007046 D-loop; other site 583345007047 H-loop/switch region; other site 583345007048 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 583345007049 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 583345007050 FtsX-like permease family; Region: FtsX; pfam02687 583345007051 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 583345007052 TolR protein; Region: tolR; TIGR02801 583345007053 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 583345007054 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 583345007055 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 583345007056 Hemin uptake protein hemP; Region: hemP; pfam10636 583345007057 Hemin uptake protein hemP; Region: hemP; pfam10636 583345007058 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 583345007059 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 583345007060 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 583345007061 RNA binding surface [nucleotide binding]; other site 583345007062 putative protease; Provisional; Region: PRK15452 583345007063 Peptidase family U32; Region: Peptidase_U32; pfam01136 583345007064 Uncharacterized conserved protein [Function unknown]; Region: COG0432 583345007065 Predicted secreted protein [Function unknown]; Region: COG5501 583345007066 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 583345007067 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 583345007068 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 583345007069 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 583345007070 dimer interface [polypeptide binding]; other site 583345007071 putative metal binding site [ion binding]; other site 583345007072 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345007073 active site 583345007074 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 583345007075 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 583345007076 dimer interface [polypeptide binding]; other site 583345007077 anticodon binding site; other site 583345007078 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 583345007079 homodimer interface [polypeptide binding]; other site 583345007080 motif 1; other site 583345007081 active site 583345007082 motif 2; other site 583345007083 GAD domain; Region: GAD; pfam02938 583345007084 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 583345007085 motif 3; other site 583345007086 Uncharacterized conserved protein [Function unknown]; Region: COG2928 583345007087 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 583345007088 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 583345007089 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 583345007090 PAS fold; Region: PAS_3; pfam08447 583345007091 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 583345007092 heme pocket [chemical binding]; other site 583345007093 putative active site [active] 583345007094 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 583345007095 PAS fold; Region: PAS_3; pfam08447 583345007096 putative active site [active] 583345007097 heme pocket [chemical binding]; other site 583345007098 PAS fold; Region: PAS_4; pfam08448 583345007099 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 583345007100 PAS domain; Region: PAS_9; pfam13426 583345007101 putative active site [active] 583345007102 heme pocket [chemical binding]; other site 583345007103 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345007104 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345007105 metal binding site [ion binding]; metal-binding site 583345007106 active site 583345007107 I-site; other site 583345007108 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 583345007109 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 583345007110 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 583345007111 molybdate transporter periplasmic protein; Provisional; Region: modA; PRK10677 583345007112 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 583345007113 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 583345007114 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 583345007115 dimer interface [polypeptide binding]; other site 583345007116 conserved gate region; other site 583345007117 putative PBP binding loops; other site 583345007118 ABC-ATPase subunit interface; other site 583345007119 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 583345007120 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 583345007121 Walker A/P-loop; other site 583345007122 ATP binding site [chemical binding]; other site 583345007123 Q-loop/lid; other site 583345007124 ABC transporter signature motif; other site 583345007125 Walker B; other site 583345007126 D-loop; other site 583345007127 H-loop/switch region; other site 583345007128 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 583345007129 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 583345007130 dimer interface [polypeptide binding]; other site 583345007131 ssDNA binding site [nucleotide binding]; other site 583345007132 tetramer (dimer of dimers) interface [polypeptide binding]; other site 583345007133 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 583345007134 Major Facilitator Superfamily; Region: MFS_1; pfam07690 583345007135 putative substrate translocation pore; other site 583345007136 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 583345007137 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 583345007138 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 583345007139 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 583345007140 HDOD domain; Region: HDOD; pfam08668 583345007141 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 583345007142 Transglycosylase; Region: Transgly; cl17702 583345007143 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 583345007144 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 583345007145 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 583345007146 shikimate binding site; other site 583345007147 NAD(P) binding site [chemical binding]; other site 583345007148 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 583345007149 active site residue [active] 583345007150 glutamine synthetase; Provisional; Region: glnA; PRK09469 583345007151 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 583345007152 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 583345007153 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 583345007154 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 583345007155 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 583345007156 putative active site [active] 583345007157 heme pocket [chemical binding]; other site 583345007158 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 