-- dump date 20140618_205856 -- class Genbank::misc_feature -- table misc_feature_note -- id note 62928000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 62928000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 62928000003 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 62928000004 Walker A motif; other site 62928000005 ATP binding site [chemical binding]; other site 62928000006 Walker B motif; other site 62928000007 arginine finger; other site 62928000008 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 62928000009 DnaA box-binding interface [nucleotide binding]; other site 62928000010 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 62928000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 62928000012 putative DNA binding surface [nucleotide binding]; other site 62928000013 dimer interface [polypeptide binding]; other site 62928000014 beta-clamp/clamp loader binding surface; other site 62928000015 beta-clamp/translesion DNA polymerase binding surface; other site 62928000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 62928000017 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 62928000018 ATP binding site [chemical binding]; other site 62928000019 Mg2+ binding site [ion binding]; other site 62928000020 G-X-G motif; other site 62928000021 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 62928000022 anchoring element; other site 62928000023 dimer interface [polypeptide binding]; other site 62928000024 ATP binding site [chemical binding]; other site 62928000025 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 62928000026 active site 62928000027 putative metal-binding site [ion binding]; other site 62928000028 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 62928000029 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 62928000030 HsdM N-terminal domain; Region: HsdM_N; pfam12161 62928000031 Methyltransferase domain; Region: Methyltransf_26; pfam13659 62928000032 Divergent AAA domain; Region: AAA_4; pfam04326 62928000033 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 62928000034 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 62928000035 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 62928000036 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 62928000037 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 62928000038 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea; Region: GIY-YIG_unchar_2; cd10447 62928000039 putative active site [active] 62928000040 GIY-YIG motif/motif A; other site 62928000041 putative metal binding site [ion binding]; other site 62928000042 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 62928000043 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 62928000044 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 62928000045 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 62928000046 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 62928000047 ATP binding site [chemical binding]; other site 62928000048 putative Mg++ binding site [ion binding]; other site 62928000049 short chain dehydrogenase; Provisional; Region: PRK06180 62928000050 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 62928000051 NADP binding site [chemical binding]; other site 62928000052 active site 62928000053 steroid binding site; other site 62928000054 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928000055 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928000056 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 62928000057 putative effector binding pocket; other site 62928000058 dimerization interface [polypeptide binding]; other site 62928000059 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 62928000060 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 62928000061 active site 62928000062 flavodoxin FldA; Validated; Region: PRK09267 62928000063 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 62928000064 MOSC domain; Region: MOSC; pfam03473 62928000065 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 62928000066 putative metal binding site [ion binding]; other site 62928000067 intracellular protease, PfpI family; Region: PfpI; TIGR01382 62928000068 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 62928000069 conserved cys residue [active] 62928000070 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928000071 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 62928000072 putative ligand binding site [chemical binding]; other site 62928000073 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928000074 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 62928000075 putative effector binding pocket; other site 62928000076 putative dimerization interface [polypeptide binding]; other site 62928000077 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 62928000078 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 62928000079 catalytic loop [active] 62928000080 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 62928000081 iron binding site [ion binding]; other site 62928000082 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 62928000083 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 62928000084 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 62928000085 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 62928000086 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 62928000087 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 62928000088 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 62928000089 XdhC Rossmann domain; Region: XdhC_C; pfam13478 62928000090 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 62928000091 Ligand binding site; other site 62928000092 metal-binding site 62928000093 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 62928000094 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 62928000095 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 62928000096 NAD binding site [chemical binding]; other site 62928000097 putative substrate binding site 2 [chemical binding]; other site 62928000098 putative substrate binding site 1 [chemical binding]; other site 62928000099 active site 62928000100 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 62928000101 active site 62928000102 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 62928000103 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 62928000104 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928000105 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928000106 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 62928000107 dimerization interface [polypeptide binding]; other site 62928000108 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 62928000109 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 62928000110 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 62928000111 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 62928000112 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 62928000113 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 62928000114 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 62928000115 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928000116 short chain dehydrogenase; Validated; Region: PRK07069 62928000117 NAD(P) binding site [chemical binding]; other site 62928000118 active site 62928000119 YcaO domain protein; Region: TIGR03549 62928000120 OsmC-like protein; Region: OsmC; pfam02566 62928000121 YcaO-like family; Region: YcaO; pfam02624 62928000122 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928000123 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928000124 short chain dehydrogenase; Provisional; Region: PRK06172 62928000125 classical (c) SDRs; Region: SDR_c; cd05233 62928000126 NAD(P) binding site [chemical binding]; other site 62928000127 active site 62928000128 Protein of unknown function (DUF1134); Region: DUF1134; pfam06577 62928000129 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 62928000130 putative active site [active] 62928000131 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 62928000132 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 62928000133 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 62928000134 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928000135 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 62928000136 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 62928000137 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 62928000138 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 62928000139 Predicted secreted protein [Function unknown]; Region: COG5445 62928000140 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 62928000141 Predicted secreted protein [Function unknown]; Region: COG5445 62928000142 Stage II sporulation protein; Region: SpoIID; pfam08486 62928000143 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 62928000144 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 62928000145 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 62928000146 Mechanosensitive ion channel; Region: MS_channel; pfam00924 62928000147 PGAP1-like protein; Region: PGAP1; pfam07819 62928000148 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928000149 Alpha/beta hydrolase of unknown function (DUF915); Region: DUF915; pfam06028 62928000150 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 62928000151 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 62928000152 dimer interface [polypeptide binding]; other site 62928000153 phosphorylation site [posttranslational modification] 62928000154 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 62928000155 ATP binding site [chemical binding]; other site 62928000156 Mg2+ binding site [ion binding]; other site 62928000157 G-X-G motif; other site 62928000158 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928000159 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 62928000160 active site 62928000161 phosphorylation site [posttranslational modification] 62928000162 intermolecular recognition site; other site 62928000163 dimerization interface [polypeptide binding]; other site 62928000164 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 62928000165 DNA binding site [nucleotide binding] 62928000166 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928000167 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 62928000168 Walker A/P-loop; other site 62928000169 ATP binding site [chemical binding]; other site 62928000170 Q-loop/lid; other site 62928000171 ABC transporter signature motif; other site 62928000172 Walker B; other site 62928000173 D-loop; other site 62928000174 H-loop/switch region; other site 62928000175 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 62928000176 FtsX-like permease family; Region: FtsX; pfam02687 62928000177 MG2 domain; Region: A2M_N; pfam01835 62928000178 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 62928000179 Alpha-2-macroglobulin family; Region: A2M; pfam00207 62928000180 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 62928000181 Protein of unknown function (DUF1175); Region: DUF1175; pfam06672 62928000182 Uncharacterized protein conserved in bacteria (DUF2138); Region: DUF2138; pfam09909 62928000183 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 62928000184 Protein of unknown function DUF86; Region: DUF86; cl01031 62928000185 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 62928000186 Domain of unknown function DUF20; Region: UPF0118; pfam01594 62928000187 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 62928000188 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 62928000189 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928000190 substrate binding site [chemical binding]; other site 62928000191 oxyanion hole (OAH) forming residues; other site 62928000192 trimer interface [polypeptide binding]; other site 62928000193 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 62928000194 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 62928000195 active site 62928000196 catalytic site [active] 62928000197 substrate binding site [chemical binding]; other site 62928000198 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 62928000199 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 62928000200 heme-binding site [chemical binding]; other site 62928000201 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928000202 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 62928000203 active site 62928000204 phosphorylation site [posttranslational modification] 62928000205 intermolecular recognition site; other site 62928000206 dimerization interface [polypeptide binding]; other site 62928000207 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 62928000208 Walker A motif; other site 62928000209 ATP binding site [chemical binding]; other site 62928000210 Walker B motif; other site 62928000211 arginine finger; other site 62928000212 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928000213 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 62928000214 dimer interface [polypeptide binding]; other site 62928000215 phosphorylation site [posttranslational modification] 62928000216 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 62928000217 ATP binding site [chemical binding]; other site 62928000218 Mg2+ binding site [ion binding]; other site 62928000219 G-X-G motif; other site 62928000220 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 62928000221 putative substrate translocation pore; other site 62928000222 von Willebrand factor; Region: vWF_A; pfam12450 62928000223 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 62928000224 VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b...; Region: vWA_subgroup; cd01465 62928000225 metal ion-dependent adhesion site (MIDAS); other site 62928000226 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 62928000227 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928000228 RNA polymerase sigma factor, SigM family; Region: SigM_subfam; TIGR02950 62928000229 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 62928000230 DNA binding residues [nucleotide binding] 62928000231 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 62928000232 hypothetical protein; Reviewed; Region: PRK09588 62928000233 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 62928000234 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 62928000235 G1 box; other site 62928000236 putative GEF interaction site [polypeptide binding]; other site 62928000237 GTP/Mg2+ binding site [chemical binding]; other site 62928000238 Switch I region; other site 62928000239 G2 box; other site 62928000240 G3 box; other site 62928000241 Switch II region; other site 62928000242 G4 box; other site 62928000243 G5 box; other site 62928000244 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 62928000245 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 62928000246 catalytic motif [active] 62928000247 Catalytic residue [active] 62928000248 recombination associated protein; Reviewed; Region: rdgC; PRK00321 62928000249 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 62928000250 putative hydrophobic ligand binding site [chemical binding]; other site 62928000251 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 62928000252 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 62928000253 active site 62928000254 uracil binding [chemical binding]; other site 62928000255 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 62928000256 elongation factor P; Validated; Region: PRK00529 62928000257 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 62928000258 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 62928000259 RNA binding site [nucleotide binding]; other site 62928000260 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 62928000261 RNA binding site [nucleotide binding]; other site 62928000262 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 62928000263 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928000264 Walker A/P-loop; other site 62928000265 ATP binding site [chemical binding]; other site 62928000266 Q-loop/lid; other site 62928000267 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 62928000268 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928000269 Walker A/P-loop; other site 62928000270 ATP binding site [chemical binding]; other site 62928000271 Q-loop/lid; other site 62928000272 ABC transporter signature motif; other site 62928000273 Walker B; other site 62928000274 D-loop; other site 62928000275 H-loop/switch region; other site 62928000276 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 62928000277 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 62928000278 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 62928000279 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928000280 Walker A/P-loop; other site 62928000281 ATP binding site [chemical binding]; other site 62928000282 Q-loop/lid; other site 62928000283 ABC transporter signature motif; other site 62928000284 Walker B; other site 62928000285 D-loop; other site 62928000286 H-loop/switch region; other site 62928000287 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 62928000288 Cytochrome C' Region: Cytochrom_C_2; pfam01322 62928000289 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 62928000290 dimerization interface [polypeptide binding]; other site 62928000291 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928000292 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928000293 dimer interface [polypeptide binding]; other site 62928000294 putative CheW interface [polypeptide binding]; other site 62928000295 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 62928000296 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928000297 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 62928000298 protein binding site [polypeptide binding]; other site 62928000299 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 62928000300 protein binding site [polypeptide binding]; other site 62928000301 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928000302 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 62928000303 N-terminal plug; other site 62928000304 ligand-binding site [chemical binding]; other site 62928000305 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928000306 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928000307 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 62928000308 dimerization interface [polypeptide binding]; other site 62928000309 DNA topoisomerase III; Validated; Region: PRK08173 62928000310 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 62928000311 active site 62928000312 putative interdomain interaction site [polypeptide binding]; other site 62928000313 putative metal-binding site [ion binding]; other site 62928000314 putative nucleotide binding site [chemical binding]; other site 62928000315 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 62928000316 domain I; other site 62928000317 DNA binding groove [nucleotide binding] 62928000318 phosphate binding site [ion binding]; other site 62928000319 domain II; other site 62928000320 domain III; other site 62928000321 nucleotide binding site [chemical binding]; other site 62928000322 catalytic site [active] 62928000323 domain IV; other site 62928000324 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 62928000325 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 62928000326 Protein of unknown function (DUF494); Region: DUF494; pfam04361 62928000327 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 62928000328 DNA protecting protein DprA; Region: dprA; TIGR00732 62928000329 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 62928000330 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 62928000331 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 62928000332 active site 62928000333 catalytic residues [active] 62928000334 metal binding site [ion binding]; metal-binding site 62928000335 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 62928000336 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 62928000337 putative active site [active] 62928000338 substrate binding site [chemical binding]; other site 62928000339 putative cosubstrate binding site; other site 62928000340 catalytic site [active] 62928000341 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 62928000342 substrate binding site [chemical binding]; other site 62928000343 M48 family peptidase; Provisional; Region: PRK03001 62928000344 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 62928000345 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 62928000346 catalytic residues [active] 62928000347 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 62928000348 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 62928000349 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928000350 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928000351 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 62928000352 dimer interface [polypeptide binding]; other site 62928000353 catalytic triad [active] 62928000354 peroxidatic and resolving cysteines [active] 62928000355 EamA-like transporter family; Region: EamA; pfam00892 62928000356 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 62928000357 EamA-like transporter family; Region: EamA; pfam00892 62928000358 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 62928000359 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 62928000360 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 62928000361 putative active site [active] 62928000362 dimerization interface [polypeptide binding]; other site 62928000363 putative tRNAtyr binding site [nucleotide binding]; other site 62928000364 Pirin-related protein [General function prediction only]; Region: COG1741 62928000365 Pirin; Region: Pirin; pfam02678 62928000366 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 62928000367 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 62928000368 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD2; cd08298 62928000369 putative NAD(P) binding site [chemical binding]; other site 62928000370 putative substrate binding site [chemical binding]; other site 62928000371 catalytic Zn binding site [ion binding]; other site 62928000372 structural Zn binding site [ion binding]; other site 62928000373 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928000374 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928000375 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 62928000376 putative effector binding pocket; other site 62928000377 putative dimerization interface [polypeptide binding]; other site 62928000378 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 62928000379 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 62928000380 putative C-terminal domain interface [polypeptide binding]; other site 62928000381 putative GSH binding site (G-site) [chemical binding]; other site 62928000382 putative dimer interface [polypeptide binding]; other site 62928000383 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 62928000384 putative N-terminal domain interface [polypeptide binding]; other site 62928000385 putative dimer interface [polypeptide binding]; other site 62928000386 putative substrate binding pocket (H-site) [chemical binding]; other site 62928000387 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 62928000388 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 62928000389 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 62928000390 putative active site [active] 62928000391 putative catalytic site [active] 62928000392 AMP nucleosidase; Provisional; Region: PRK08292 62928000393 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 62928000394 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 62928000395 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928000396 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928000397 Walker A/P-loop; other site 62928000398 ATP binding site [chemical binding]; other site 62928000399 Q-loop/lid; other site 62928000400 ABC transporter signature motif; other site 62928000401 Walker B; other site 62928000402 D-loop; other site 62928000403 H-loop/switch region; other site 62928000404 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928000405 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928000406 Walker A/P-loop; other site 62928000407 ATP binding site [chemical binding]; other site 62928000408 Q-loop/lid; other site 62928000409 ABC transporter signature motif; other site 62928000410 Walker B; other site 62928000411 D-loop; other site 62928000412 H-loop/switch region; other site 62928000413 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928000414 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 62928000415 putative ligand binding site [chemical binding]; other site 62928000416 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928000417 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928000418 TM-ABC transporter signature motif; other site 62928000419 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928000420 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928000421 TM-ABC transporter signature motif; other site 62928000422 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 62928000423 Protein of Unknown function (DUF2784); Region: DUF2784; pfam10861 62928000424 TfoX C-terminal domain; Region: TfoX_C; pfam04994 62928000425 Uncharacterized conserved protein [Function unknown]; Region: COG5470 62928000426 Protein of unknown function (DUF1622); Region: DUF1622; pfam07784 62928000427 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 62928000428 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 62928000429 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928000430 dimer interface [polypeptide binding]; other site 62928000431 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 62928000432 putative CheW interface [polypeptide binding]; other site 62928000433 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 62928000434 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928000435 HAMP domain; Region: HAMP; pfam00672 62928000436 dimerization interface [polypeptide binding]; other site 62928000437 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928000438 dimer interface [polypeptide binding]; other site 62928000439 putative CheW interface [polypeptide binding]; other site 62928000440 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 62928000441 active site 1 [active] 62928000442 dimer interface [polypeptide binding]; other site 62928000443 hexamer interface [polypeptide binding]; other site 62928000444 active site 2 [active] 62928000445 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 62928000446 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928000447 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 62928000448 dimerization interface [polypeptide binding]; other site 62928000449 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 62928000450 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cd00449 62928000451 homodimer interface [polypeptide binding]; other site 62928000452 substrate-cofactor binding pocket; other site 62928000453 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928000454 catalytic residue [active] 62928000455 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928000456 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 62928000457 active site 62928000458 phosphorylation site [posttranslational modification] 62928000459 intermolecular recognition site; other site 62928000460 dimerization interface [polypeptide binding]; other site 62928000461 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 62928000462 PAS domain; Region: PAS_9; pfam13426 62928000463 putative active site [active] 62928000464 heme pocket [chemical binding]; other site 62928000465 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928000466 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928000467 metal binding site [ion binding]; metal-binding site 62928000468 active site 62928000469 I-site; other site 62928000470 Response regulator receiver domain; Region: Response_reg; pfam00072 62928000471 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 62928000472 active site 62928000473 phosphorylation site [posttranslational modification] 62928000474 intermolecular recognition site; other site 62928000475 dimerization interface [polypeptide binding]; other site 62928000476 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 62928000477 dimerization interface [polypeptide binding]; other site 62928000478 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 62928000479 dimer interface [polypeptide binding]; other site 62928000480 phosphorylation site [posttranslational modification] 62928000481 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928000482 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 62928000483 ATP binding site [chemical binding]; other site 62928000484 Mg2+ binding site [ion binding]; other site 62928000485 G-X-G motif; other site 62928000486 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928000487 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 62928000488 putative ligand binding site [chemical binding]; other site 62928000489 putative lipid kinase; Reviewed; Region: PRK13057 62928000490 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 62928000491 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 62928000492 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 62928000493 putative active site [active] 62928000494 putative metal binding site [ion binding]; other site 62928000495 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4398 62928000496 FIST N domain; Region: FIST; pfam08495 62928000497 FIST C domain; Region: FIST_C; pfam10442 62928000498 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 62928000499 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 62928000500 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 62928000501 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 62928000502 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 62928000503 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 62928000504 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 62928000505 P-loop; other site 62928000506 Magnesium ion binding site [ion binding]; other site 62928000507 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 62928000508 Magnesium ion binding site [ion binding]; other site 62928000509 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 62928000510 active site 62928000511 NTP binding site [chemical binding]; other site 62928000512 metal binding triad [ion binding]; metal-binding site 62928000513 antibiotic binding site [chemical binding]; other site 62928000514 Protein of unknown function DUF86; Region: DUF86; cl01031 62928000515 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 62928000516 ParB-like nuclease domain; Region: ParB; smart00470 62928000517 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 62928000518 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 62928000519 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 62928000520 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928000521 putative substrate translocation pore; other site 62928000522 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 62928000523 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 62928000524 putative acyl-acceptor binding pocket; other site 62928000525 Amidohydrolase; Region: Amidohydro_2; pfam04909 62928000526 active site 62928000527 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 62928000528 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 62928000529 putative acyl-acceptor binding pocket; other site 62928000530 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 62928000531 acyl-activating enzyme (AAE) consensus motif; other site 62928000532 putative AMP binding site [chemical binding]; other site 62928000533 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 62928000534 dimerization interface [polypeptide binding]; other site 62928000535 putative DNA binding site [nucleotide binding]; other site 62928000536 putative Zn2+ binding site [ion binding]; other site 62928000537 ATP synthase I chain; Region: ATP_synt_I; pfam03899 62928000538 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 62928000539 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 62928000540 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 62928000541 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 62928000542 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 62928000543 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 62928000544 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 62928000545 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 62928000546 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 62928000547 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 62928000548 beta subunit interaction interface [polypeptide binding]; other site 62928000549 Walker A motif; other site 62928000550 ATP binding site [chemical binding]; other site 62928000551 Walker B motif; other site 62928000552 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 62928000553 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 62928000554 core domain interface [polypeptide binding]; other site 62928000555 delta subunit interface [polypeptide binding]; other site 62928000556 epsilon subunit interface [polypeptide binding]; other site 62928000557 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 62928000558 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 62928000559 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 62928000560 alpha subunit interaction interface [polypeptide binding]; other site 62928000561 Walker A motif; other site 62928000562 ATP binding site [chemical binding]; other site 62928000563 Walker B motif; other site 62928000564 inhibitor binding site; inhibition site 62928000565 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 62928000566 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 62928000567 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 62928000568 gamma subunit interface [polypeptide binding]; other site 62928000569 epsilon subunit interface [polypeptide binding]; other site 62928000570 LBP interface [polypeptide binding]; other site 62928000571 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 62928000572 SCP-2 sterol transfer family; Region: SCP2; pfam02036 62928000573 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 62928000574 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 62928000575 S-adenosylmethionine binding site [chemical binding]; other site 62928000576 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 62928000577 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 62928000578 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 62928000579 active site 62928000580 phosphorylation site [posttranslational modification] 62928000581 intermolecular recognition site; other site 62928000582 dimerization interface [polypeptide binding]; other site 62928000583 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 62928000584 DNA binding site [nucleotide binding] 62928000585 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 62928000586 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 62928000587 dimer interface [polypeptide binding]; other site 62928000588 phosphorylation site [posttranslational modification] 62928000589 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 62928000590 ATP binding site [chemical binding]; other site 62928000591 Mg2+ binding site [ion binding]; other site 62928000592 G-X-G motif; other site 62928000593 Munc13 (mammalian uncoordinated) homology domain; Region: Membr_traf_MHD; pfam10540 62928000594 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 62928000595 nucleotide binding site/active site [active] 62928000596 HIT family signature motif; other site 62928000597 catalytic residue [active] 62928000598 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 62928000599 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 62928000600 putative active site [active] 62928000601 putative dimer interface [polypeptide binding]; other site 62928000602 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 62928000603 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 62928000604 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 62928000605 GatB domain; Region: GatB_Yqey; smart00845 62928000606 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 62928000607 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 62928000608 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 62928000609 rod shape-determining protein MreB; Provisional; Region: PRK13927 62928000610 MreB and similar proteins; Region: MreB_like; cd10225 62928000611 nucleotide binding site [chemical binding]; other site 62928000612 Mg binding site [ion binding]; other site 62928000613 putative protofilament interaction site [polypeptide binding]; other site 62928000614 RodZ interaction site [polypeptide binding]; other site 62928000615 rod shape-determining protein MreC; Provisional; Region: PRK13922 62928000616 rod shape-determining protein MreC; Region: MreC; pfam04085 62928000617 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 62928000618 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 62928000619 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 62928000620 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 62928000621 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 62928000622 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 62928000623 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 62928000624 Sporulation related domain; Region: SPOR; pfam05036 62928000625 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 62928000626 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 62928000627 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 62928000628 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 62928000629 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 62928000630 homodimer interface [polypeptide binding]; other site 62928000631 substrate-cofactor binding pocket; other site 62928000632 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928000633 catalytic residue [active] 62928000634 Protein of unknown function (DUF493); Region: DUF493; cl01102 62928000635 lipoate-protein ligase B; Provisional; Region: PRK14343 62928000636 lipoyl synthase; Provisional; Region: PRK05481 62928000637 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 62928000638 FeS/SAM binding site; other site 62928000639 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 62928000640 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 62928000641 Part of AAA domain; Region: AAA_19; pfam13245 62928000642 Family description; Region: UvrD_C_2; pfam13538 62928000643 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 62928000644 short chain dehydrogenase; Provisional; Region: PRK07023 62928000645 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928000646 NAD(P) binding site [chemical binding]; other site 62928000647 active site 62928000648 Nucleoid-associated protein [General function prediction only]; Region: COG3081 62928000649 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 62928000650 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 62928000651 putative active site [active] 62928000652 putative catalytic site [active] 62928000653 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 62928000654 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 62928000655 thioredoxin 2; Provisional; Region: PRK10996 62928000656 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 62928000657 catalytic residues [active] 62928000658 H-NS histone family; Region: Histone_HNS; pfam00816 62928000659 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 62928000660 Predicted transcriptional regulator [Transcription]; Region: COG2378 62928000661 HTH domain; Region: HTH_11; pfam08279 62928000662 WYL domain; Region: WYL; pfam13280 62928000663 aminodeoxychorismate synthase; Provisional; Region: PRK07508 62928000664 chorismate binding enzyme; Region: Chorismate_bind; cl10555 62928000665 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 62928000666 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 62928000667 substrate-cofactor binding pocket; other site 62928000668 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928000669 catalytic residue [active] 62928000670 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 62928000671 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 62928000672 active site 62928000673 metal binding site [ion binding]; metal-binding site 62928000674 DNA binding site [nucleotide binding] 62928000675 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 62928000676 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 62928000677 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 62928000678 Walker A/P-loop; other site 62928000679 ATP binding site [chemical binding]; other site 62928000680 Q-loop/lid; other site 62928000681 ABC transporter signature motif; other site 62928000682 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 62928000683 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 62928000684 ABC transporter signature motif; other site 62928000685 Walker B; other site 62928000686 D-loop; other site 62928000687 H-loop/switch region; other site 62928000688 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928000689 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 62928000690 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 62928000691 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 62928000692 putative ligand binding site [chemical binding]; other site 62928000693 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 62928000694 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 62928000695 metal binding site [ion binding]; metal-binding site 62928000696 putative dimer interface [polypeptide binding]; other site 62928000697 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928000698 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928000699 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928000700 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 62928000701 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 62928000702 putative active site [active] 62928000703 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 62928000704 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 62928000705 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 62928000706 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928000707 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 62928000708 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 62928000709 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 62928000710 putative DNA binding site [nucleotide binding]; other site 62928000711 putative Zn2+ binding site [ion binding]; other site 62928000712 AsnC family; Region: AsnC_trans_reg; pfam01037 62928000713 hypothetical protein; Provisional; Region: PRK05965 62928000714 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 62928000715 inhibitor-cofactor binding pocket; inhibition site 62928000716 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928000717 catalytic residue [active] 62928000718 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 62928000719 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928000720 Coenzyme A binding pocket [chemical binding]; other site 62928000721 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 62928000722 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 62928000723 NAD(P) binding site [chemical binding]; other site 62928000724 catalytic residues [active] 62928000725 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 62928000726 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 62928000727 motif II; other site 62928000728 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 62928000729 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 62928000730 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_17; cd08503 62928000731 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 62928000732 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 62928000733 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 62928000734 dimer interface [polypeptide binding]; other site 62928000735 conserved gate region; other site 62928000736 putative PBP binding loops; other site 62928000737 ABC-ATPase subunit interface; other site 62928000738 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 62928000739 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 62928000740 dimer interface [polypeptide binding]; other site 62928000741 conserved gate region; other site 62928000742 ABC-ATPase subunit interface; other site 62928000743 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 62928000744 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 62928000745 Walker A/P-loop; other site 62928000746 ATP binding site [chemical binding]; other site 62928000747 Q-loop/lid; other site 62928000748 ABC transporter signature motif; other site 62928000749 Walker B; other site 62928000750 D-loop; other site 62928000751 H-loop/switch region; other site 62928000752 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 62928000753 Walker A/P-loop; other site 62928000754 ATP binding site [chemical binding]; other site 62928000755 Q-loop/lid; other site 62928000756 ABC transporter signature motif; other site 62928000757 Walker B; other site 62928000758 D-loop; other site 62928000759 H-loop/switch region; other site 62928000760 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 62928000761 succinic semialdehyde dehydrogenase; Region: PLN02278 62928000762 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 62928000763 tetramerization interface [polypeptide binding]; other site 62928000764 NAD(P) binding site [chemical binding]; other site 62928000765 catalytic residues [active] 62928000766 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928000767 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928000768 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 62928000769 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 62928000770 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 62928000771 N-terminal plug; other site 62928000772 ligand-binding site [chemical binding]; other site 62928000773 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 62928000774 Predicted membrane protein [Function unknown]; Region: COG3503 62928000775 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 62928000776 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 62928000777 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 62928000778 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 62928000779 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 62928000780 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 62928000781 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 62928000782 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 62928000783 active site 62928000784 purine riboside binding site [chemical binding]; other site 62928000785 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 62928000786 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 62928000787 Double zinc ribbon; Region: DZR; pfam12773 62928000788 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 62928000789 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 62928000790 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 62928000791 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 62928000792 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 62928000793 DctM-like transporters; Region: DctM; pfam06808 62928000794 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 62928000795 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928000796 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928000797 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 62928000798 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928000799 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928000800 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928000801 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 62928000802 Protein export membrane protein; Region: SecD_SecF; cl14618 62928000803 Protein export membrane protein; Region: SecD_SecF; cl14618 62928000804 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 62928000805 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 62928000806 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 62928000807 heme binding site [chemical binding]; other site 62928000808 ferroxidase pore; other site 62928000809 ferroxidase diiron center [ion binding]; other site 62928000810 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 62928000811 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 62928000812 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 62928000813 FMN-binding pocket [chemical binding]; other site 62928000814 flavin binding motif; other site 62928000815 phosphate binding motif [ion binding]; other site 62928000816 beta-alpha-beta structure motif; other site 62928000817 NAD binding pocket [chemical binding]; other site 62928000818 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 62928000819 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 62928000820 G1 box; other site 62928000821 GTP/Mg2+ binding site [chemical binding]; other site 62928000822 G2 box; other site 62928000823 Switch I region; other site 62928000824 G3 box; other site 62928000825 Switch II region; other site 62928000826 G4 box; other site 62928000827 G5 box; other site 62928000828 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 62928000829 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 62928000830 S-adenosylmethionine binding site [chemical binding]; other site 62928000831 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 62928000832 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 62928000833 NodB motif; other site 62928000834 active site 62928000835 catalytic site [active] 62928000836 metal binding site [ion binding]; metal-binding site 62928000837 Predicted exporter [General function prediction only]; Region: COG4258 62928000838 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 62928000839 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 62928000840 putative acyl-acceptor binding pocket; other site 62928000841 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 62928000842 active site 2 [active] 62928000843 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 62928000844 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928000845 AMP binding site [chemical binding]; other site 62928000846 active site 62928000847 acyl-activating enzyme (AAE) consensus motif; other site 62928000848 CoA binding site [chemical binding]; other site 62928000849 Predicted membrane protein [Function unknown]; Region: COG4648 62928000850 Phosphopantetheine attachment site; Region: PP-binding; cl09936 62928000851 sensor protein QseC; Provisional; Region: PRK10337 62928000852 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 62928000853 dimer interface [polypeptide binding]; other site 62928000854 phosphorylation site [posttranslational modification] 62928000855 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 62928000856 ATP binding site [chemical binding]; other site 62928000857 Mg2+ binding site [ion binding]; other site 62928000858 G-X-G motif; other site 62928000859 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 62928000860 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 62928000861 active site 62928000862 phosphorylation site [posttranslational modification] 62928000863 intermolecular recognition site; other site 62928000864 dimerization interface [polypeptide binding]; other site 62928000865 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 62928000866 DNA binding site [nucleotide binding] 62928000867 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 62928000868 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 62928000869 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928000870 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928000871 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 62928000872 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 62928000873 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 62928000874 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 62928000875 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 62928000876 FeS/SAM binding site; other site 62928000877 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 62928000878 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928000879 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 62928000880 DNA binding residues [nucleotide binding] 62928000881 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 62928000882 Domain of unknown function (DUF802); Region: DUF802; pfam05650 62928000883 Domain of unknown function (DUF802); Region: DUF802; pfam05650 62928000884 hypothetical protein; Provisional; Region: PRK09040 62928000885 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928000886 ligand binding site [chemical binding]; other site 62928000887 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 62928000888 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 62928000889 active site 62928000890 Phosphopantetheine attachment site; Region: PP-binding; cl09936 62928000891 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 62928000892 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 62928000893 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 62928000894 ABC-2 type transporter; Region: ABC2_membrane; cl17235 62928000895 PIN domain of the hypothetical protein MT3492 of Mycobacterium tuberculosis CDC1551 and other uncharacterized, annotated PilT protein domain proteins; Region: PIN_MT3492; cd09874 62928000896 putative active site [active] 62928000897 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 62928000898 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 62928000899 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928000900 Walker A/P-loop; other site 62928000901 ATP binding site [chemical binding]; other site 62928000902 Q-loop/lid; other site 62928000903 ABC transporter signature motif; other site 62928000904 Walker B; other site 62928000905 D-loop; other site 62928000906 H-loop/switch region; other site 62928000907 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 62928000908 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 62928000909 "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are...; Region: init_cond_enzymes; cd00827 62928000910 dimer interface [polypeptide binding]; other site 62928000911 active site 62928000912 Beta-lactamase; Region: Beta-lactamase; pfam00144 62928000913 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 62928000914 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928000915 Cupin domain; Region: Cupin_2; pfam07883 62928000916 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 62928000917 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 62928000918 putative trimer interface [polypeptide binding]; other site 62928000919 putative metal binding site [ion binding]; other site 62928000920 phenylacetic acid degradation protein paaN; Region: PaaN_2; TIGR02288 62928000921 Phenylacetic acid degradation proteins PaaZ (Escherichia coli) and PaaN (Pseudomonas putida)-like; Region: ALDH_PAD-PaaZ; cd07127 62928000922 NADP binding site [chemical binding]; other site 62928000923 catalytic residues [active] 62928000924 enoyl-CoA hydratase; Provisional; Region: PRK08140 62928000925 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928000926 substrate binding site [chemical binding]; other site 62928000927 oxyanion hole (OAH) forming residues; other site 62928000928 trimer interface [polypeptide binding]; other site 62928000929 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 62928000930 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 62928000931 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928000932 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928000933 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 62928000934 CoenzymeA binding site [chemical binding]; other site 62928000935 subunit interaction site [polypeptide binding]; other site 62928000936 PHB binding site; other site 62928000937 Phenylacetate-CoA ligase (also known as PaaK); Region: PaaK; cd05913 62928000938 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 62928000939 active site 62928000940 AMP binding site [chemical binding]; other site 62928000941 homodimer interface [polypeptide binding]; other site 62928000942 acyl-activating enzyme (AAE) consensus motif; other site 62928000943 CoA binding site [chemical binding]; other site 62928000944 phenylacetate-CoA oxygenase subunit PaaA; Provisional; Region: paaA; PRK13778 62928000945 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 62928000946 phenylacetate-CoA oxygenase subunit PaaB; Provisional; Region: paaB; PRK13781 62928000947 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; pfam05138 62928000948 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 62928000949 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 62928000950 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 62928000951 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 62928000952 FAD binding pocket [chemical binding]; other site 62928000953 FAD binding motif [chemical binding]; other site 62928000954 phosphate binding motif [ion binding]; other site 62928000955 beta-alpha-beta structure motif; other site 62928000956 NAD(p) ribose binding residues [chemical binding]; other site 62928000957 NAD binding pocket [chemical binding]; other site 62928000958 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 62928000959 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 62928000960 catalytic loop [active] 62928000961 iron binding site [ion binding]; other site 62928000962 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928000963 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928000964 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 62928000965 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928000966 dimer interface [polypeptide binding]; other site 62928000967 active site 62928000968 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 62928000969 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928000970 putative ligand binding site [chemical binding]; other site 62928000971 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928000972 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928000973 TM-ABC transporter signature motif; other site 62928000974 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928000975 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928000976 TM-ABC transporter signature motif; other site 62928000977 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928000978 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928000979 Walker A/P-loop; other site 62928000980 ATP binding site [chemical binding]; other site 62928000981 Q-loop/lid; other site 62928000982 ABC transporter signature motif; other site 62928000983 Walker B; other site 62928000984 D-loop; other site 62928000985 H-loop/switch region; other site 62928000986 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928000987 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928000988 Walker A/P-loop; other site 62928000989 ATP binding site [chemical binding]; other site 62928000990 Q-loop/lid; other site 62928000991 ABC transporter signature motif; other site 62928000992 Walker B; other site 62928000993 D-loop; other site 62928000994 H-loop/switch region; other site 62928000995 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 62928000996 IHF dimer interface [polypeptide binding]; other site 62928000997 IHF - DNA interface [nucleotide binding]; other site 62928000998 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 62928000999 DEAD-like helicases superfamily; Region: DEXDc; smart00487 62928001000 ATP binding site [chemical binding]; other site 62928001001 Mg++ binding site [ion binding]; other site 62928001002 motif III; other site 62928001003 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 62928001004 nucleotide binding region [chemical binding]; other site 62928001005 ATP-binding site [chemical binding]; other site 62928001006 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 62928001007 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 62928001008 homopentamer interface [polypeptide binding]; other site 62928001009 active site 62928001010 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 62928001011 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 62928001012 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 62928001013 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 62928001014 Lumazine binding domain; Region: Lum_binding; pfam00677 62928001015 Lumazine binding domain; Region: Lum_binding; pfam00677 62928001016 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 62928001017 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 62928001018 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 62928001019 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 62928001020 DsbD alpha interface [polypeptide binding]; other site 62928001021 catalytic residues [active] 62928001022 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 62928001023 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 62928001024 FMN binding site [chemical binding]; other site 62928001025 substrate binding site [chemical binding]; other site 62928001026 putative catalytic residue [active] 62928001027 Domain of unknown function (DUF1992); Region: DUF1992; pfam09350 62928001028 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 62928001029 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 62928001030 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 62928001031 FAD binding pocket [chemical binding]; other site 62928001032 FAD binding motif [chemical binding]; other site 62928001033 phosphate binding motif [ion binding]; other site 62928001034 beta-alpha-beta structure motif; other site 62928001035 NAD binding pocket [chemical binding]; other site 62928001036 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 62928001037 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928001038 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928001039 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 62928001040 putative ligand binding site [chemical binding]; other site 62928001041 Domain of unknown function (DUF3291); Region: DUF3291; pfam11695 62928001042 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 62928001043 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928001044 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 62928001045 dimerization interface [polypeptide binding]; other site 62928001046 substrate binding pocket [chemical binding]; other site 62928001047 Hemerythrin-like domain; Region: Hr-like; cd12108 62928001048 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 62928001049 nucleophile elbow; other site 62928001050 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 62928001051 nucleophile elbow; other site 62928001052 Patatin phospholipase; Region: DUF3734; pfam12536 62928001053 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 62928001054 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 62928001055 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 62928001056 PAS domain; Region: PAS_9; pfam13426 62928001057 putative active site [active] 62928001058 heme pocket [chemical binding]; other site 62928001059 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 62928001060 PAS domain; Region: PAS_9; pfam13426 62928001061 putative active site [active] 62928001062 heme pocket [chemical binding]; other site 62928001063 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928001064 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928001065 metal binding site [ion binding]; metal-binding site 62928001066 active site 62928001067 I-site; other site 62928001068 PBP superfamily domain; Region: PBP_like_2; cl17296 62928001069 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 62928001070 PEGA domain; Region: PEGA; pfam08308 62928001071 Cytochrome C' Region: Cytochrom_C_2; pfam01322 62928001072 Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NhoA; COG2162 62928001073 ParA-like protein; Provisional; Region: PHA02518 62928001074 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 62928001075 P-loop; other site 62928001076 Magnesium ion binding site [ion binding]; other site 62928001077 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 62928001078 Part of AAA domain; Region: AAA_19; pfam13245 62928001079 Family description; Region: UvrD_C_2; pfam13538 62928001080 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 62928001081 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 62928001082 hypothetical protein; Validated; Region: PRK08238 62928001083 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 62928001084 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 62928001085 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 62928001086 ABC-2 type transporter; Region: ABC2_membrane; cl17235 62928001087 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 62928001088 Virulence-associated protein and related proteins [Function unknown]; Region: VagC; COG4456 62928001089 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 62928001090 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 62928001091 cofactor binding site; other site 62928001092 DNA binding site [nucleotide binding] 62928001093 substrate interaction site [chemical binding]; other site 62928001094 Restriction endonuclease; Region: Mrr_cat; pfam04471 62928001095 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 62928001096 additional DNA contacts [nucleotide binding]; other site 62928001097 mismatch recognition site; other site 62928001098 active site 62928001099 zinc binding site [ion binding]; other site 62928001100 DNA intercalation site [nucleotide binding]; other site 62928001101 FliP family; Region: FliP; cl00593 62928001102 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 62928001103 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 62928001104 ATP binding site [chemical binding]; other site 62928001105 Mg2+ binding site [ion binding]; other site 62928001106 G-X-G motif; other site 62928001107 Nuclease-related domain; Region: NERD; pfam08378 62928001108 nodulation ABC transporter NodI; Provisional; Region: PRK13537 62928001109 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 62928001110 Walker A/P-loop; other site 62928001111 ATP binding site [chemical binding]; other site 62928001112 Q-loop/lid; other site 62928001113 ABC transporter signature motif; other site 62928001114 Walker B; other site 62928001115 D-loop; other site 62928001116 H-loop/switch region; other site 62928001117 putative glutathione S-transferase; Provisional; Region: PRK10357 62928001118 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 62928001119 putative C-terminal domain interface [polypeptide binding]; other site 62928001120 putative GSH binding site (G-site) [chemical binding]; other site 62928001121 putative dimer interface [polypeptide binding]; other site 62928001122 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 62928001123 dimer interface [polypeptide binding]; other site 62928001124 N-terminal domain interface [polypeptide binding]; other site 62928001125 putative substrate binding pocket (H-site) [chemical binding]; other site 62928001126 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 62928001127 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 62928001128 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 62928001129 dimer interface [polypeptide binding]; other site 62928001130 [2Fe-2S] cluster binding site [ion binding]; other site 62928001131 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 62928001132 active site residue [active] 62928001133 serine O-acetyltransferase; Region: cysE; TIGR01172 62928001134 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 62928001135 trimer interface [polypeptide binding]; other site 62928001136 active site 62928001137 substrate binding site [chemical binding]; other site 62928001138 CoA binding site [chemical binding]; other site 62928001139 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 62928001140 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 62928001141 non-specific DNA binding site [nucleotide binding]; other site 62928001142 salt bridge; other site 62928001143 sequence-specific DNA binding site [nucleotide binding]; other site 62928001144 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 62928001145 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 62928001146 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928001147 catalytic residue [active] 62928001148 Predicted membrane protein [Function unknown]; Region: COG2119 62928001149 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 62928001150 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 62928001151 SCP-2 sterol transfer family; Region: SCP2; cl01225 62928001152 putative protease; Provisional; Region: PRK15447 62928001153 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 62928001154 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 62928001155 Peptidase family U32; Region: Peptidase_U32; pfam01136 62928001156 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 62928001157 Na binding site [ion binding]; other site 62928001158 putative glycosylation site [posttranslational modification]; other site 62928001159 putative glycosylation site [posttranslational modification]; other site 62928001160 Arginase family; Region: Arginase; cd09989 62928001161 active site 62928001162 Mn binding site [ion binding]; other site 62928001163 oligomer interface [polypeptide binding]; other site 62928001164 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 62928001165 ornithine aminotransferase; Region: Orn_aminotrans; TIGR01885 62928001166 inhibitor-cofactor binding pocket; inhibition site 62928001167 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928001168 catalytic residue [active] 62928001169 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 62928001170 ABC1 family; Region: ABC1; pfam03109 62928001171 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 62928001172 active site 62928001173 ATP binding site [chemical binding]; other site 62928001174 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928001175 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 62928001176 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 62928001177 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 62928001178 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 62928001179 active site 62928001180 HIGH motif; other site 62928001181 nucleotide binding site [chemical binding]; other site 62928001182 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 62928001183 KMSK motif region; other site 62928001184 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 62928001185 tRNA binding surface [nucleotide binding]; other site 62928001186 anticodon binding site; other site 62928001187 Sporulation related domain; Region: SPOR; pfam05036 62928001188 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 62928001189 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 62928001190 catalytic residues [active] 62928001191 hinge region; other site 62928001192 alpha helical domain; other site 62928001193 short chain dehydrogenase; Provisional; Region: PRK07024 62928001194 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928001195 NAD(P) binding site [chemical binding]; other site 62928001196 active site 62928001197 PilZ domain; Region: PilZ; pfam07238 62928001198 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 62928001199 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 62928001200 intersubunit interface [polypeptide binding]; other site 62928001201 PIN domain; Region: PIN_3; pfam13470 62928001202 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 62928001203 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 62928001204 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 62928001205 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 62928001206 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928001207 DNA binding residues [nucleotide binding] 62928001208 putative dimer interface [polypeptide binding]; other site 62928001209 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 62928001210 CoenzymeA binding site [chemical binding]; other site 62928001211 subunit interaction site [polypeptide binding]; other site 62928001212 PHB binding site; other site 62928001213 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 62928001214 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928001215 dimer interface [polypeptide binding]; other site 62928001216 active site 62928001217 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 62928001218 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 62928001219 FAD binding site [chemical binding]; other site 62928001220 homotetramer interface [polypeptide binding]; other site 62928001221 substrate binding pocket [chemical binding]; other site 62928001222 catalytic base [active] 62928001223 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 62928001224 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 62928001225 putative catalytic residue [active] 62928001226 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 62928001227 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 62928001228 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928001229 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 62928001230 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 62928001231 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 62928001232 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 62928001233 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 62928001234 active site 62928001235 phosphorylation site [posttranslational modification] 62928001236 intermolecular recognition site; other site 62928001237 dimerization interface [polypeptide binding]; other site 62928001238 CheB methylesterase; Region: CheB_methylest; pfam01339 62928001239 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 62928001240 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 62928001241 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 62928001242 CheD chemotactic sensory transduction; Region: CheD; cl00810 62928001243 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 62928001244 putative CheA interaction surface; other site 62928001245 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928001246 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928001247 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 62928001248 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928001249 dimer interface [polypeptide binding]; other site 62928001250 putative CheW interface [polypeptide binding]; other site 62928001251 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 62928001252 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 62928001253 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928001254 dimer interface [polypeptide binding]; other site 62928001255 putative CheW interface [polypeptide binding]; other site 62928001256 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 62928001257 putative binding surface; other site 62928001258 active site 62928001259 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 62928001260 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 62928001261 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 62928001262 ATP binding site [chemical binding]; other site 62928001263 Mg2+ binding site [ion binding]; other site 62928001264 G-X-G motif; other site 62928001265 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 62928001266 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 62928001267 anti sigma factor interaction site; other site 62928001268 regulatory phosphorylation site [posttranslational modification]; other site 62928001269 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928001270 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928001271 dimer interface [polypeptide binding]; other site 62928001272 putative CheW interface [polypeptide binding]; other site 62928001273 Response regulator receiver domain; Region: Response_reg; pfam00072 62928001274 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 62928001275 active site 62928001276 phosphorylation site [posttranslational modification] 62928001277 intermolecular recognition site; other site 62928001278 dimerization interface [polypeptide binding]; other site 62928001279 Predicted transporter component [General function prediction only]; Region: COG2391 62928001280 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 62928001281 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 62928001282 Ligand Binding Site [chemical binding]; other site 62928001283 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 62928001284 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 62928001285 FeS/SAM binding site; other site 62928001286 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 62928001287 Tetratricopeptide repeat; Region: TPR_6; pfam13174 62928001288 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 62928001289 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928001290 ligand binding site [chemical binding]; other site 62928001291 translocation protein TolB; Provisional; Region: tolB; PRK02889 62928001292 TolB amino-terminal domain; Region: TolB_N; pfam04052 62928001293 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 62928001294 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 62928001295 TolA protein; Region: tolA_full; TIGR02794 62928001296 TonB C terminal; Region: TonB_2; pfam13103 62928001297 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 62928001298 TolR protein; Region: tolR; TIGR02801 62928001299 TolQ protein; Region: tolQ; TIGR02796 62928001300 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 62928001301 active site 62928001302 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 62928001303 anti sigma factor interaction site; other site 62928001304 regulatory phosphorylation site [posttranslational modification]; other site 62928001305 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 62928001306 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 62928001307 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 62928001308 active site 62928001309 HslU subunit interaction site [polypeptide binding]; other site 62928001310 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 62928001311 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 62928001312 Walker A motif; other site 62928001313 ATP binding site [chemical binding]; other site 62928001314 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 62928001315 Walker B motif; other site 62928001316 arginine finger; other site 62928001317 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 62928001318 Membrane transport protein; Region: Mem_trans; cl09117 62928001319 CHASE domain; Region: CHASE; pfam03924 62928001320 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 62928001321 PAS fold; Region: PAS; pfam00989 62928001322 putative active site [active] 62928001323 heme pocket [chemical binding]; other site 62928001324 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928001325 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928001326 metal binding site [ion binding]; metal-binding site 62928001327 active site 62928001328 I-site; other site 62928001329 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 62928001330 RNA binding surface [nucleotide binding]; other site 62928001331 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 62928001332 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 62928001333 CysD dimerization site [polypeptide binding]; other site 62928001334 G1 box; other site 62928001335 putative GEF interaction site [polypeptide binding]; other site 62928001336 GTP/Mg2+ binding site [chemical binding]; other site 62928001337 Switch I region; other site 62928001338 G2 box; other site 62928001339 G3 box; other site 62928001340 Switch II region; other site 62928001341 G4 box; other site 62928001342 G5 box; other site 62928001343 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 62928001344 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 62928001345 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 62928001346 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 62928001347 Active Sites [active] 62928001348 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 62928001349 Active Sites [active] 62928001350 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 62928001351 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 62928001352 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 62928001353 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 62928001354 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 62928001355 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 62928001356 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928001357 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 62928001358 substrate binding site [chemical binding]; other site 62928001359 dimerization interface [polypeptide binding]; other site 62928001360 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 62928001361 active site 62928001362 homodimer interface [polypeptide binding]; other site 62928001363 homotetramer interface [polypeptide binding]; other site 62928001364 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 62928001365 Aspartase; Region: Aspartase; cd01357 62928001366 active sites [active] 62928001367 tetramer interface [polypeptide binding]; other site 62928001368 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 62928001369 homodimer interface [polypeptide binding]; other site 62928001370 active site 62928001371 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 62928001372 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 62928001373 Walker A/P-loop; other site 62928001374 ATP binding site [chemical binding]; other site 62928001375 Q-loop/lid; other site 62928001376 ABC transporter signature motif; other site 62928001377 Walker B; other site 62928001378 D-loop; other site 62928001379 H-loop/switch region; other site 62928001380 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 62928001381 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 62928001382 dimer interface [polypeptide binding]; other site 62928001383 conserved gate region; other site 62928001384 putative PBP binding loops; other site 62928001385 ABC-ATPase subunit interface; other site 62928001386 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 62928001387 dimer interface [polypeptide binding]; other site 62928001388 conserved gate region; other site 62928001389 putative PBP binding loops; other site 62928001390 ABC-ATPase subunit interface; other site 62928001391 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 62928001392 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 62928001393 substrate binding pocket [chemical binding]; other site 62928001394 membrane-bound complex binding site; other site 62928001395 hinge residues; other site 62928001396 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 62928001397 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928001398 ATP-dependent DNA ligase; Validated; Region: PRK09247 62928001399 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 62928001400 active site 62928001401 DNA binding site [nucleotide binding] 62928001402 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 62928001403 DNA binding site [nucleotide binding] 62928001404 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 62928001405 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 62928001406 ATP binding site [chemical binding]; other site 62928001407 putative Mg++ binding site [ion binding]; other site 62928001408 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 62928001409 nucleotide binding region [chemical binding]; other site 62928001410 ATP-binding site [chemical binding]; other site 62928001411 DEAD/H associated; Region: DEAD_assoc; pfam08494 62928001412 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 62928001413 putative active site [active] 62928001414 putative metal binding site [ion binding]; other site 62928001415 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928001416 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 62928001417 active site 62928001418 phosphorylation site [posttranslational modification] 62928001419 intermolecular recognition site; other site 62928001420 dimerization interface [polypeptide binding]; other site 62928001421 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 62928001422 Walker A motif; other site 62928001423 ATP binding site [chemical binding]; other site 62928001424 Walker B motif; other site 62928001425 arginine finger; other site 62928001426 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928001427 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 62928001428 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 62928001429 dimer interface [polypeptide binding]; other site 62928001430 phosphorylation site [posttranslational modification] 62928001431 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 62928001432 ATP binding site [chemical binding]; other site 62928001433 Mg2+ binding site [ion binding]; other site 62928001434 G-X-G motif; other site 62928001435 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 62928001436 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 62928001437 TrkA-N domain; Region: TrkA_N; pfam02254 62928001438 CHASE domain; Region: CHASE; cl01369 62928001439 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 62928001440 PAS domain; Region: PAS_9; pfam13426 62928001441 putative active site [active] 62928001442 heme pocket [chemical binding]; other site 62928001443 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928001444 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928001445 metal binding site [ion binding]; metal-binding site 62928001446 active site 62928001447 I-site; other site 62928001448 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 62928001449 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928001450 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928001451 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 62928001452 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 62928001453 Walker A/P-loop; other site 62928001454 ATP binding site [chemical binding]; other site 62928001455 Q-loop/lid; other site 62928001456 ABC transporter signature motif; other site 62928001457 Walker B; other site 62928001458 D-loop; other site 62928001459 H-loop/switch region; other site 62928001460 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 62928001461 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 62928001462 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 62928001463 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 62928001464 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928001465 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 62928001466 active site 62928001467 phosphorylation site [posttranslational modification] 62928001468 intermolecular recognition site; other site 62928001469 dimerization interface [polypeptide binding]; other site 62928001470 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 62928001471 DNA binding site [nucleotide binding] 62928001472 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928001473 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 62928001474 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 62928001475 dimer interface [polypeptide binding]; other site 62928001476 phosphorylation site [posttranslational modification] 62928001477 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 62928001478 ATP binding site [chemical binding]; other site 62928001479 Mg2+ binding site [ion binding]; other site 62928001480 G-X-G motif; other site 62928001481 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 62928001482 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 62928001483 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 62928001484 ligand binding site [chemical binding]; other site 62928001485 flexible hinge region; other site 62928001486 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; cl17320 62928001487 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 62928001488 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 62928001489 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 62928001490 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 62928001491 active site 62928001492 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 62928001493 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 62928001494 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928001495 dimer interface [polypeptide binding]; other site 62928001496 active site 62928001497 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928001498 substrate binding site [chemical binding]; other site 62928001499 oxyanion hole (OAH) forming residues; other site 62928001500 trimer interface [polypeptide binding]; other site 62928001501 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 62928001502 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 62928001503 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928001504 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 62928001505 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 