583345007159 dimer interface [polypeptide binding]; other site 583345007160 phosphorylation site [posttranslational modification] 583345007161 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 583345007162 ATP binding site [chemical binding]; other site 583345007163 Mg2+ binding site [ion binding]; other site 583345007164 G-X-G motif; other site 583345007165 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 583345007166 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 583345007167 active site 583345007168 phosphorylation site [posttranslational modification] 583345007169 intermolecular recognition site; other site 583345007170 dimerization interface [polypeptide binding]; other site 583345007171 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 583345007172 Walker A motif; other site 583345007173 ATP binding site [chemical binding]; other site 583345007174 Walker B motif; other site 583345007175 arginine finger; other site 583345007176 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345007177 Gram-negative porin; Region: Porin_4; pfam13609 583345007178 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 583345007179 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345007180 Zn2+ binding site [ion binding]; other site 583345007181 Mg2+ binding site [ion binding]; other site 583345007182 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 583345007183 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 583345007184 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 583345007185 active site 583345007186 dimer interface [polypeptide binding]; other site 583345007187 metal binding site [ion binding]; metal-binding site 583345007188 shikimate kinase; Reviewed; Region: aroK; PRK00131 583345007189 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 583345007190 ADP binding site [chemical binding]; other site 583345007191 magnesium binding site [ion binding]; other site 583345007192 putative shikimate binding site; other site 583345007193 AMIN domain; Region: AMIN; pfam11741 583345007194 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 583345007195 Secretin and TonB N terminus short domain; Region: STN; smart00965 583345007196 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 583345007197 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 583345007198 Pilus assembly protein, PilP; Region: PilP; pfam04351 583345007199 Pilus assembly protein, PilO; Region: PilO; pfam04350 583345007200 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 583345007201 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 583345007202 Cell division protein FtsA; Region: FtsA; cl17206 583345007203 Competence protein A; Region: Competence_A; pfam11104 583345007204 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 583345007205 nucleotide binding site [chemical binding]; other site 583345007206 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 583345007207 Transglycosylase; Region: Transgly; pfam00912 583345007208 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 583345007209 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 583345007210 putative catalytic site [active] 583345007211 putative phosphate binding site [ion binding]; other site 583345007212 active site 583345007213 metal binding site A [ion binding]; metal-binding site 583345007214 DNA binding site [nucleotide binding] 583345007215 putative AP binding site [nucleotide binding]; other site 583345007216 putative metal binding site B [ion binding]; other site 583345007217 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 583345007218 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 583345007219 motif II; other site 583345007220 thiopurine S-methyltransferase, Se/Te detoxification family; Region: TMPT_Se_Te; TIGR03840 583345007221 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 583345007222 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 583345007223 active site 583345007224 Zn binding site [ion binding]; other site 583345007225 Tic20-like protein; Region: Tic20; pfam09685 583345007226 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 583345007227 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 583345007228 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 583345007229 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 583345007230 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 583345007231 dimerization domain swap beta strand [polypeptide binding]; other site 583345007232 regulatory protein interface [polypeptide binding]; other site 583345007233 active site 583345007234 regulatory phosphorylation site [posttranslational modification]; other site 583345007235 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 583345007236 active pocket/dimerization site; other site 583345007237 active site 583345007238 phosphorylation site [posttranslational modification] 583345007239 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 583345007240 HPr kinase/phosphorylase; Provisional; Region: PRK05428 583345007241 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 583345007242 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 583345007243 Hpr binding site; other site 583345007244 active site 583345007245 homohexamer subunit interaction site [polypeptide binding]; other site 583345007246 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 583345007247 30S subunit binding site; other site 583345007248 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 583345007249 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 583345007250 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 583345007251 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 583345007252 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 583345007253 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 583345007254 Walker A/P-loop; other site 583345007255 ATP binding site [chemical binding]; other site 583345007256 Q-loop/lid; other site 583345007257 ABC transporter signature motif; other site 583345007258 Walker B; other site 583345007259 D-loop; other site 583345007260 H-loop/switch region; other site 583345007261 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 583345007262 OstA-like protein; Region: OstA; pfam03968 583345007263 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 583345007264 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 583345007265 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 583345007266 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 583345007267 active site 583345007268 motif I; other site 583345007269 motif II; other site 583345007270 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 583345007271 