62928001506 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 62928001507 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 62928001508 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928001509 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 62928001510 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928001511 substrate binding site [chemical binding]; other site 62928001512 oxyanion hole (OAH) forming residues; other site 62928001513 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 62928001514 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928001515 dimer interface [polypeptide binding]; other site 62928001516 active site 62928001517 enoyl-CoA hydratase; Provisional; Region: PRK06688 62928001518 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928001519 substrate binding site [chemical binding]; other site 62928001520 oxyanion hole (OAH) forming residues; other site 62928001521 trimer interface [polypeptide binding]; other site 62928001522 Uncharacterized conserved protein [Function unknown]; Region: COG1434 62928001523 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 62928001524 putative active site [active] 62928001525 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 62928001526 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 62928001527 homodimer interface [polypeptide binding]; other site 62928001528 substrate-cofactor binding pocket; other site 62928001529 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928001530 catalytic residue [active] 62928001531 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 62928001532 Sporulation related domain; Region: SPOR; pfam05036 62928001533 flagellar assembly protein FliW; Provisional; Region: PRK13284 62928001534 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 62928001535 homotrimer interaction site [polypeptide binding]; other site 62928001536 putative active site [active] 62928001537 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 62928001538 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 62928001539 generic binding surface II; other site 62928001540 ssDNA binding site; other site 62928001541 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 62928001542 ATP binding site [chemical binding]; other site 62928001543 putative Mg++ binding site [ion binding]; other site 62928001544 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 62928001545 nucleotide binding region [chemical binding]; other site 62928001546 ATP-binding site [chemical binding]; other site 62928001547 Chorismate lyase; Region: Chor_lyase; cl01230 62928001548 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 62928001549 UbiA prenyltransferase family; Region: UbiA; pfam01040 62928001550 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 62928001551 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 62928001552 FAD binding domain; Region: FAD_binding_4; pfam01565 62928001553 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 62928001554 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 62928001555 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 62928001556 Cysteine-rich domain; Region: CCG; pfam02754 62928001557 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 62928001558 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 62928001559 homotrimer interaction site [polypeptide binding]; other site 62928001560 putative active site [active] 62928001561 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 62928001562 psiF repeat; Region: PsiF_repeat; pfam07769 62928001563 psiF repeat; Region: PsiF_repeat; pfam07769 62928001564 cyclase homology domain; Region: CHD; cd07302 62928001565 nucleotidyl binding site; other site 62928001566 metal binding site [ion binding]; metal-binding site 62928001567 dimer interface [polypeptide binding]; other site 62928001568 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 62928001569 phosphopeptide binding site; other site 62928001570 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 62928001571 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 62928001572 Ligand Binding Site [chemical binding]; other site 62928001573 pteridine reductase; Provisional; Region: PRK09135 62928001574 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928001575 NAD(P) binding site [chemical binding]; other site 62928001576 active site 62928001577 Uncharacterized conserved protein [Function unknown]; Region: COG1565 62928001578 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928001579 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 62928001580 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 62928001581 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 62928001582 C-terminal domain interface [polypeptide binding]; other site 62928001583 GSH binding site (G-site) [chemical binding]; other site 62928001584 dimer interface [polypeptide binding]; other site 62928001585 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 62928001586 N-terminal domain interface [polypeptide binding]; other site 62928001587 putative dimer interface [polypeptide binding]; other site 62928001588 active site 62928001589 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 62928001590 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 62928001591 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 62928001592 active site 62928001593 NTP binding site [chemical binding]; other site 62928001594 metal binding triad [ion binding]; metal-binding site 62928001595 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 62928001596 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928001597 Zn2+ binding site [ion binding]; other site 62928001598 Mg2+ binding site [ion binding]; other site 62928001599 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 62928001600 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 62928001601 putative C-terminal domain interface [polypeptide binding]; other site 62928001602 putative GSH binding site (G-site) [chemical binding]; other site 62928001603 putative dimer interface [polypeptide binding]; other site 62928001604 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 62928001605 putative substrate binding pocket (H-site) [chemical binding]; other site 62928001606 putative N-terminal domain interface [polypeptide binding]; other site 62928001607 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 62928001608 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 62928001609 putative NAD(P) binding site [chemical binding]; other site 62928001610 active site 62928001611 lytic murein transglycosylase; Provisional; Region: PRK11619 62928001612 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 62928001613 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928001614 catalytic residue [active] 62928001615 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 62928001616 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 62928001617 PAS fold; Region: PAS_3; pfam08447 62928001618 putative active site [active] 62928001619 heme pocket [chemical binding]; other site 62928001620 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 62928001621 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 62928001622 putative active site [active] 62928001623 heme pocket [chemical binding]; other site 62928001624 PAS domain; Region: PAS; smart00091 62928001625 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928001626 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928001627 metal binding site [ion binding]; metal-binding site 62928001628 active site 62928001629 I-site; other site 62928001630 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 62928001631 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 62928001632 substrate binding pocket [chemical binding]; other site 62928001633 membrane-bound complex binding site; other site 62928001634 hinge residues; other site 62928001635 threonine dehydratase; Reviewed; Region: PRK09224 62928001636 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 62928001637 tetramer interface [polypeptide binding]; other site 62928001638 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928001639 catalytic residue [active] 62928001640 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 62928001641 putative Ile/Val binding site [chemical binding]; other site 62928001642 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 62928001643 putative Ile/Val binding site [chemical binding]; other site 62928001644 HPr kinase/phosphorylase; Provisional; Region: PRK05428 62928001645 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 62928001646 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 62928001647 Hpr binding site; other site 62928001648 active site 62928001649 homohexamer subunit interaction site [polypeptide binding]; other site 62928001650 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 62928001651 active site 62928001652 phosphorylation site [posttranslational modification] 62928001653 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 62928001654 30S subunit binding site; other site 62928001655 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 62928001656 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 62928001657 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 62928001658 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 62928001659 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 62928001660 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 62928001661 Walker A/P-loop; other site 62928001662 ATP binding site [chemical binding]; other site 62928001663 Q-loop/lid; other site 62928001664 ABC transporter signature motif; other site 62928001665 Walker B; other site 62928001666 D-loop; other site 62928001667 H-loop/switch region; other site 62928001668 recombination regulator RecX; Reviewed; Region: recX; PRK00117 62928001669 recombinase A; Provisional; Region: recA; PRK09354 62928001670 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 62928001671 hexamer interface [polypeptide binding]; other site 62928001672 Walker A motif; other site 62928001673 ATP binding site [chemical binding]; other site 62928001674 Walker B motif; other site 62928001675 Competence-damaged protein; Region: CinA; cl00666 62928001676 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 62928001677 tetramer interfaces [polypeptide binding]; other site 62928001678 binuclear metal-binding site [ion binding]; other site 62928001679 thiamine monophosphate kinase; Provisional; Region: PRK05731 62928001680 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 62928001681 ATP binding site [chemical binding]; other site 62928001682 dimerization interface [polypeptide binding]; other site 62928001683 RnfH family Ubiquitin; Region: Ub-RnfH; pfam03658 62928001684 electron transport complex RsxE subunit; Provisional; Region: PRK12405 62928001685 electron transport complex, RnfABCDGE type, G subunit; Region: rnfG; TIGR01947 62928001686 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 62928001687 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 62928001688 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 62928001689 SLBB domain; Region: SLBB; pfam10531 62928001690 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 62928001691 electron transport complex protein RnfB; Provisional; Region: PRK05113 62928001692 4Fe-4S binding domain; Region: Fer4; pfam00037 62928001693 electron transport complex protein RsxA; Provisional; Region: PRK05151 62928001694 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 62928001695 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 62928001696 putative active site [active] 62928001697 heme pocket [chemical binding]; other site 62928001698 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 62928001699 ATP binding site [chemical binding]; other site 62928001700 Mg2+ binding site [ion binding]; other site 62928001701 G-X-G motif; other site 62928001702 Nif-specific regulatory protein; Region: nifA; TIGR01817 62928001703 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928001704 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 62928001705 Walker A motif; other site 62928001706 ATP binding site [chemical binding]; other site 62928001707 Walker B motif; other site 62928001708 arginine finger; other site 62928001709 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928001710 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 62928001711 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 62928001712 E-class dimer interface [polypeptide binding]; other site 62928001713 P-class dimer interface [polypeptide binding]; other site 62928001714 active site 62928001715 Cu2+ binding site [ion binding]; other site 62928001716 Zn2+ binding site [ion binding]; other site 62928001717 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 62928001718 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 62928001719 FeS/SAM binding site; other site 62928001720 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 62928001721 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 62928001722 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 62928001723 ArsC family; Region: ArsC; pfam03960 62928001724 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 62928001725 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928001726 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 62928001727 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 62928001728 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 62928001729 catalytic loop [active] 62928001730 iron binding site [ion binding]; other site 62928001731 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 62928001732 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 62928001733 catalytic loop [active] 62928001734 iron binding site [ion binding]; other site 62928001735 NifQ; Region: NifQ; pfam04891 62928001736 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 62928001737 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 62928001738 putative active site [active] 62928001739 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 62928001740 TPR repeat; Region: TPR_11; pfam13414 62928001741 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 62928001742 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 62928001743 Sel1-like repeats; Region: SEL1; smart00671 62928001744 Hemerythrin; Region: Hemerythrin; cd12107 62928001745 Fe binding site [ion binding]; other site 62928001746 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 62928001747 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 62928001748 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 62928001749 nitrogenase iron protein; Region: nifH; TIGR01287 62928001750 Nucleotide-binding sites [chemical binding]; other site 62928001751 Walker A motif; other site 62928001752 Switch I region of nucleotide binding site; other site 62928001753 Fe4S4 binding sites [ion binding]; other site 62928001754 Switch II region of nucleotide binding site; other site 62928001755 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 62928001756 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 62928001757 MoFe protein alpha/beta subunit interactions; other site 62928001758 Alpha subunit P cluster binding residues; other site 62928001759 FeMoco binding residues [chemical binding]; other site 62928001760 MoFe protein alpha subunit/Fe protein contacts; other site 62928001761 MoFe protein dimer/ dimer interactions; other site 62928001762 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 62928001763 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 62928001764 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 62928001765 MoFe protein beta/alpha subunit interactions; other site 62928001766 Beta subunit P cluster binding residues; other site 62928001767 MoFe protein beta subunit/Fe protein contacts; other site 62928001768 MoFe protein dimer/ dimer interactions; other site 62928001769 NifT/FixU protein; Region: NifT; pfam06988 62928001770 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 62928001771 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 62928001772 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928001773 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928001774 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928001775 dimer interface [polypeptide binding]; other site 62928001776 putative CheW interface [polypeptide binding]; other site 62928001777 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 62928001778 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 62928001779 NifZ domain; Region: NifZ; pfam04319 62928001780 Nitrogen fixation protein NifW; Region: NifW; pfam03206 62928001781 serine O-acetyltransferase; Region: cysE; TIGR01172 62928001782 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 62928001783 trimer interface [polypeptide binding]; other site 62928001784 active site 62928001785 substrate binding site [chemical binding]; other site 62928001786 CoA binding site [chemical binding]; other site 62928001787 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 62928001788 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 62928001789 active site 62928001790 catalytic residues [active] 62928001791 metal binding site [ion binding]; metal-binding site 62928001792 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 62928001793 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 62928001794 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928001795 catalytic residue [active] 62928001796 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 62928001797 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 62928001798 trimerization site [polypeptide binding]; other site 62928001799 active site 62928001800 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 62928001801 NifU-like domain; Region: NifU; pfam01106 62928001802 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 62928001803 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 62928001804 Rop-like; Region: Rop-like; pfam05082 62928001805 probable nitrogen fixation protein; Region: TIGR02935 62928001806 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 62928001807 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 62928001808 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 62928001809 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 62928001810 nitrogenase molybdenum-cofactor biosynthesis protein NifE; Provisional; Region: PRK14478 62928001811 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 62928001812 LRV protein FeS4 cluster; Region: LRV_FeS; pfam05484 62928001813 MgtE intracellular N domain; Region: MgtE_N; cl15244 62928001814 HEAT repeats; Region: HEAT_2; pfam13646 62928001815 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 62928001816 PAS domain; Region: PAS_9; pfam13426 62928001817 putative active site [active] 62928001818 heme pocket [chemical binding]; other site 62928001819 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928001820 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928001821 metal binding site [ion binding]; metal-binding site 62928001822 active site 62928001823 I-site; other site 62928001824 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 62928001825 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 62928001826 CHASE3 domain; Region: CHASE3; pfam05227 62928001827 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 62928001828 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 62928001829 ATP binding site [chemical binding]; other site 62928001830 G-X-G motif; other site 62928001831 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928001832 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 62928001833 active site 62928001834 phosphorylation site [posttranslational modification] 62928001835 intermolecular recognition site; other site 62928001836 dimerization interface [polypeptide binding]; other site 62928001837 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 62928001838 DNA binding residues [nucleotide binding] 62928001839 dimerization interface [polypeptide binding]; other site 62928001840 Esterase PHB depolymerase; Region: Esterase_phd; pfam10503 62928001841 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 62928001842 active site 62928001843 putative DNA-binding cleft [nucleotide binding]; other site 62928001844 dimer interface [polypeptide binding]; other site 62928001845 hypothetical protein; Provisional; Region: PRK02877 62928001846 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 62928001847 EamA-like transporter family; Region: EamA; pfam00892 62928001848 EamA-like transporter family; Region: EamA; pfam00892 62928001849 hypothetical protein; Validated; Region: PRK00110 62928001850 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 62928001851 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 62928001852 Walker A motif; other site 62928001853 ATP binding site [chemical binding]; other site 62928001854 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928001855 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928001856 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 62928001857 putative effector binding pocket; other site 62928001858 dimerization interface [polypeptide binding]; other site 62928001859 EamA-like transporter family; Region: EamA; pfam00892 62928001860 EamA-like transporter family; Region: EamA; pfam00892 62928001861 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928001862 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 62928001863 dimerization interface [polypeptide binding]; other site 62928001864 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928001865 dimer interface [polypeptide binding]; other site 62928001866 putative CheW interface [polypeptide binding]; other site 62928001867 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 62928001868 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 62928001869 putative substrate translocation pore; other site 62928001870 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928001871 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928001872 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 62928001873 putative effector binding pocket; other site 62928001874 dimerization interface [polypeptide binding]; other site 62928001875 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 62928001876 FAD binding site [chemical binding]; other site 62928001877 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 62928001878 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 62928001879 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 62928001880 homotetramer interface [polypeptide binding]; other site 62928001881 ligand binding site [chemical binding]; other site 62928001882 catalytic site [active] 62928001883 NAD binding site [chemical binding]; other site 62928001884 S-adenosylmethionine synthetase; Validated; Region: PRK05250 62928001885 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 62928001886 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 62928001887 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 62928001888 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 62928001889 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 62928001890 putative acyl-acceptor binding pocket; other site 62928001891 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 62928001892 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 62928001893 putative acyl-acceptor binding pocket; other site 62928001894 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 62928001895 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 62928001896 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 62928001897 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 62928001898 Protein of unknown function, DUF484; Region: DUF484; cl17449 62928001899 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 62928001900 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 62928001901 active site 62928001902 DNA binding site [nucleotide binding] 62928001903 Int/Topo IB signature motif; other site 62928001904 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; cl17320 62928001905 DNA binding site [nucleotide binding] 62928001906 sequence specific DNA binding site [nucleotide binding]; other site 62928001907 putative cAMP binding site [chemical binding]; other site 62928001908 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 62928001909 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 62928001910 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 62928001911 putative RNA binding site [nucleotide binding]; other site 62928001912 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 62928001913 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 62928001914 Walker A motif; other site 62928001915 ATP binding site [chemical binding]; other site 62928001916 Walker B motif; other site 62928001917 arginine finger; other site 62928001918 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 62928001919 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 62928001920 RuvA N terminal domain; Region: RuvA_N; pfam01330 62928001921 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 62928001922 AzlC protein; Region: AzlC; pfam03591 62928001923 FeoA domain; Region: FeoA; pfam04023 62928001924 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 62928001925 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 62928001926 G1 box; other site 62928001927 GTP/Mg2+ binding site [chemical binding]; other site 62928001928 G2 box; other site 62928001929 Switch I region; other site 62928001930 G3 box; other site 62928001931 Switch II region; other site 62928001932 G4 box; other site 62928001933 Nucleoside recognition; Region: Gate; pfam07670 62928001934 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 62928001935 Nucleoside recognition; Region: Gate; pfam07670 62928001936 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 62928001937 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 62928001938 N-terminal plug; other site 62928001939 ligand-binding site [chemical binding]; other site 62928001940 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 62928001941 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 62928001942 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 62928001943 active site 62928001944 substrate binding site [chemical binding]; other site 62928001945 FMN binding site [chemical binding]; other site 62928001946 putative catalytic residues [active] 62928001947 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 62928001948 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 62928001949 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928001950 Walker A/P-loop; other site 62928001951 ATP binding site [chemical binding]; other site 62928001952 Q-loop/lid; other site 62928001953 ABC transporter signature motif; other site 62928001954 Walker B; other site 62928001955 D-loop; other site 62928001956 H-loop/switch region; other site 62928001957 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928001958 FtsX-like permease family; Region: FtsX; pfam02687 62928001959 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928001960 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 62928001961 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928001962 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 62928001963 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 62928001964 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 62928001965 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 62928001966 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 62928001967 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 62928001968 heme binding site [chemical binding]; other site 62928001969 ferroxidase pore; other site 62928001970 ferroxidase diiron center [ion binding]; other site 62928001971 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 62928001972 Hemin uptake protein hemP; Region: hemP; pfam10636 62928001973 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 62928001974 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 62928001975 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 62928001976 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928001977 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 62928001978 dimerization interface [polypeptide binding]; other site 62928001979 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 62928001980 PAS fold; Region: PAS_3; pfam08447 62928001981 putative active site [active] 62928001982 heme pocket [chemical binding]; other site 62928001983 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928001984 metal binding site [ion binding]; metal-binding site 62928001985 active site 62928001986 I-site; other site 62928001987 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 62928001988 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 62928001989 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 62928001990 PAS fold; Region: PAS_3; pfam08447 62928001991 putative active site [active] 62928001992 heme pocket [chemical binding]; other site 62928001993 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 62928001994 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 62928001995 Protein of unknown function, DUF480; Region: DUF480; pfam04337 62928001996 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria; Region: CHASE2; smart01080 62928001997 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 62928001998 cyclase homology domain; Region: CHD; cd07302 62928001999 nucleotidyl binding site; other site 62928002000 metal binding site [ion binding]; metal-binding site 62928002001 dimer interface [polypeptide binding]; other site 62928002002 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 62928002003 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928002004 ligand binding site [chemical binding]; other site 62928002005 FecR protein; Region: FecR; pfam04773 62928002006 GAF