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 583345007272 putative active site [active] 583345007273 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 583345007274 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 583345007275 putative cation:proton antiport protein; Provisional; Region: PRK10669 583345007276 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 583345007277 TrkA-N domain; Region: TrkA_N; pfam02254 583345007278 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 583345007279 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 583345007280 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 583345007281 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 583345007282 glutamine binding [chemical binding]; other site 583345007283 catalytic triad [active] 583345007284 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 583345007285 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 583345007286 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 583345007287 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 583345007288 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 583345007289 active site 583345007290 ribulose/triose binding site [chemical binding]; other site 583345007291 phosphate binding site [ion binding]; other site 583345007292 substrate (anthranilate) binding pocket [chemical binding]; other site 583345007293 product (indole) binding pocket [chemical binding]; other site 583345007294 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 583345007295 dimer interface [polypeptide binding]; other site 583345007296 allosteric magnesium binding site [ion binding]; other site 583345007297 active site 583345007298 aspartate-rich active site metal binding site; other site 583345007299 Schiff base residues; other site 583345007300 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 583345007301 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 583345007302 active site 583345007303 phosphorylation site [posttranslational modification] 583345007304 intermolecular recognition site; other site 583345007305 dimerization interface [polypeptide binding]; other site 583345007306 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 583345007307 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 583345007308 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 583345007309 dimerization interface [polypeptide binding]; other site 583345007310 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 583345007311 dimer interface [polypeptide binding]; other site 583345007312 phosphorylation site [posttranslational modification] 583345007313 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 583345007314 ATP binding site [chemical binding]; other site 583345007315 Mg2+ binding site [ion binding]; other site 583345007316 G-X-G motif; other site 583345007317 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 583345007318 16S rRNA methyltransferase B; Provisional; Region: PRK10901 583345007319 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 583345007320 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 583345007321 S-adenosylmethionine binding site [chemical binding]; other site 583345007322 M48 family peptidase; Provisional; Region: PRK03001 583345007323 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 583345007324 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 583345007325 putative active site [active] 583345007326 substrate binding site [chemical binding]; other site 583345007327 putative cosubstrate binding site; other site 583345007328 catalytic site [active] 583345007329 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 583345007330 substrate binding site [chemical binding]; other site 583345007331 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 583345007332 active site 583345007333 catalytic residues [active] 583345007334 metal binding site [ion binding]; metal-binding site 583345007335 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 583345007336 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 583345007337 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 583345007338 DNA protecting protein DprA; Region: dprA; TIGR00732 583345007339 Protein of unknown function (DUF494); Region: DUF494; pfam04361 583345007340 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 583345007341 FAD binding site [chemical binding]; other site 583345007342 Membrane protein of unknown function; Region: DUF360; pfam04020 583345007343 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 583345007344 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 583345007345 homotetramer interface [polypeptide binding]; other site 583345007346 ligand binding site [chemical binding]; other site 583345007347 catalytic site [active] 583345007348 NAD binding site [chemical binding]; other site 583345007349 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 583345007350 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 583345007351 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 583345007352 Zn2+ binding site [ion binding]; other site 583345007353 Mg2+ binding site [ion binding]; other site 583345007354 S-adenosylmethionine synthetase; Validated; Region: PRK05250 583345007355 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 583345007356 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 583345007357 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 583345007358 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 583345007359 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 583345007360 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 583345007361 Protein of unknown function, DUF484; Region: DUF484; cl17449 583345007362 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 583345007363 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 583345007364 active site 583345007365 DNA binding site [nucleotide binding] 583345007366 Int/Topo IB signature motif; other site 583345007367 superoxide dismutase; Provisional; Region: PRK10543 583345007368 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 583345007369 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 583345007370 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 583345007371 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 583345007372 N-terminal plug; other site 583345007373 ligand-binding site [chemical binding]; other site 583345007374 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 583345007375 oxidative damage protection protein; Provisional; Region: PRK05408 583345007376 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 583345007377 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 