domain; Region: GAF; pfam01590 62928002007 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 62928002008 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928002009 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 62928002010 TIGR02449 family protein; Region: TIGR02449 62928002011 Cell division protein ZapA; Region: ZapA; pfam05164 62928002012 EVE domain; Region: EVE; cl00728 62928002013 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 62928002014 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 62928002015 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 62928002016 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 62928002017 metal binding site [ion binding]; metal-binding site 62928002018 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 62928002019 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 62928002020 ABC-ATPase subunit interface; other site 62928002021 dimer interface [polypeptide binding]; other site 62928002022 putative PBP binding regions; other site 62928002023 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 62928002024 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 62928002025 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 62928002026 metal binding site 2 [ion binding]; metal-binding site 62928002027 putative DNA binding helix; other site 62928002028 metal binding site 1 [ion binding]; metal-binding site 62928002029 dimer interface [polypeptide binding]; other site 62928002030 structural Zn2+ binding site [ion binding]; other site 62928002031 PilZ domain; Region: PilZ; pfam07238 62928002032 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 62928002033 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 62928002034 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928002035 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 62928002036 Walker A/P-loop; other site 62928002037 ATP binding site [chemical binding]; other site 62928002038 Q-loop/lid; other site 62928002039 ABC transporter signature motif; other site 62928002040 Walker B; other site 62928002041 D-loop; other site 62928002042 H-loop/switch region; other site 62928002043 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 62928002044 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928002045 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928002046 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928002047 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 62928002048 DNA binding residues [nucleotide binding] 62928002049 dimerization interface [polypeptide binding]; other site 62928002050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 62928002051 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928002052 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 62928002053 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 62928002054 dimerization interface [polypeptide binding]; other site 62928002055 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 62928002056 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 62928002057 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 62928002058 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 62928002059 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928002060 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 62928002061 dimer interface [polypeptide binding]; other site 62928002062 phosphorylation site [posttranslational modification] 62928002063 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 62928002064 ATP binding site [chemical binding]; other site 62928002065 Mg2+ binding site [ion binding]; other site 62928002066 G-X-G motif; other site 62928002067 Response regulator receiver domain; Region: Response_reg; pfam00072 62928002068 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 62928002069 active site 62928002070 phosphorylation site [posttranslational modification] 62928002071 intermolecular recognition site; other site 62928002072 dimerization interface [polypeptide binding]; other site 62928002073 Response regulator receiver domain; Region: Response_reg; pfam00072 62928002074 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 62928002075 active site 62928002076 phosphorylation site [posttranslational modification] 62928002077 intermolecular recognition site; other site 62928002078 dimerization interface [polypeptide binding]; other site 62928002079 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 62928002080 DNA binding residues [nucleotide binding] 62928002081 dimerization interface [polypeptide binding]; other site 62928002082 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 62928002083 glutathione reductase; Validated; Region: PRK06116 62928002084 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928002085 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928002086 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 62928002087 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 62928002088 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928002089 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 62928002090 Walker A/P-loop; other site 62928002091 ATP binding site [chemical binding]; other site 62928002092 Q-loop/lid; other site 62928002093 ABC transporter signature motif; other site 62928002094 Walker B; other site 62928002095 D-loop; other site 62928002096 H-loop/switch region; other site 62928002097 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 62928002098 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 62928002099 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 62928002100 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 62928002101 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 62928002102 Putative methyltransferase; Region: Methyltransf_20; pfam12147 62928002103 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 62928002104 active site 62928002105 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 62928002106 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 62928002107 putative acyl-acceptor binding pocket; other site 62928002108 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]; Region: COG4589 62928002109 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 62928002110 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 62928002111 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 62928002112 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 62928002113 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 62928002114 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 62928002115 [4Fe-4S] binding site [ion binding]; other site 62928002116 molybdopterin cofactor binding site; other site 62928002117 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 62928002118 molybdopterin cofactor binding site; other site 62928002119 NapD protein; Region: NapD; pfam03927 62928002120 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 62928002121 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928002122 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 62928002123 putative ligand binding site [chemical binding]; other site 62928002124 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928002125 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928002126 TM-ABC transporter signature motif; other site 62928002127 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928002128 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928002129 TM-ABC transporter signature motif; other site 62928002130 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 62928002131 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928002132 Walker A/P-loop; other site 62928002133 ATP binding site [chemical binding]; other site 62928002134 Q-loop/lid; other site 62928002135 ABC transporter signature motif; other site 62928002136 Walker B; other site 62928002137 D-loop; other site 62928002138 H-loop/switch region; other site 62928002139 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 62928002140 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928002141 Walker A/P-loop; other site 62928002142 ATP binding site [chemical binding]; other site 62928002143 Q-loop/lid; other site 62928002144 ABC transporter signature motif; other site 62928002145 Walker B; other site 62928002146 D-loop; other site 62928002147 H-loop/switch region; other site 62928002148 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928002149 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928002150 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_4; cd08463 62928002151 putative substrate binding pocket [chemical binding]; other site 62928002152 putative dimerization interface [polypeptide binding]; other site 62928002153 enoyl-CoA hydratase; Provisional; Region: PRK06127 62928002154 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928002155 substrate binding site [chemical binding]; other site 62928002156 oxyanion hole (OAH) forming residues; other site 62928002157 trimer interface [polypeptide binding]; other site 62928002158 Protein of unknown function, DUF485; Region: DUF485; pfam04341 62928002159 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 62928002160 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 62928002161 Na binding site [ion binding]; other site 62928002162 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 62928002163 Domain of unknown function DUF21; Region: DUF21; pfam01595 62928002164 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 62928002165 Transporter associated domain; Region: CorC_HlyC; smart01091 62928002166 Transcriptional regulators [Transcription]; Region: GntR; COG1802 62928002167 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928002168 DNA-binding site [nucleotide binding]; DNA binding site 62928002169 FCD domain; Region: FCD; pfam07729 62928002170 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 62928002171 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 62928002172 active site 62928002173 substrate binding site [chemical binding]; other site 62928002174 coenzyme B12 binding site [chemical binding]; other site 62928002175 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 62928002176 B12 binding site [chemical binding]; other site 62928002177 cobalt ligand [ion binding]; other site 62928002178 membrane ATPase/protein kinase; Provisional; Region: PRK09435 62928002179 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 62928002180 Walker A; other site 62928002181 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 62928002182 G4 box; other site 62928002183 G5 box; other site 62928002184 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 62928002185 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 62928002186 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 62928002187 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 62928002188 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 62928002189 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 62928002190 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 62928002191 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 62928002192 carboxyltransferase (CT) interaction site; other site 62928002193 biotinylation site [posttranslational modification]; other site 62928002194 PAS fold; Region: PAS_4; pfam08448 62928002195 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 62928002196 putative active site [active] 62928002197 heme pocket [chemical binding]; other site 62928002198 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 62928002199 PAS fold; Region: PAS_3; pfam08447 62928002200 putative active site [active] 62928002201 heme pocket [chemical binding]; other site 62928002202 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 62928002203 PAS domain; Region: PAS_9; pfam13426 62928002204 putative active site [active] 62928002205 heme pocket [chemical binding]; other site 62928002206 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928002207 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928002208 metal binding site [ion binding]; metal-binding site 62928002209 active site 62928002210 I-site; other site 62928002211 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 62928002212 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 62928002213 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 62928002214 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928002215 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928002216 metal binding site [ion binding]; metal-binding site 62928002217 active site 62928002218 I-site; other site 62928002219 Predicted metalloprotease [General function prediction only]; Region: COG2321 62928002220 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 62928002221 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928002222 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 62928002223 dimer interface [polypeptide binding]; other site 62928002224 substrate binding site [chemical binding]; other site 62928002225 metal binding site [ion binding]; metal-binding site 62928002226 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928002227 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 62928002228 active site 62928002229 phosphorylation site [posttranslational modification] 62928002230 intermolecular recognition site; other site 62928002231 dimerization interface [polypeptide binding]; other site 62928002232 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 62928002233 DNA binding site [nucleotide binding] 62928002234 PAS fold; Region: PAS_7; pfam12860 62928002235 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 62928002236 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 62928002237 putative active site [active] 62928002238 heme pocket [chemical binding]; other site 62928002239 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 62928002240 dimer interface [polypeptide binding]; other site 62928002241 phosphorylation site [posttranslational modification] 62928002242 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 62928002243 ATP binding site [chemical binding]; other site 62928002244 G-X-G motif; other site 62928002245 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 62928002246 phosphorylation site [posttranslational modification] 62928002247 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 62928002248 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928002249 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928002250 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 62928002251 B12 binding site [chemical binding]; other site 62928002252 cobalt ligand [ion binding]; other site 62928002253 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 62928002254 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 62928002255 Walker A; other site 62928002256 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, unknown subfamily 1; composed of uncharacterized bacterial proteins containing a C-terminal MCM domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The...; Region: MM_CoA_mutase_1; cd03678 62928002257 putative active site [active] 62928002258 putative substrate binding site [chemical binding]; other site 62928002259 putative coenzyme B12 binding site [chemical binding]; other site 62928002260 fumarate hydratase; Reviewed; Region: fumC; PRK00485 62928002261 Class II fumarases; Region: Fumarase_classII; cd01362 62928002262 active site 62928002263 tetramer interface [polypeptide binding]; other site 62928002264 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 62928002265 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 62928002266 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 62928002267 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 62928002268 inner membrane protein; Provisional; Region: PRK11715 62928002269 sensory histidine kinase CreC; Provisional; Region: PRK11100 62928002270 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 62928002271 dimer interface [polypeptide binding]; other site 62928002272 phosphorylation site [posttranslational modification] 62928002273 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 62928002274 ATP binding site [chemical binding]; other site 62928002275 Mg2+ binding site [ion binding]; other site 62928002276 G-X-G motif; other site 62928002277 DNA-binding response regulator CreB; Provisional; Region: PRK11083 62928002278 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 62928002279 active site 62928002280 phosphorylation site [posttranslational modification] 62928002281 intermolecular recognition site; other site 62928002282 dimerization interface [polypeptide binding]; other site 62928002283 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 62928002284 DNA binding site [nucleotide binding] 62928002285 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 62928002286 MgtE intracellular N domain; Region: MgtE_N; smart00924 62928002287 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 62928002288 Divalent cation transporter; Region: MgtE; cl00786 62928002289 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 62928002290 Transglycosylase; Region: Transgly; cl17702 62928002291 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 62928002292 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 62928002293 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 62928002294 NAD(P) binding site [chemical binding]; other site 62928002295 shikimate binding site; other site 62928002296 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 62928002297 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 62928002298 RNB domain; Region: RNB; pfam00773 62928002299 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 62928002300 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 62928002301 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 62928002302 Flagellin N-methylase; Region: FliB; cl00497 62928002303 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 62928002304 Methyltransferase domain; Region: Methyltransf_23; pfam13489 62928002305 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 62928002306 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 62928002307 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 62928002308 ATP binding site [chemical binding]; other site 62928002309 putative Mg++ binding site [ion binding]; other site 62928002310 nucleotide binding region [chemical binding]; other site 62928002311 helicase superfamily c-terminal domain; Region: HELICc; smart00490 62928002312 ATP-binding site [chemical binding]; other site 62928002313 Helicase associated domain (HA2); Region: HA2; pfam04408 62928002314 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 62928002315 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 62928002316 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 62928002317 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 62928002318 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 62928002319 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 62928002320 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 62928002321 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 62928002322 replicative DNA helicase; Region: DnaB; TIGR00665 62928002323 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 62928002324 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 62928002325 Walker A motif; other site 62928002326 ATP binding site [chemical binding]; other site 62928002327 Walker B motif; other site 62928002328 DNA binding loops [nucleotide binding] 62928002329 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608 62928002330 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 62928002331 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 62928002332 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 62928002333 dimerization domain [polypeptide binding]; other site 62928002334 dimer interface [polypeptide binding]; other site 62928002335 catalytic residues [active] 62928002336 MltA specific insert domain; Region: MltA; smart00925 62928002337 3D domain; Region: 3D; pfam06725 62928002338 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 62928002339 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 62928002340 Walker A motif; other site 62928002341 ATP binding site [chemical binding]; other site 62928002342 Walker B motif; other site 62928002343 arginine finger; other site 62928002344 hypothetical protein; Provisional; Region: PRK08999 62928002345 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 62928002346 active site 62928002347 8-oxo-dGMP binding site [chemical binding]; other site 62928002348 nudix motif; other site 62928002349 metal binding site [ion binding]; metal-binding site 62928002350 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 62928002351 active site 62928002352 thiamine phosphate binding site [chemical binding]; other site 62928002353 pyrophosphate binding site [ion binding]; other site 62928002354 Domain of unknown function (DUF329); Region: DUF329; pfam03884 62928002355 hypothetical protein; Provisional; Region: PRK05287 62928002356 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 62928002357 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 62928002358 CoA-binding site [chemical binding]; other site 62928002359 Sporulation related domain; Region: SPOR; pfam05036 62928002360 pantothenate kinase; Reviewed; Region: PRK13329 62928002361 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 62928002362 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 62928002363 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 62928002364 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 62928002365 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 62928002366 active site 62928002367 phosphorylation site [posttranslational modification] 62928002368 intermolecular recognition site; other site 62928002369 dimerization interface [polypeptide binding]; other site 62928002370 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 62928002371 Walker A motif; other site 62928002372 ATP binding site [chemical binding]; other site 62928002373 Walker B motif; other site 62928002374 arginine finger; other site 62928002375 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928002376 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 62928002377 PAS domain; Region: PAS; smart00091 62928002378 putative active site [active] 62928002379 heme pocket [chemical binding]; other site 62928002380 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 62928002381 dimer interface [polypeptide binding]; other site 62928002382 phosphorylation site [posttranslational modification] 62928002383 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 62928002384 ATP binding site [chemical binding]; other site 62928002385 Mg2+ binding site [ion binding]; other site 62928002386 G-X-G motif; other site 62928002387 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 62928002388 glutamine synthetase; Provisional; Region: glnA; PRK09469 62928002389 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 62928002390 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 62928002391 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 62928002392 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 62928002393 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 62928002394 active site residue [active] 62928002395 quinolinate synthetase; Provisional; Region: PRK09375 62928002396 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 62928002397 putative catalytic site [active] 62928002398 putative metal binding site [ion binding]; other site 62928002399 putative phosphate binding site [ion binding]; other site 62928002400 cardiolipin synthase 2; Provisional; Region: PRK11263 62928002401 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 62928002402 putative active site [active] 62928002403 catalytic site [active] 62928002404 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 62928002405 putative active site [active] 62928002406 catalytic site [active] 62928002407 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 62928002408 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 62928002409 active site 62928002410 HIGH motif; other site 62928002411 nucleotide binding site [chemical binding]; other site 62928002412 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 62928002413 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 62928002414 BNR repeat-like domain; Region: BNR_2; pfam13088 62928002415 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 62928002416 putative active site [active] 62928002417 YdjC motif; other site 62928002418 Mg binding site [ion binding]; other site 62928002419 putative homodimer interface [polypeptide binding]; other site 62928002420 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 62928002421 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 62928002422 Ligand binding site; other site 62928002423 Putative Catalytic site; other site 62928002424 DXD motif; other site 62928002425 Predicted membrane protein [Function unknown]; Region: COG2246 62928002426 GtrA-like protein; Region: GtrA; pfam04138 62928002427 GTP-binding protein YchF; Reviewed; Region: PRK09601 62928002428 YchF GTPase; Region: YchF; cd01900 62928002429 G1 box; other site 62928002430 GTP/Mg2+ binding site [chemical binding]; other site 62928002431 Switch I region; other site 62928002432 G2 box; other site 62928002433 Switch II region; other site 62928002434 G3 box; other site 62928002435 G4 box; other site 62928002436 G5 box; other site 62928002437 Protein of unknown function (DUF933); Region: YchF-GTPase_C; pfam06071 62928002438 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 62928002439 putative active site [active] 62928002440 catalytic residue [active] 62928002441 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 62928002442 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 62928002443 5S rRNA interface [nucleotide binding]; other site 62928002444 CTC domain interface [polypeptide binding]; other site 62928002445 L16 interface [polypeptide binding]; other site 62928002446 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 62928002447 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 62928002448 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928002449 active site 62928002450 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 62928002451 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 62928002452 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 62928002453 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 62928002454 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 62928002455 binding surface 62928002456 TPR motif; other site 62928002457 TPR repeat; Region: TPR_11; pfam13414 62928002458 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 62928002459 binding surface 62928002460 TPR motif; other site 62928002461 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 62928002462 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 62928002463 DNA binding site [nucleotide binding] 62928002464 catalytic residue [active] 62928002465 H2TH interface [polypeptide binding]; other site 62928002466 putative catalytic residues [active] 62928002467 turnover-facilitating residue; other site 62928002468 intercalation triad [nucleotide binding]; other site 62928002469 8OG recognition residue [nucleotide binding]; other site 62928002470 putative reading head residues; other site 62928002471 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 62928002472 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 62928002473 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 62928002474 Dynamin family; Region: Dynamin_N; pfam00350 62928002475 G1 box; other site 62928002476 GTP/Mg2+ binding site [chemical binding]; other site 62928002477 G2 box; other site 62928002478 Switch I region; other site 62928002479 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 62928002480 G3 box; other site 62928002481 Switch II region; other site 62928002482 GTP/Mg2+ binding site [chemical binding]; other site 62928002483 G4 box; other site 62928002484 G5 box; other site 62928002485 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 62928002486 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 62928002487 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 62928002488 active site 62928002489 (T/H)XGH motif; other site 62928002490 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 62928002491 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 62928002492 S-adenosylmethionine binding site [chemical binding]; other site 62928002493 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 62928002494 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 62928002495 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 62928002496 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 62928002497 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 62928002498 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 62928002499 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 62928002500 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 62928002501 P loop; other site 62928002502 GTP binding site [chemical binding]; other site 62928002503 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 62928002504 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928002505 Walker A/P-loop; other site 62928002506 ATP binding site [chemical binding]; other site 62928002507 Q-loop/lid; other site 62928002508 ABC transporter signature motif; other site 62928002509 Walker B; other site 62928002510 D-loop; other site 62928002511 H-loop/switch region; other site 62928002512 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 62928002513 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 62928002514 peroxiredoxin; Region: AhpC; TIGR03137 62928002515 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 62928002516 dimer interface [polypeptide binding]; other site 62928002517 decamer (pentamer of dimers) interface [polypeptide binding]; other site 62928002518 catalytic triad [active] 62928002519 peroxidatic and resolving cysteines [active] 62928002520 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 62928002521 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 62928002522 catalytic residue [active] 62928002523 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 62928002524 catalytic residues [active] 62928002525 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928002526 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928002527 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 62928002528 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 62928002529 cofactor binding site; other site 62928002530 DNA binding site [nucleotide binding] 62928002531 substrate interaction site [chemical binding]; other site 62928002532 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 62928002533 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 62928002534 RNA/DNA hybrid binding site [nucleotide binding]; other site 62928002535 active site 62928002536 AntA/AntB antirepressor; Region: AntA; pfam08346 62928002537 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 62928002538 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 62928002539 catalytic residues [active] 62928002540 catalytic nucleophile [active] 62928002541 Presynaptic Site I dimer interface [polypeptide binding]; other site 62928002542 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 62928002543 Synaptic Flat tetramer interface [polypeptide binding]; other site 62928002544 Synaptic Site I dimer interface [polypeptide binding]; other site 62928002545 DNA binding site [nucleotide binding] 62928002546 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 62928002547 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 62928002548 active site 62928002549 DNA binding site [nucleotide binding] 62928002550 Int/Topo IB signature motif; other site 62928002551 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 62928002552 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 62928002553 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 62928002554 FeS/SAM binding site; other site 62928002555 TRAM domain; Region: TRAM; pfam01938 62928002556 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 62928002557 PhoH-like protein; Region: PhoH; pfam02562 62928002558 unkown domain/putative metalloprotease fusion protein; Provisional; Region: PRK13963 62928002559 FOG: CBS domain [General function prediction only]; Region: COG0517 62928002560 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 62928002561 Transporter associated domain; Region: CorC_HlyC; smart01091 62928002562 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 62928002563 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 62928002564 putative active site [active] 62928002565 catalytic triad [active] 62928002566 putative dimer interface [polypeptide binding]; other site 62928002567 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928002568 PTS_IIA, PTS system, glucose/sucrose 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_glc; cl00162 62928002569 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928002570 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 62928002571 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 62928002572 dimer interface [polypeptide binding]; other site 62928002573 motif 1; other site 62928002574 active site 62928002575 motif 2; other site 62928002576 motif 3; other site 62928002577 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 62928002578 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 62928002579 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 62928002580 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 62928002581 active site 62928002582 motif I; other site 62928002583 motif II; other site 62928002584 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 62928002585 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 62928002586 putative acyl-acceptor binding pocket; other site 62928002587 Phasin protein; Region: Phasin_2; pfam09361 62928002588 enoyl-CoA hydratase; Provisional; Region: PRK05862 62928002589 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928002590 substrate binding site [chemical binding]; other site 62928002591 oxyanion hole (OAH) forming residues; other site 62928002592 trimer interface [polypeptide binding]; other site 62928002593 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 62928002594 OstA-like protein; Region: OstA; pfam03968 62928002595 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 62928002596 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 62928002597 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 62928002598 KpsF/GutQ family protein; Region: kpsF; TIGR00393 62928002599 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 62928002600 putative active site [active] 62928002601 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 62928002602 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 62928002603 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 62928002604 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 62928002605 TrkA-N domain; Region: TrkA_N; pfam02254 62928002606 TrkA-C domain; Region: TrkA_C; pfam02080 62928002607 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 62928002608 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 62928002609 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 62928002610 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 62928002611 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 62928002612 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 62928002613 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 62928002614 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 62928002615 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 62928002616 Walker A motif; other site 62928002617 ATP binding site [chemical binding]; other site 62928002618 Walker B motif; other site 62928002619 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 62928002620 binding surface 62928002621 TPR motif; other site 62928002622 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 62928002623 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 62928002624 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 62928002625 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 62928002626 Walker A/P-loop; other site 62928002627 ATP binding site [chemical binding]; other site 62928002628 Q-loop/lid; other site 62928002629 ABC transporter signature motif; other site 62928002630 Walker B; other site 62928002631 D-loop; other site 62928002632 H-loop/switch region; other site 62928002633 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 62928002634 Permease; Region: Permease; pfam02405 62928002635 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 62928002636 mce related protein; Region: MCE; pfam02470 62928002637 VacJ like lipoprotein; Region: VacJ; cl01073 62928002638 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 62928002639 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 62928002640 anti sigma factor interaction site; other site 62928002641 regulatory phosphorylation site [posttranslational modification]; other site 62928002642 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 62928002643 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 62928002644 Walker A/P-loop; other site 62928002645 ATP binding site [chemical binding]; other site 62928002646 Q-loop/lid; other site 62928002647 ABC transporter signature motif; other site 62928002648 Walker B; other site 62928002649 D-loop; other site 62928002650 H-loop/switch region; other site 62928002651 ABC-2 type transporter; Region: ABC2_membrane; cl17235 62928002652 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 62928002653 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 62928002654 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 62928002655 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 62928002656 hinge; other site 62928002657 active site 62928002658 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 62928002659 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 62928002660 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 62928002661 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 62928002662 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 62928002663 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 62928002664 NAD binding site [chemical binding]; other site 62928002665 dimerization interface [polypeptide binding]; other site 62928002666 product binding site; other site 62928002667 substrate binding site [chemical binding]; other site 62928002668 zinc binding site [ion binding]; other site 62928002669 catalytic residues [active] 62928002670 hypothetical protein; Provisional; Region: PRK08960 62928002671 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 62928002672 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928002673 homodimer interface [polypeptide binding]; other site 62928002674 catalytic residue [active] 62928002675 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 62928002676 active site 62928002677 substrate-binding site [chemical binding]; other site 62928002678 metal-binding site [ion binding] 62928002679 GTP binding site [chemical binding]; other site 62928002680 malic enzyme; Reviewed; Region: PRK12862 62928002681 Malic enzyme, N-terminal domain; Region: malic; pfam00390 62928002682 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 62928002683 putative NAD(P) binding site [chemical binding]; other site 62928002684 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 62928002685 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 62928002686 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 62928002687 nucleophile elbow; other site 62928002688 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 62928002689 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 62928002690 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 62928002691 Transcriptional regulator [Transcription]; Region: IclR; COG1414 62928002692 Bacterial transcriptional regulator; Region: IclR; pfam01614 62928002693 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 62928002694 glycerate dehydrogenase; Provisional; Region: PRK06487 62928002695 putative ligand binding site [chemical binding]; other site 62928002696 putative NAD binding site [chemical binding]; other site 62928002697 catalytic site [active] 62928002698 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 62928002699 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 62928002700 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 62928002701 RNA binding surface [nucleotide binding]; other site 62928002702 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 62928002703 active site 62928002704 NADH dehydrogenase subunit B; Validated; Region: PRK06411 62928002705 Helix-turn-helix domain; Region: HTH_18; pfam12833 62928002706 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928002707 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 62928002708 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928002709 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 62928002710 FtsX-like permease family; Region: FtsX; pfam02687 62928002711 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 62928002712 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928002713 Walker A/P-loop; other site 62928002714 ATP binding site [chemical binding]; other site 62928002715 Q-loop/lid; other site 62928002716 ABC transporter signature motif; other site 62928002717 Walker B; other site 62928002718 D-loop; other site 62928002719 H-loop/switch region; other site 62928002720 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 62928002721 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928002722 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928002723 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 62928002724 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 62928002725 active site 62928002726 HIGH motif; other site 62928002727 nucleotide binding site [chemical binding]; other site 62928002728 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 62928002729 active site 62928002730 KMSKS motif; other site 62928002731 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 62928002732 chromosome condensation membrane protein; Provisional; Region: PRK14196 62928002733 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 62928002734 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928002735 ligand binding site [chemical binding]; other site 62928002736 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 62928002737 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 62928002738 ATP binding site [chemical binding]; other site 62928002739 putative Mg++ binding site [ion binding]; other site 62928002740 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 62928002741 nucleotide binding region [chemical binding]; other site 62928002742 ATP-binding site [chemical binding]; other site 62928002743 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 62928002744 ThiC-associated domain; Region: ThiC-associated; pfam13667 62928002745 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 62928002746 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 62928002747 dimer interface [polypeptide binding]; other site 62928002748 substrate binding site [chemical binding]; other site 62928002749 ATP binding site [chemical binding]; other site 62928002750 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 62928002751 active site 62928002752 zinc binding site [ion binding]; other site 62928002753 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 62928002754 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928002755 DNA-binding site [nucleotide binding]; DNA binding site 62928002756 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 62928002757 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928002758 homodimer interface [polypeptide binding]; other site 62928002759 catalytic residue [active] 62928002760 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928002761 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928002762 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928002763 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928002764 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928002765 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 62928002766 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 62928002767 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 62928002768 S-adenosylmethionine binding site [chemical binding]; other site 62928002769 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 62928002770 active site residue [active] 62928002771 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 62928002772 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 62928002773 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 62928002774 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 62928002775 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 62928002776 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 62928002777 putative NAD(P) binding site [chemical binding]; other site 62928002778 active site 62928002779 putative substrate binding site [chemical binding]; other site 62928002780 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 62928002781 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 62928002782 active site 62928002783 metal binding site [ion binding]; metal-binding site 62928002784 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 62928002785 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 62928002786 putative acyl-acceptor binding pocket; other site 62928002787 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 62928002788 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 62928002789 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 62928002790 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 62928002791 substrate binding site [chemical binding]; other site 62928002792 ATP binding site [chemical binding]; other site 62928002793 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 62928002794 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 62928002795 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 62928002796 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 62928002797 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 62928002798 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 62928002799 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 62928002800 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 62928002801 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 62928002802 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 62928002803 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 62928002804 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 62928002805 carboxyltransferase (CT) interaction site; other site 62928002806 biotinylation site [posttranslational modification]; other site 62928002807 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 62928002808 Dehydroquinase class II; Region: DHquinase_II; pfam01220 62928002809 trimer interface [polypeptide binding]; other site 62928002810 active site 62928002811 dimer interface [polypeptide binding]; other site 62928002812 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 62928002813 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 62928002814 catalytic residues [active] 62928002815 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 62928002816 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 62928002817 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 62928002818 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 62928002819 BON domain; Region: BON; pfam04972 62928002820 BON domain; Region: BON; pfam04972 62928002821 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 62928002822 dimer interface [polypeptide binding]; other site 62928002823 active site 62928002824 hypothetical protein; Reviewed; Region: PRK12497 62928002825 Predicted methyltransferases [General function prediction only]; Region: COG0313 62928002826 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 62928002827 putative SAM binding site [chemical binding]; other site 62928002828 putative homodimer interface [polypeptide binding]; other site 62928002829 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 62928002830 active site 62928002831 substrate binding pocket [chemical binding]; other site 62928002832 dimer interface [polypeptide binding]; other site 62928002833 cell division protein MraZ; Reviewed; Region: PRK00326 62928002834 MraZ protein; Region: MraZ; pfam02381 62928002835 MraZ protein; Region: MraZ; pfam02381 62928002836 MraW methylase family; Region: Methyltransf_5; cl17771 62928002837 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 62928002838 Cell division protein FtsL; Region: FtsL; pfam04999 62928002839 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 62928002840 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 62928002841 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 62928002842 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 62928002843 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 62928002844 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 62928002845 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 62928002846 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 62928002847 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 62928002848 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 62928002849 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 62928002850 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 62928002851 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 62928002852 Mg++ binding site [ion binding]; other site 62928002853 putative catalytic motif [active] 62928002854 putative substrate binding site [chemical binding]; other site 62928002855 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 62928002856 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 62928002857 cell division protein FtsW; Region: ftsW; TIGR02614 62928002858 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 62928002859 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 62928002860 active site 62928002861 homodimer interface [polypeptide binding]; other site 62928002862 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 62928002863 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 62928002864 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 62928002865 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 62928002866 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 62928002867 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 62928002868 ATP-grasp domain; Region: ATP-grasp_4; cl17255 62928002869 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 62928002870 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 62928002871 Cell division protein FtsQ; Region: FtsQ; pfam03799 62928002872 cell division protein FtsA; Region: ftsA; TIGR01174 62928002873 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 62928002874 nucleotide binding site [chemical binding]; other site 62928002875 Cell division protein FtsA; Region: FtsA; pfam14450 62928002876 cell division protein FtsZ; Validated; Region: PRK09330 62928002877 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 62928002878 nucleotide binding site [chemical binding]; other site 62928002879 SulA interaction site; other site 62928002880 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 62928002881 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 62928002882 Protein of unknown function (DUF721); Region: DUF721; pfam05258 62928002883 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 62928002884 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 62928002885 SEC-C motif; Region: SEC-C; pfam02810 62928002886 HDOD domain; Region: HDOD; pfam08668 62928002887 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928002888 GAF domain; Region: GAF; pfam01590 62928002889 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 62928002890 heterotetramer interface [polypeptide binding]; other site 62928002891 active site pocket [active] 62928002892 cleavage site 62928002893 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 62928002894 active site 62928002895 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 62928002896 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 62928002897 TPR motif; other site 62928002898 binding surface 62928002899 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928002900 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928002901 active site 62928002902 ATP binding site [chemical binding]; other site 62928002903 substrate binding site [chemical binding]; other site 62928002904 activation loop (A-loop); other site 62928002905 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928002906 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 62928002907 dimerization interface [polypeptide binding]; other site 62928002908 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 62928002909 phosphopeptide binding site; other site 62928002910 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 62928002911 adenylosuccinate lyase; Provisional; Region: PRK09285 62928002912 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 62928002913 tetramer interface [polypeptide binding]; other site 62928002914 active site 62928002915 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 62928002916 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 62928002917 Protein export membrane protein; Region: SecD_SecF; pfam02355 62928002918 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 62928002919 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 62928002920 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 62928002921 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 62928002922 HDOD domain; Region: HDOD; pfam08668 62928002923 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 62928002924 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 62928002925 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 62928002926 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 62928002927 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928002928 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 62928002929 putative dimerization interface [polypeptide binding]; other site 62928002930 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 62928002931 YccA-like proteins; Region: YccA_like; cd10433 62928002932 putative cation:proton antiport protein; Provisional; Region: PRK10669 62928002933 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 62928002934 TrkA-N domain; Region: TrkA_N; pfam02254 62928002935 Domain of unknown function DUF21; Region: DUF21; pfam01595 62928002936 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 62928002937 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 62928002938 Transporter associated domain; Region: CorC_HlyC; smart01091 62928002939 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 62928002940 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 62928002941 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 62928002942 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 62928002943 Ligand Binding Site [chemical binding]; other site 62928002944 TilS substrate binding domain; Region: TilS; pfam09179 62928002945 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 62928002946 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 62928002947 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 62928002948 active site 62928002949 phosphorylation site [posttranslational modification] 62928002950 intermolecular recognition site; other site 62928002951 dimerization interface [polypeptide binding]; other site 62928002952 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 62928002953 dimerization interface [polypeptide binding]; other site 62928002954 DNA binding residues [nucleotide binding] 62928002955 PAS domain S-box; Region: sensory_box; TIGR00229 62928002956 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 62928002957 putative active site [active] 62928002958 heme pocket [chemical binding]; other site 62928002959 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 62928002960 dimer interface [polypeptide binding]; other site 62928002961 phosphorylation site [posttranslational modification] 62928002962 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 62928002963 ATP binding site [chemical binding]; other site 62928002964 Mg2+ binding site [ion binding]; other site 62928002965 G-X-G motif; other site 62928002966 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 62928002967 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 62928002968 membrane-bound complex binding site; other site 62928002969 hinge residues; other site 62928002970 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 62928002971 DctM-like transporters; Region: DctM; pfam06808 62928002972 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 62928002973 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 62928002974 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 62928002975 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 62928002976 active site 62928002977 multimer interface [polypeptide binding]; other site 62928002978 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 62928002979 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 62928002980 FeS/SAM binding site; other site 62928002981 Tetratricopeptide repeat; Region: TPR_16; pfam13432 62928002982 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 62928002983 TPR motif; other site 62928002984 binding surface 62928002985 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 62928002986 TPR motif; other site 62928002987 binding surface 62928002988 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 62928002989 non-specific DNA binding site [nucleotide binding]; other site 62928002990 salt bridge; other site 62928002991 sequence-specific DNA binding site [nucleotide binding]; other site 62928002992 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 62928002993 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 62928002994 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 62928002995 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 62928002996 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 62928002997 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 62928002998 dimer interface [polypeptide binding]; other site 62928002999 motif 1; other site 62928003000 active site 62928003001 motif 2; other site 62928003002 motif 3; other site 62928003003 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 62928003004 anticodon binding site; other site 62928003005 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 62928003006 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 62928003007 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 62928003008 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 62928003009 Trp docking motif [polypeptide binding]; other site 62928003010 active site 62928003011 GTP-binding protein Der; Reviewed; Region: PRK00093 62928003012 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 62928003013 G1 box; other site 62928003014 GTP/Mg2+ binding site [chemical binding]; other site 62928003015 Switch I region; other site 62928003016 G2 box; other site 62928003017 Switch II region; other site 62928003018 G3 box; other site 62928003019 G4 box; other site 62928003020 G5 box; other site 62928003021 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 62928003022 G1 box; other site 62928003023 GTP/Mg2+ binding site [chemical binding]; other site 62928003024 Switch I region; other site 62928003025 G2 box; other site 62928003026 G3 box; other site 62928003027 Switch II region; other site 62928003028 G4 box; other site 