583345007378 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 583345007379 lipoyl attachment site [posttranslational modification]; other site 583345007380 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 583345007381 multifunctional aminopeptidase A; Provisional; Region: PRK00913 583345007382 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 583345007383 interface (dimer of trimers) [polypeptide binding]; other site 583345007384 Substrate-binding/catalytic site; other site 583345007385 Zn-binding sites [ion binding]; other site 583345007386 Predicted permeases [General function prediction only]; Region: COG0795 583345007387 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 583345007388 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 583345007389 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 583345007390 RDD family; Region: RDD; pfam06271 583345007391 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 583345007392 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 583345007393 RNA polymerase factor sigma-70; Validated; Region: PRK09047 583345007394 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 583345007395 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 583345007396 DNA binding residues [nucleotide binding] 583345007397 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 583345007398 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 583345007399 dimer interface [polypeptide binding]; other site 583345007400 phosphorylation site [posttranslational modification] 583345007401 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 583345007402 ATP binding site [chemical binding]; other site 583345007403 Mg2+ binding site [ion binding]; other site 583345007404 G-X-G motif; other site 583345007405 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 583345007406 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 583345007407 active site 583345007408 phosphorylation site [posttranslational modification] 583345007409 intermolecular recognition site; other site 583345007410 dimerization interface [polypeptide binding]; other site 583345007411 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 583345007412 Walker A motif; other site 583345007413 ATP binding site [chemical binding]; other site 583345007414 Walker B motif; other site 583345007415 arginine finger; other site 583345007416 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 583345007417 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 583345007418 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 583345007419 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 583345007420 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 583345007421 amidase catalytic site [active] 583345007422 Zn binding residues [ion binding]; other site 583345007423 substrate binding site [chemical binding]; other site 583345007424 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345007425 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345007426 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345007427 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 583345007428 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 583345007429 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 583345007430 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 583345007431 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 583345007432 S-adenosylmethionine binding site [chemical binding]; other site 583345007433 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 583345007434 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 583345007435 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 583345007436 dimerization interface [polypeptide binding]; other site 583345007437 putative ATP binding site [chemical binding]; other site 583345007438 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 583345007439 Domain of unknown function DUF20; Region: UPF0118; pfam01594 583345007440 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 583345007441 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 583345007442 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 583345007443 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 583345007444 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 583345007445 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 583345007446 catalytic residue [active] 583345007447 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 583345007448 catalytic residues [active] 583345007449 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 583345007450 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 583345007451 peroxiredoxin; Region: AhpC; TIGR03137 583345007452 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 583345007453 dimer interface [polypeptide binding]; other site 583345007454 decamer (pentamer of dimers) interface [polypeptide binding]; other site 583345007455 catalytic triad [active] 583345007456 peroxidatic and resolving cysteines [active] 583345007457 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 583345007458 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 583345007459 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 583345007460 Peptidase family M48; Region: Peptidase_M48; pfam01435 583345007461 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 583345007462 trimer interface [polypeptide binding]; other site 583345007463 dimer interface [polypeptide binding]; other site 583345007464 putative active site [active] 583345007465 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 583345007466 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345007467 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345007468 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345007469 Outer membrane efflux protein; Region: OEP; pfam02321 583345007470 Outer membrane efflux protein; Region: OEP; pfam02321 583345007471 MASE1; Region: MASE1; pfam05231 583345007472 PAS domain S-box; Region: sensory_box; TIGR00229 583345007473 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 583345007474 putative active site [active] 583345007475 heme pocket [chemical binding]; other site 583345007476 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 583345007477 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 583345007478 metal binding site [ion binding]; metal-binding site 583345007479 active site 583345007480 I-site; other site 583345007481 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 583345007482 anthranilate synthase component I; Provisional; Region: PRK13565 583345007483 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 583345007484 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 583345007485 phosphoglycolate phosphatase; Provisional; Region: PRK13222 583345007486 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 583345007487 motif II; other site 583345007488 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 583345007489 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 583345007490 substrate binding site [chemical binding]; other site 583345007491 hexamer interface [polypeptide binding]; other site 583345007492 metal binding site [ion binding]; metal-binding site 583345007493 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 583345007494 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 583345007495 tRNA; other site 583345007496 putative tRNA binding site [nucleotide binding]; other site 583345007497 putative NADP binding site [chemical binding]; other site 583345007498 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 583345007499 peptide chain release factor 1; Validated; Region: prfA; PRK00591 583345007500 This domain is found in peptide chain release factors; Region: PCRF; smart00937 583345007501 RF-1 domain; Region: RF-1; pfam00472 583345007502 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 583345007503 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 583345007504 S-adenosylmethionine binding site [chemical binding]; other site 583345007505 Sensors of blue-light using FAD; Region: BLUF; pfam04940 583345007506 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 583345007507 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 583345007508 Methyltransferase domain; Region: Methyltransf_31; pfam13847 583345007509 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 583345007510 S-adenosylmethionine binding site [chemical binding]; other site 583345007511 muropeptide transporter; Reviewed; Region: ampG; PRK11902 583345007512 AmpG-like permease; Region: 2A0125; TIGR00901 583345007513 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 583345007514 putative active site [active] 583345007515 putative catalytic site [active] 583345007516 putative DNA binding site [nucleotide binding]; other site 583345007517 putative phosphate binding site [ion binding]; other site 583345007518 metal binding site A [ion binding]; metal-binding site 583345007519 putative AP binding site [nucleotide binding]; other site 583345007520 putative metal binding site B [ion binding]; other site 583345007521 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 583345007522 active site 583345007523 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 583345007524 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 583345007525 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 583345007526 GatB domain; Region: GatB_Yqey; smart00845 583345007527 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 583345007528 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 583345007529 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 583345007530 rod shape-determining protein MreB; Provisional; Region: PRK13927 583345007531 MreB and similar proteins; Region: MreB_like; cd10225 583345007532 nucleotide binding site [chemical binding]; other site 583345007533 Mg binding site [ion binding]; other site 583345007534 putative protofilament interaction site [polypeptide binding]; other site 583345007535 RodZ interaction site [polypeptide binding]; other site 583345007536 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 583345007537 rod shape-determining protein MreC; Region: MreC; pfam04085 583345007538 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 583345007539 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 583345007540 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 583345007541 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 583345007542 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 583345007543 rare lipoprotein A; Provisional; Region: PRK10672 583345007544 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 583345007545 Sporulation related domain; Region: SPOR; pfam05036 583345007546 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 583345007547 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 583345007548 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 583345007549 Protein of unknown function (DUF493); Region: DUF493; pfam04359 583345007550 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 583345007551 lipoyl synthase; Provisional; Region: PRK05481 583345007552 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 583345007553 FeS/SAM binding site; other site 583345007554 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 583345007555 Glutamate-cysteine ligase; Region: GshA; pfam08886 583345007556 glutathione synthetase; Provisional; Region: PRK05246 583345007557 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 583345007558 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 583345007559 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 583345007560 ApbE family; Region: ApbE; pfam02424 583345007561 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 583345007562 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 583345007563 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 583345007564 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 583345007565 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 583345007566 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 583345007567 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 583345007568 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 583345007569 Type II transport protein GspH; Region: GspH; pfam12019 583345007570 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 583345007571 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 583345007572 diaminopimelate decarboxylase; Region: lysA; TIGR01048 583345007573 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 583345007574 active site 583345007575 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 583345007576 substrate binding site [chemical binding]; other site 583345007577 catalytic residues [active] 583345007578 dimer interface [polypeptide binding]; other site 583345007579 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 583345007580 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 583345007581 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 583345007582 putative active site [active] 583345007583 putative substrate binding site [chemical binding]; other site 583345007584 putative cosubstrate binding site; other site 583345007585 catalytic site [active] 583345007586 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 583345007587 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 583345007588 