62928003029 G5 box; other site 62928003030 bacterial Hfq-like; Region: Hfq; cd01716 62928003031 hexamer interface [polypeptide binding]; other site 62928003032 Sm1 motif; other site 62928003033 RNA binding site [nucleotide binding]; other site 62928003034 Sm2 motif; other site 62928003035 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 62928003036 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 62928003037 HflX GTPase family; Region: HflX; cd01878 62928003038 G1 box; other site 62928003039 GTP/Mg2+ binding site [chemical binding]; other site 62928003040 Switch I region; other site 62928003041 G2 box; other site 62928003042 G3 box; other site 62928003043 Switch II region; other site 62928003044 G4 box; other site 62928003045 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 62928003046 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 62928003047 HflK protein; Region: hflK; TIGR01933 62928003048 FtsH protease regulator HflC; Provisional; Region: PRK11029 62928003049 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 62928003050 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 62928003051 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 62928003052 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 62928003053 motif 1; other site 62928003054 dimer interface [polypeptide binding]; other site 62928003055 active site 62928003056 motif 2; other site 62928003057 motif 3; other site 62928003058 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 62928003059 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 62928003060 GDP-binding site [chemical binding]; other site 62928003061 ACT binding site; other site 62928003062 IMP binding site; other site 62928003063 ribonuclease R; Region: RNase_R; TIGR02063 62928003064 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 62928003065 RNB domain; Region: RNB; pfam00773 62928003066 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 62928003067 RNA binding site [nucleotide binding]; other site 62928003068 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 62928003069 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 62928003070 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 62928003071 Nitrate and nitrite sensing; Region: NIT; pfam08376 62928003072 ANTAR domain; Region: ANTAR; pfam03861 62928003073 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 62928003074 NMT1-like family; Region: NMT1_2; pfam13379 62928003075 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 62928003076 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 62928003077 dimer interface [polypeptide binding]; other site 62928003078 conserved gate region; other site 62928003079 putative PBP binding loops; other site 62928003080 ABC-ATPase subunit interface; other site 62928003081 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 62928003082 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 62928003083 Walker A/P-loop; other site 62928003084 ATP binding site [chemical binding]; other site 62928003085 Q-loop/lid; other site 62928003086 ABC transporter signature motif; other site 62928003087 Walker B; other site 62928003088 D-loop; other site 62928003089 H-loop/switch region; other site 62928003090 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 62928003091 active site 62928003092 SAM binding site [chemical binding]; other site 62928003093 homodimer interface [polypeptide binding]; other site 62928003094 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 62928003095 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928003096 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 62928003097 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 62928003098 [4Fe-4S] binding site [ion binding]; other site 62928003099 molybdopterin cofactor binding site; other site 62928003100 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 62928003101 molybdopterin cofactor binding site; other site 62928003102 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 62928003103 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928003104 dimer interface [polypeptide binding]; other site 62928003105 Nitrate and nitrite sensing; Region: NIT; pfam08376 62928003106 PAS domain S-box; Region: sensory_box; TIGR00229 62928003107 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 62928003108 putative active site [active] 62928003109 heme pocket [chemical binding]; other site 62928003110 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928003111 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928003112 metal binding site [ion binding]; metal-binding site 62928003113 active site 62928003114 I-site; other site 62928003115 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 62928003116 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 62928003117 Restriction endonuclease; Region: Mrr_cat; pfam04471 62928003118 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 62928003119 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 62928003120 dimer interface [polypeptide binding]; other site 62928003121 FMN binding site [chemical binding]; other site 62928003122 NADPH bind site [chemical binding]; other site 62928003123 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 62928003124 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 62928003125 cyclopropane fatty acyl phospholipid synthase; Provisional; Region: PRK11705 62928003126 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 62928003127 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 62928003128 S-adenosylmethionine binding site [chemical binding]; other site 62928003129 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 62928003130 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 62928003131 Walker A motif; other site 62928003132 ATP binding site [chemical binding]; other site 62928003133 Walker B motif; other site 62928003134 arginine finger; other site 62928003135 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 62928003136 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 62928003137 hypothetical protein; Validated; Region: PRK00153 62928003138 recombination protein RecR; Reviewed; Region: recR; PRK00076 62928003139 RecR protein; Region: RecR; pfam02132 62928003140 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 62928003141 putative active site [active] 62928003142 putative metal-binding site [ion binding]; other site 62928003143 tetramer interface [polypeptide binding]; other site 62928003144 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 62928003145 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 62928003146 [2Fe-2S] cluster binding site [ion binding]; other site 62928003147 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 62928003148 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 62928003149 Qi binding site; other site 62928003150 intrachain domain interface; other site 62928003151 interchain domain interface [polypeptide binding]; other site 62928003152 heme bH binding site [chemical binding]; other site 62928003153 heme bL binding site [chemical binding]; other site 62928003154 Qo binding site; other site 62928003155 interchain domain interface [polypeptide binding]; other site 62928003156 intrachain domain interface; other site 62928003157 Qi binding site; other site 62928003158 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 62928003159 Qo binding site; other site 62928003160 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 62928003161 stringent starvation protein A; Provisional; Region: sspA; PRK09481 62928003162 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 62928003163 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 62928003164 dimer interface [polypeptide binding]; other site 62928003165 N-terminal domain interface [polypeptide binding]; other site 62928003166 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 62928003167 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 62928003168 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 62928003169 putative ADP-binding pocket [chemical binding]; other site 62928003170 Hemerythrin; Region: Hemerythrin; cd12107 62928003171 Fe binding site [ion binding]; other site 62928003172 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 62928003173 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928003174 hydroxyglutarate oxidase; Provisional; Region: PRK11728 62928003175 fructose-1,6-bisphosphatase family protein; Region: PLN02628 62928003176 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 62928003177 AMP binding site [chemical binding]; other site 62928003178 metal binding site [ion binding]; metal-binding site 62928003179 active site 62928003180 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 62928003181 Surface antigen; Region: Bac_surface_Ag; pfam01103 62928003182 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 62928003183 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 62928003184 zinc binding site [ion binding]; other site 62928003185 putative ligand binding site [chemical binding]; other site 62928003186 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 62928003187 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928003188 TM-ABC transporter signature motif; other site 62928003189 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 62928003190 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928003191 Walker A/P-loop; other site 62928003192 ATP binding site [chemical binding]; other site 62928003193 Q-loop/lid; other site 62928003194 ABC transporter signature motif; other site 62928003195 Walker B; other site 62928003196 D-loop; other site 62928003197 H-loop/switch region; other site 62928003198 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 62928003199 oligomerisation interface [polypeptide binding]; other site 62928003200 mobile loop; other site 62928003201 roof hairpin; other site 62928003202 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 62928003203 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 62928003204 ring oligomerisation interface [polypeptide binding]; other site 62928003205 ATP/Mg binding site [chemical binding]; other site 62928003206 stacking interactions; other site 62928003207 hinge regions; other site 62928003208 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928003209 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 62928003210 active site 62928003211 phosphorylation site [posttranslational modification] 62928003212 intermolecular recognition site; other site 62928003213 dimerization interface [polypeptide binding]; other site 62928003214 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 62928003215 DNA binding site [nucleotide binding] 62928003216 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 62928003217 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 62928003218 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 62928003219 dimerization interface [polypeptide binding]; other site 62928003220 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 62928003221 dimer interface [polypeptide binding]; other site 62928003222 phosphorylation site [posttranslational modification] 62928003223 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 62928003224 ATP binding site [chemical binding]; other site 62928003225 Mg2+ binding site [ion binding]; other site 62928003226 G-X-G motif; other site 62928003227 Protein of unknown function, DUF485; Region: DUF485; pfam04341 62928003228 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 62928003229 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 62928003230 Na binding site [ion binding]; other site 62928003231 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928003232 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 62928003233 active site 62928003234 phosphorylation site [posttranslational modification] 62928003235 intermolecular recognition site; other site 62928003236 dimerization interface [polypeptide binding]; other site 62928003237 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 62928003238 DNA binding site [nucleotide binding] 62928003239 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 62928003240 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 62928003241 tRNA; other site 62928003242 putative tRNA binding site [nucleotide binding]; other site 62928003243 putative NADP binding site [chemical binding]; other site 62928003244 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 62928003245 peptide chain release factor 1; Validated; Region: prfA; PRK00591 62928003246 This domain is found in peptide chain release factors; Region: PCRF; smart00937 62928003247 RF-1 domain; Region: RF-1; pfam00472 62928003248 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 62928003249 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 62928003250 S-adenosylmethionine binding site [chemical binding]; other site 62928003251 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 62928003252 putative GSH binding site [chemical binding]; other site 62928003253 catalytic residues [active] 62928003254 HprK-related kinase A; Region: HprK_rel_A; TIGR04352 62928003255 PqqD family protein, HPr-rel-A system; Region: PqqD_rel_X; TIGR04353 62928003256 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 62928003257 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928003258 active site 62928003259 ATP binding site [chemical binding]; other site 62928003260 substrate binding site [chemical binding]; other site 62928003261 activation loop (A-loop); other site 62928003262 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 62928003263 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 62928003264 argininosuccinate lyase; Provisional; Region: PRK00855 62928003265 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 62928003266 active sites [active] 62928003267 tetramer interface [polypeptide binding]; other site 62928003268 Histidine kinase; Region: His_kinase; pfam06580 62928003269 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 62928003270 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 62928003271 active site 62928003272 phosphorylation site [posttranslational modification] 62928003273 intermolecular recognition site; other site 62928003274 dimerization interface [polypeptide binding]; other site 62928003275 LytTr DNA-binding domain; Region: LytTR; smart00850 62928003276 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 62928003277 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 62928003278 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 62928003279 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 62928003280 domain interfaces; other site 62928003281 active site 62928003282 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 62928003283 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 62928003284 active site 62928003285 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 62928003286 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 62928003287 Transcriptional regulators [Transcription]; Region: FadR; COG2186 62928003288 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928003289 DNA-binding site [nucleotide binding]; DNA binding site 62928003290 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 62928003291 FAD binding domain; Region: FAD_binding_4; pfam01565 62928003292 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 62928003293 FAD binding domain; Region: FAD_binding_4; pfam01565 62928003294 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 62928003295 Cysteine-rich domain; Region: CCG; pfam02754 62928003296 Cysteine-rich domain; Region: CCG; pfam02754 62928003297 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 62928003298 active site 62928003299 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 62928003300 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 62928003301 ligand binding site [chemical binding]; other site 62928003302 homodimer interface [polypeptide binding]; other site 62928003303 NAD(P) binding site [chemical binding]; other site 62928003304 trimer interface B [polypeptide binding]; other site 62928003305 trimer interface A [polypeptide binding]; other site 62928003306 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 62928003307 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 62928003308 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 62928003309 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 62928003310 putative active site [active] 62928003311 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 62928003312 PAS domain; Region: PAS_9; pfam13426 62928003313 putative active site [active] 62928003314 heme pocket [chemical binding]; other site 62928003315 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928003316 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928003317 metal binding site [ion binding]; metal-binding site 62928003318 active site 62928003319 I-site; other site 62928003320 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 62928003321 helicase 45; Provisional; Region: PTZ00424 62928003322 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 62928003323 ATP binding site [chemical binding]; other site 62928003324 Mg++ binding site [ion binding]; other site 62928003325 motif III; other site 62928003326 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 62928003327 nucleotide binding region [chemical binding]; other site 62928003328 ATP-binding site [chemical binding]; other site 62928003329 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 62928003330 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 62928003331 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 62928003332 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 62928003333 active site 62928003334 catalytic tetrad [active] 62928003335 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 62928003336 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 62928003337 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 62928003338 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 62928003339 active site 62928003340 catalytic site [active] 62928003341 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 62928003342 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 62928003343 substrate binding pocket [chemical binding]; other site 62928003344 chain length determination region; other site 62928003345 substrate-Mg2+ binding site; other site 62928003346 catalytic residues [active] 62928003347 aspartate-rich region 1; other site 62928003348 active site lid residues [active] 62928003349 aspartate-rich region 2; other site 62928003350 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 62928003351 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928003352 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 62928003353 dimerization interface [polypeptide binding]; other site 62928003354 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 62928003355 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 62928003356 phosphate binding site [ion binding]; other site 62928003357 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 62928003358 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 62928003359 binding surface 62928003360 TPR motif; other site 62928003361 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 62928003362 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 62928003363 RNA binding surface [nucleotide binding]; other site 62928003364 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 62928003365 active site 62928003366 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 62928003367 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 62928003368 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 62928003369 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 62928003370 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 62928003371 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 62928003372 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 62928003373 NAD(P) binding site [chemical binding]; other site 62928003374 homotetramer interface [polypeptide binding]; other site 62928003375 homodimer interface [polypeptide binding]; other site 62928003376 active site 62928003377 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 62928003378 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 62928003379 NAD(P) binding site [chemical binding]; other site 62928003380 homotetramer interface [polypeptide binding]; other site 62928003381 homodimer interface [polypeptide binding]; other site 62928003382 active site 62928003383 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 62928003384 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 62928003385 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 62928003386 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 62928003387 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 62928003388 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 62928003389 TRAM domain; Region: TRAM; cl01282 62928003390 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 62928003391 nucleophile elbow; other site 62928003392 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 62928003393 FAD binding domain; Region: FAD_binding_4; pfam01565 62928003394 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 62928003395 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 62928003396 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928003397 transcription termination factor Rho; Provisional; Region: rho; PRK09376 62928003398 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 62928003399 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 62928003400 RNA binding site [nucleotide binding]; other site 62928003401 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 62928003402 multimer interface [polypeptide binding]; other site 62928003403 Walker A motif; other site 62928003404 ATP binding site [chemical binding]; other site 62928003405 Walker B motif; other site 62928003406 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 62928003407 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 62928003408 catalytic residues [active] 62928003409 Ferredoxin [Energy production and conversion]; Region: COG1146 62928003410 4Fe-4S binding domain; Region: Fer4; cl02805 62928003411 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 62928003412 FOG: CBS domain [General function prediction only]; Region: COG0517 62928003413 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_12; cd04625 62928003414 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 62928003415 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 62928003416 acyl-activating enzyme (AAE) consensus motif; other site 62928003417 putative AMP binding site [chemical binding]; other site 62928003418 putative active site [active] 62928003419 putative CoA binding site [chemical binding]; other site 62928003420 acetolactate synthase catalytic subunit; Validated; Region: PRK08155 62928003421 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 62928003422 PYR/PP interface [polypeptide binding]; other site 62928003423 dimer interface [polypeptide binding]; other site 62928003424 TPP binding site [chemical binding]; other site 62928003425 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 62928003426 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 62928003427 TPP-binding site [chemical binding]; other site 62928003428 dimer interface [polypeptide binding]; other site 62928003429 Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]; Region: IlvH; COG0440 62928003430 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 62928003431 putative valine binding site [chemical binding]; other site 62928003432 dimer interface [polypeptide binding]; other site 62928003433 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 62928003434 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 62928003435 Tetramer interface [polypeptide binding]; other site 62928003436 active site 62928003437 FMN-binding site [chemical binding]; other site 62928003438 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 62928003439 MFS_1 like family; Region: MFS_1_like; pfam12832 62928003440 Peptidase family M48; Region: Peptidase_M48; pfam01435 62928003441 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 62928003442 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 62928003443 substrate binding site [chemical binding]; other site 62928003444 ligand binding site [chemical binding]; other site 62928003445 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 62928003446 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 62928003447 substrate binding site [chemical binding]; other site 62928003448 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 62928003449 tartrate dehydrogenase; Region: TTC; TIGR02089 62928003450 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 62928003451 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 62928003452 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 62928003453 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 62928003454 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 62928003455 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 62928003456 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 62928003457 dimerization interface 3.5A [polypeptide binding]; other site 62928003458 active site 62928003459 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 62928003460 active site 62928003461 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 62928003462 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 62928003463 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928003464 catalytic residue [active] 62928003465 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 62928003466 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 62928003467 substrate binding site [chemical binding]; other site 62928003468 active site 62928003469 catalytic residues [active] 62928003470 heterodimer interface [polypeptide binding]; other site 62928003471 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 62928003472 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 62928003473 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 62928003474 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 62928003475 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 62928003476 Sporulation related domain; Region: SPOR; pfam05036 62928003477 Colicin V production protein; Region: Colicin_V; pfam02674 62928003478 amidophosphoribosyltransferase; Provisional; Region: PRK09246 62928003479 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 62928003480 active site 62928003481 tetramer interface [polypeptide binding]; other site 62928003482 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928003483 active site 62928003484 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 62928003485 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 62928003486 homodimer interface [polypeptide binding]; other site 62928003487 substrate-cofactor binding pocket; other site 62928003488 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928003489 catalytic residue [active] 62928003490 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 62928003491 putative active site [active] 62928003492 putative metal binding site [ion binding]; other site 62928003493 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 62928003494 substrate binding site [chemical binding]; other site 62928003495 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 62928003496 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 62928003497 substrate binding site [chemical binding]; other site 62928003498 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 62928003499 TPR repeat; Region: TPR_11; pfam13414 62928003500 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 62928003501 binding surface 62928003502 TPR motif; other site 62928003503 Tetratricopeptide repeat; Region: TPR_16; pfam13432 62928003504 SnoaL-like domain; Region: SnoaL_3; pfam13474 62928003505 SnoaL-like domain; Region: SnoaL_4; cl17707 62928003506 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 62928003507 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 62928003508 active site 62928003509 HIGH motif; other site 62928003510 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 62928003511 KMSKS motif; other site 62928003512 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 62928003513 tRNA binding surface [nucleotide binding]; other site 62928003514 anticodon binding site; other site 62928003515 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928003516 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 62928003517 putative ligand binding site [chemical binding]; other site 62928003518 chaperone protein DnaJ; Provisional; Region: PRK10767 62928003519 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 62928003520 HSP70 interaction site [polypeptide binding]; other site 62928003521 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 62928003522 substrate binding site [polypeptide binding]; other site 62928003523 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 62928003524 Zn binding sites [ion binding]; other site 62928003525 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 62928003526 dimer interface [polypeptide binding]; other site 62928003527 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 62928003528 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 62928003529 nucleotide binding site [chemical binding]; other site 62928003530 NEF interaction site [polypeptide binding]; other site 62928003531 SBD interface [polypeptide binding]; other site 62928003532 GrpE; Region: GrpE; pfam01025 62928003533 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 62928003534 dimer interface [polypeptide binding]; other site 62928003535 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 62928003536 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 62928003537 DNA gyrase subunit A; Validated; Region: PRK05560 