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_7; cd04664 583345007589 nudix motif; other site 583345007590 quinolinate synthetase; Provisional; Region: PRK09375 583345007591 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 583345007592 HIT family signature motif; other site 583345007593 catalytic residue [active] 583345007594 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 583345007595 dimer interface [polypeptide binding]; other site 583345007596 [2Fe-2S] cluster binding site [ion binding]; other site 583345007597 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 583345007598 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 583345007599 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 583345007600 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 583345007601 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 583345007602 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 583345007603 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 583345007604 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 583345007605 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 583345007606 substrate binding pocket [chemical binding]; other site 583345007607 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 583345007608 B12 binding site [chemical binding]; other site 583345007609 cobalt ligand [ion binding]; other site 583345007610 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 583345007611 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 583345007612 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 583345007613 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 583345007614 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 583345007615 Membrane fusogenic activity; Region: BMFP; pfam04380 583345007616 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 583345007617 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 583345007618 Nitrogen regulatory protein P-II; Region: P-II; smart00938 583345007619 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 583345007620 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 583345007621 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 583345007622 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345007623 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345007624 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345007625 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 583345007626 dimerization interface [polypeptide binding]; other site 583345007627 putative DNA binding site [nucleotide binding]; other site 583345007628 putative Zn2+ binding site [ion binding]; other site 583345007629 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 583345007630 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 583345007631 putative acyl-acceptor binding pocket; other site 583345007632 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 583345007633 acyl-activating enzyme (AAE) consensus motif; other site 583345007634 putative AMP binding site [chemical binding]; other site 583345007635 H+ Antiporter protein; Region: 2A0121; TIGR00900 583345007636 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 583345007637 Sulfatase; Region: Sulfatase; pfam00884 583345007638 MltA specific insert domain; Region: MltA; smart00925 583345007639 3D domain; Region: 3D; pfam06725 583345007640 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 583345007641 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 583345007642 ThiS interaction site; other site 583345007643 putative active site [active] 583345007644 tetramer interface [polypeptide binding]; other site 583345007645 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 583345007646 thiS-thiF/thiG interaction site; other site 583345007647 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 583345007648 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 583345007649 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 583345007650 substrate binding site [chemical binding]; other site 583345007651 active site 583345007652 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 583345007653 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 583345007654 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 583345007655 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 583345007656 active site 583345007657 dimer interface [polypeptide binding]; other site 583345007658 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 583345007659 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 583345007660 active site 583345007661 FMN binding site [chemical binding]; other site 583345007662 substrate binding site [chemical binding]; other site 583345007663 3Fe-4S cluster binding site [ion binding]; other site 583345007664 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 583345007665 domain interface; other site 583345007666 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 583345007667 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 583345007668 inhibitor-cofactor binding pocket; inhibition site 583345007669 pyridoxal 5'-phosphate binding site [chemical binding]; other site 583345007670 catalytic residue [active] 583345007671 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 583345007672 thiamine phosphate binding site [chemical binding]; other site 583345007673 active site 583345007674 pyrophosphate binding site [ion binding]; other site 583345007675 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 583345007676 substrate binding site [chemical binding]; other site 583345007677 dimer interface [polypeptide binding]; other site 583345007678 ATP binding site [chemical binding]; other site 583345007679 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 583345007680 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 583345007681 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 583345007682 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 583345007683 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 583345007684 HlyD family secretion protein; Region: HlyD_3; pfam13437 583345007685 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 583345007686 Nitrogen regulatory protein P-II; Region: P-II; smart00938 583345007687 primosome assembly protein PriA; Validated; Region: PRK05580 583345007688 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 583345007689 ATP binding site [chemical binding]; other site 583345007690 putative Mg++ binding site [ion binding]; other site 583345007691 helicase superfamily c-terminal domain; Region: HELICc; smart00490 583345007692 ATP-binding site [chemical binding]; other site 583345007693 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 583345007694 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 583345007695 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 583345007696 active site 583345007697 HIGH motif; other site 583345007698 KMSK motif region; other site 583345007699 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 583345007700 tRNA binding surface [nucleotide binding]; other site 583345007701 anticodon binding site; other site 583345007702 Sporulation related domain; Region: SPOR; pfam05036 583345007703 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 583345007704 catalytic residues [active] 583345007705 hinge region; other site 583345007706 alpha helical domain; other site 583345007707 short chain dehydrogenase; Provisional; Region: PRK07024 583345007708 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 583345007709 NAD(P) binding site [chemical binding]; other site 583345007710 active site 583345007711 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 583345007712 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345007713 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345007714 ABC transporter; Region: ABC_tran_2; pfam12848 583345007715 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 583345007716 YaeQ protein; Region: YaeQ; pfam07152 583345007717 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 583345007718 cyclase homology domain; Region: CHD; cd07302 583345007719 nucleotidyl binding site; other site 583345007720 metal binding site [ion binding]; metal-binding site 583345007721 dimer interface [polypeptide binding]; other site 583345007722 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 583345007723 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 583345007724 glutaminase active site [active] 583345007725 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 583345007726 dimer interface [polypeptide binding]; other site 583345007727 active site 583345007728 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 583345007729 dimer interface [polypeptide binding]; other site 583345007730 active site 583345007731 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 583345007732 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 583345007733 Substrate binding site; other site 583345007734 Mg++ binding site; other site 583345007735 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 583345007736 active site 583345007737 substrate binding site [chemical binding]; other site 583345007738 CoA binding site [chemical binding]; other site 583345007739 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 583345007740 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 583345007741 gamma subunit interface [polypeptide binding]; other site 583345007742 epsilon subunit interface [polypeptide binding]; other site 583345007743 LBP interface [polypeptide binding]; other site 583345007744 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 583345007745 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 583345007746 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 583345007747 alpha subunit interaction interface [polypeptide binding]; other site 583345007748 Walker A motif; other site 583345007749 ATP binding site [chemical binding]; other site 583345007750 Walker B motif; other site 583345007751 inhibitor binding site; inhibition site 583345007752 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 583345007753 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 583345007754 core domain interface [polypeptide binding]; other site 583345007755 delta subunit interface [polypeptide binding]; other site 583345007756 epsilon subunit interface [polypeptide binding]; other site 583345007757 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 583345007758 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 583345007759 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 583345007760 beta subunit interaction interface [polypeptide binding]; other site 583345007761 Walker A motif; other site 583345007762 ATP binding site [chemical binding]; other site 583345007763 Walker B motif; other site 583345007764 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 583345007765 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 583345007766 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 583345007767 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 583345007768 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 583345007769 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 583345007770 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 583345007771 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 583345007772 ParB-like nuclease domain; Region: ParBc; pfam02195 583345007773 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 583345007774 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 583345007775 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 583345007776 P-loop; other site 583345007777 Magnesium ion binding site [ion binding]; other site 583345007778 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 583345007779 Magnesium ion binding site [ion binding]; other site 583345007780 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 583345007781 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 583345007782 S-adenosylmethionine binding site [chemical binding]; other site 583345007783 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 583345007784 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 583345007785 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 583345007786 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 583345007787 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 583345007788 Uncharacterized conserved protein [Function unknown]; Region: COG3422 583345007789 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 583345007790 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 583345007791 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 583345007792 trmE is a tRNA modification GTPase; Region: trmE; cd04164 583345007793 G1 box; other site 583345007794 GTP/Mg2+ binding site [chemical binding]; other site 583345007795 Switch I region; other site 583345007796 G2 box; other site 583345007797 Switch II region; other site 583345007798 G3 box; other site 583345007799 G4 box; other site 583345007800 G5 box; other site 583345007801 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 583345007802 membrane protein insertase; Provisional; Region: PRK01318 583345007803 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 583345007804 Haemolytic domain; Region: Haemolytic; pfam01809 583345007805 ribonuclease P; Reviewed; Region: rnpA; PRK04390 583345007806 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399