62928003538 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 62928003539 CAP-like domain; other site 62928003540 active site 62928003541 primary dimer interface [polypeptide binding]; other site 62928003542 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003543 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003544 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003545 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003546 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003547 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003548 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 62928003549 homodimer interface [polypeptide binding]; other site 62928003550 substrate-cofactor binding pocket; other site 62928003551 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928003552 catalytic residue [active] 62928003553 Chorismate mutase type II; Region: CM_2; cl00693 62928003554 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 62928003555 Prephenate dehydratase; Region: PDT; pfam00800 62928003556 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 62928003557 putative L-Phe binding site [chemical binding]; other site 62928003558 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 62928003559 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 62928003560 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928003561 homodimer interface [polypeptide binding]; other site 62928003562 catalytic residue [active] 62928003563 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 62928003564 prephenate dehydrogenase; Validated; Region: PRK08507 62928003565 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 62928003566 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 62928003567 hinge; other site 62928003568 active site 62928003569 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 62928003570 CMP-binding site; other site 62928003571 The sites determining sugar specificity; other site 62928003572 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 62928003573 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 62928003574 RNA binding site [nucleotide binding]; other site 62928003575 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 62928003576 RNA binding site [nucleotide binding]; other site 62928003577 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 62928003578 RNA binding site [nucleotide binding]; other site 62928003579 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 62928003580 RNA binding site [nucleotide binding]; other site 62928003581 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 62928003582 RNA binding site [nucleotide binding]; other site 62928003583 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 62928003584 RNA binding site [nucleotide binding]; other site 62928003585 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 62928003586 IHF dimer interface [polypeptide binding]; other site 62928003587 IHF - DNA interface [nucleotide binding]; other site 62928003588 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 62928003589 tetratricopeptide repeat protein; Provisional; Region: PRK11788 62928003590 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 62928003591 binding surface 62928003592 TPR motif; other site 62928003593 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 62928003594 binding surface 62928003595 TPR motif; other site 62928003596 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 62928003597 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 62928003598 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 62928003599 cysteine synthase B; Region: cysM; TIGR01138 62928003600 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 62928003601 dimer interface [polypeptide binding]; other site 62928003602 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928003603 catalytic residue [active] 62928003604 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 62928003605 active site 62928003606 catalytic site [active] 62928003607 substrate binding site [chemical binding]; other site 62928003608 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 62928003609 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 62928003610 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 62928003611 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 62928003612 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 62928003613 active site 62928003614 dimer interface [polypeptide binding]; other site 62928003615 motif 1; other site 62928003616 motif 2; other site 62928003617 motif 3; other site 62928003618 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 62928003619 anticodon binding site; other site 62928003620 translation initiation factor IF-3; Region: infC; TIGR00168 62928003621 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 62928003622 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 62928003623 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 62928003624 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 62928003625 23S rRNA binding site [nucleotide binding]; other site 62928003626 L21 binding site [polypeptide binding]; other site 62928003627 L13 binding site [polypeptide binding]; other site 62928003628 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 62928003629 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 62928003630 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 62928003631 dimer interface [polypeptide binding]; other site 62928003632 motif 1; other site 62928003633 active site 62928003634 motif 2; other site 62928003635 motif 3; other site 62928003636 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 62928003637 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 62928003638 putative tRNA-binding site [nucleotide binding]; other site 62928003639 B3/4 domain; Region: B3_4; pfam03483 62928003640 tRNA synthetase B5 domain; Region: B5; smart00874 62928003641 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 62928003642 dimer interface [polypeptide binding]; other site 62928003643 motif 1; other site 62928003644 motif 3; other site 62928003645 motif 2; other site 62928003646 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 62928003647 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 62928003648 IHF dimer interface [polypeptide binding]; other site 62928003649 IHF - DNA interface [nucleotide binding]; other site 62928003650 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 62928003651 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928003652 DNA binding residues [nucleotide binding] 62928003653 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 62928003654 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 62928003655 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 62928003656 S-adenosylmethionine binding site [chemical binding]; other site 62928003657 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 62928003658 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 62928003659 Peptidase family M23; Region: Peptidase_M23; pfam01551 62928003660 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 62928003661 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928003662 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 62928003663 murein hydrolase B; Provisional; Region: PRK10760; cl17906 62928003664 Transglycosylase SLT domain; Region: SLT_2; pfam13406 62928003665 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 62928003666 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 62928003667 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 62928003668 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 62928003669 Protein of unknown function DUF58; Region: DUF58; pfam01882 62928003670 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 62928003671 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 62928003672 Walker A motif; other site 62928003673 ATP binding site [chemical binding]; other site 62928003674 Walker B motif; other site 62928003675 arginine finger; other site 62928003676 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 62928003677 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 62928003678 putative active site [active] 62928003679 Zn binding site [ion binding]; other site 62928003680 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 62928003681 dihydrodipicolinate synthase; Region: dapA; TIGR00674 62928003682 dimer interface [polypeptide binding]; other site 62928003683 active site 62928003684 catalytic residue [active] 62928003685 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 62928003686 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 62928003687 Uncharacterized conserved protein [Function unknown]; Region: COG2850 62928003688 Cupin-like domain; Region: Cupin_8; pfam13621 62928003689 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 62928003690 TRAM domain; Region: TRAM; pfam01938 62928003691 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 62928003692 S-adenosylmethionine binding site [chemical binding]; other site 62928003693 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 62928003694 pseudouridine synthase; Region: TIGR00093 62928003695 active site 62928003696 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 62928003697 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 62928003698 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 62928003699 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 62928003700 FHIPEP family; Region: FHIPEP; pfam00771 62928003701 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 62928003702 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 62928003703 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 62928003704 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 62928003705 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928003706 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 62928003707 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 62928003708 DNA binding residues [nucleotide binding] 62928003709 flagellar motor protein; Reviewed; Region: motC; PRK09109 62928003710 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 62928003711 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928003712 HAMP domain; Region: HAMP; pfam00672 62928003713 dimerization interface [polypeptide binding]; other site 62928003714 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928003715 dimer interface [polypeptide binding]; other site 62928003716 putative CheW interface [polypeptide binding]; other site 62928003717 flagellar motor protein MotD; Reviewed; Region: PRK09038 62928003718 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 62928003719 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928003720 ligand binding site [chemical binding]; other site 62928003721 Hemerythrin; Region: Hemerythrin; cd12107 62928003722 Fe binding site [ion binding]; other site 62928003723 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 62928003724 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 62928003725 CAP-like domain; other site 62928003726 active site 62928003727 primary dimer interface [polypeptide binding]; other site 62928003728 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 62928003729 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 62928003730 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 62928003731 active site 62928003732 motif I; other site 62928003733 motif II; other site 62928003734 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 62928003735 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 62928003736 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 62928003737 ATP binding site [chemical binding]; other site 62928003738 Mg2+ binding site [ion binding]; other site 62928003739 G-X-G motif; other site 62928003740 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 62928003741 anchoring element; other site 62928003742 dimer interface [polypeptide binding]; other site 62928003743 ATP binding site [chemical binding]; other site 62928003744 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 62928003745 active site 62928003746 putative metal-binding site [ion binding]; other site 62928003747 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 62928003748 Predicted membrane protein [Function unknown]; Region: COG2860 62928003749 UPF0126 domain; Region: UPF0126; pfam03458 62928003750 UPF0126 domain; Region: UPF0126; pfam03458 62928003751 isocitrate lyase; Provisional; Region: PRK15063 62928003752 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 62928003753 tetramer interface [polypeptide binding]; other site 62928003754 active site 62928003755 Mg2+/Mn2+ binding site [ion binding]; other site 62928003756 LIM is a small protein-protein interaction domain, containing two zinc fingers; Region: LIM; cl02475 62928003757 Zn binding site [ion binding]; other site 62928003758 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928003759 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 62928003760 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928003761 short chain dehydrogenase; Provisional; Region: PRK08265 62928003762 classical (c) SDRs; Region: SDR_c; cd05233 62928003763 NAD(P) binding site [chemical binding]; other site 62928003764 active site 62928003765 Isochorismatase family; Region: Isochorismatase; pfam00857 62928003766 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 62928003767 catalytic triad [active] 62928003768 conserved cis-peptide bond; other site 62928003769 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 62928003770 inter-subunit interface; other site 62928003771 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 62928003772 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 62928003773 iron-sulfur cluster [ion binding]; other site 62928003774 [2Fe-2S] cluster binding site [ion binding]; other site 62928003775 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 62928003776 putative alpha subunit interface [polypeptide binding]; other site 62928003777 putative active site [active] 62928003778 putative substrate binding site [chemical binding]; other site 62928003779 Fe binding site [ion binding]; other site 62928003780 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 62928003781 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 62928003782 FMN-binding pocket [chemical binding]; other site 62928003783 flavin binding motif; other site 62928003784 phosphate binding motif [ion binding]; other site 62928003785 beta-alpha-beta structure motif; other site 62928003786 NAD binding pocket [chemical binding]; other site 62928003787 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 62928003788 catalytic loop [active] 62928003789 iron binding site [ion binding]; other site 62928003790 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928003791 TM-ABC transporter signature motif; other site 62928003792 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928003793 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928003794 TM-ABC transporter signature motif; other site 62928003795 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928003796 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928003797 Walker A/P-loop; other site 62928003798 ATP binding site [chemical binding]; other site 62928003799 Q-loop/lid; other site 62928003800 ABC transporter signature motif; other site 62928003801 Walker B; other site 62928003802 D-loop; other site 62928003803 H-loop/switch region; other site 62928003804 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928003805 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928003806 Walker A/P-loop; other site 62928003807 ATP binding site [chemical binding]; other site 62928003808 Q-loop/lid; other site 62928003809 ABC transporter signature motif; other site 62928003810 Walker B; other site 62928003811 D-loop; other site 62928003812 H-loop/switch region; other site 62928003813 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928003814 Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; Region: PBP1_Nba_like; cd06359 62928003815 putative ligand binding site [chemical binding]; other site 62928003816 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 62928003817 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 62928003818 Clp amino terminal domain; Region: Clp_N; pfam02861 62928003819 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 62928003820 Walker A motif; other site 62928003821 ATP binding site [chemical binding]; other site 62928003822 Walker B motif; other site 62928003823 arginine finger; other site 62928003824 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 62928003825 Walker A motif; other site 62928003826 ATP binding site [chemical binding]; other site 62928003827 Walker B motif; other site 62928003828 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 62928003829 Uncharacterized conserved protein [Function unknown]; Region: COG2127 62928003830 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 62928003831 DNA-binding site [nucleotide binding]; DNA binding site 62928003832 RNA-binding motif; other site 62928003833 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 62928003834 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 62928003835 hypothetical protein; Reviewed; Region: PRK00024 62928003836 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 62928003837 MPN+ (JAMM) motif; other site 62928003838 Zinc-binding site [ion binding]; other site 62928003839 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 62928003840 Flavoprotein; Region: Flavoprotein; pfam02441 62928003841 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 62928003842 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 62928003843 trimer interface [polypeptide binding]; other site 62928003844 active site 62928003845 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_24; cd04683 62928003846 nudix motif; other site 62928003847 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 62928003848 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928003849 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 62928003850 Cytochrome c; Region: Cytochrom_C; cl11414 62928003851 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 62928003852 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 62928003853 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 62928003854 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 62928003855 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 62928003856 Monomeric isocitrate dehydrogenase; Region: IDH; pfam03971 62928003857 isocitrate dehydrogenase; Validated; Region: PRK07362 62928003858 isocitrate dehydrogenase; Reviewed; Region: PRK07006 62928003859 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 62928003860 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 62928003861 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 62928003862 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 62928003863 Na binding site [ion binding]; other site 62928003864 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 62928003865 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 62928003866 elongation factor G; Reviewed; Region: PRK12740 62928003867 G1 box; other site 62928003868 putative GEF interaction site [polypeptide binding]; other site 62928003869 GTP/Mg2+ binding site [chemical binding]; other site 62928003870 Switch I region; other site 62928003871 G2 box; other site 62928003872 G3 box; other site 62928003873 Switch II region; other site 62928003874 G4 box; other site 62928003875 G5 box; other site 62928003876 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 62928003877 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 62928003878 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 62928003879 folate/biopterin transporter; Region: fbt; TIGR00788 62928003880 LrgB-like family; Region: LrgB; pfam04172 62928003881 LrgA family; Region: LrgA; pfam03788 62928003882 PTS system, glucitol/sorbitol-specific, IIBC component; Region: EIIBC-GUT; TIGR00825 62928003883 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 62928003884 FMN binding site [chemical binding]; other site 62928003885 substrate binding site [chemical binding]; other site 62928003886 putative catalytic residue [active] 62928003887 malate synthase A; Region: malate_syn_A; TIGR01344 62928003888 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 62928003889 active site 62928003890 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 62928003891 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928003892 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 62928003893 putative effector binding pocket; other site 62928003894 dimerization interface [polypeptide binding]; other site 62928003895 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 62928003896 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 62928003897 MOFRL family; Region: MOFRL; pfam05161 62928003898 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 62928003899 L-lactate permease; Provisional; Region: PRK10420 62928003900 glycolate transporter; Provisional; Region: PRK09695 62928003901 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 62928003902 FAD binding domain; Region: FAD_binding_4; pfam01565 62928003903 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 62928003904 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 62928003905 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 62928003906 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 62928003907 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 62928003908 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 62928003909 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 62928003910 Cysteine-rich domain; Region: CCG; pfam02754 62928003911 Cysteine-rich domain; Region: CCG; pfam02754 62928003912 Transcriptional regulators [Transcription]; Region: FadR; COG2186 62928003913 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928003914 DNA-binding site [nucleotide binding]; DNA binding site 62928003915 FCD domain; Region: FCD; pfam07729 62928003916 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 62928003917 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 62928003918 DNA-binding site [nucleotide binding]; DNA binding site 62928003919 RNA-binding motif; other site 62928003920 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 62928003921 nitrite reductase subunit NirD; Provisional; Region: PRK14989 62928003922 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928003923 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928003924 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 62928003925 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 62928003926 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 62928003927 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 62928003928 active site 62928003929 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 62928003930 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928003931 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928003932 active site 62928003933 ATP binding site [chemical binding]; other site 62928003934 substrate binding site [chemical binding]; other site 62928003935 activation loop (A-loop); other site 62928003936 Ureidoglycolate hydrolase [Nucleotide transport and metabolism]; Region: DAL3; COG3194 62928003937 ureidoglycolate hydrolase; Provisional; Region: PRK03606 62928003938 allantoicase; Provisional; Region: PRK13257 62928003939 Allantoicase repeat; Region: Allantoicase; pfam03561 62928003940 Allantoicase repeat; Region: Allantoicase; pfam03561 62928003941 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 62928003942 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 62928003943 active site 62928003944 catalytic site [active] 62928003945 tetramer interface [polypeptide binding]; other site 62928003946 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 62928003947 Predicted membrane protein [Function unknown]; Region: COG3748 62928003948 Protein of unknown function (DUF989); Region: DUF989; pfam06181 62928003949 Cytochrome c; Region: Cytochrom_C; pfam00034 62928003950 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 62928003951 active site 62928003952 homotetramer interface [polypeptide binding]; other site 62928003953 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 62928003954 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 62928003955 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 62928003956 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 62928003957 coenzyme PQQ biosynthesis protein PqqD; Region: PQQ_PqqD; TIGR03859 62928003958 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 62928003959 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 62928003960 FeS/SAM binding site; other site 62928003961 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 62928003962 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 62928003963 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 62928003964 dimer interface [polypeptide binding]; other site 62928003965 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 62928003966 active site 62928003967 Fe binding site [ion binding]; other site 62928003968 H+ Antiporter protein; Region: 2A0121; TIGR00900 62928003969 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 62928003970 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 62928003971 inhibitor-cofactor binding pocket; inhibition site 62928003972 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928003973 catalytic residue [active] 62928003974 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 62928003975 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 62928003976 putative GTP cyclohydrolase; Provisional; Region: PRK13674 62928003977 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 62928003978 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 62928003979 TPP-binding site; other site 62928003980 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 62928003981 PYR/PP interface [polypeptide binding]; other site 62928003982 dimer interface [polypeptide binding]; other site 62928003983 TPP binding site [chemical binding]; other site 62928003984 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 62928003985 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 62928003986 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 62928003987 substrate binding pocket [chemical binding]; other site 62928003988 chain length determination region; other site 62928003989 substrate-Mg2+ binding site; other site 62928003990 catalytic residues [active] 62928003991 aspartate-rich region 1; other site 62928003992 active site lid residues [active] 62928003993 aspartate-rich region 2; other site 62928003994 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 62928003995 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 62928003996 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 62928003997 [2Fe-2S] cluster binding site [ion binding]; other site 62928003998 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 62928003999 alpha subunit interface [polypeptide binding]; other site 62928004000 active site 62928004001 substrate binding site [chemical binding]; other site 62928004002 Fe binding site [ion binding]; other site 62928004003 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 62928004004 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 62928004005 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 62928004006 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 62928004007 lipoprotein signal peptidase; Provisional; Region: PRK14787 62928004008 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 62928004009 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 62928004010 active site 62928004011 HIGH motif; other site 62928004012 nucleotide binding site [chemical binding]; other site 62928004013 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 62928004014 active site 62928004015 KMSKS motif; other site 62928004016 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 62928004017 tRNA binding surface [nucleotide binding]; other site 62928004018 anticodon binding site; other site 62928004019 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 62928004020 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 62928004021 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 62928004022 active site 62928004023 Riboflavin kinase; Region: Flavokinase; smart00904 62928004024 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 62928004025 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 62928004026 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 62928004027 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 62928004028 FOG: WD40 repeat [General function prediction only]; Region: COG2319 62928004029 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 62928004030 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 62928004031 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 62928004032 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 62928004033 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 62928004034 intersubunit interface [polypeptide binding]; other site 62928004035 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 62928004036 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 62928004037 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 62928004038 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 62928004039 ABC-ATPase subunit interface; other site 62928004040 dimer interface [polypeptide binding]; other site 62928004041 putative PBP binding regions; other site 62928004042 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 62928004043 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 62928004044 ABC-ATPase subunit interface; other site 62928004045 dimer interface [polypeptide binding]; other site 62928004046 putative PBP binding regions; other site 62928004047 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 62928004048 dimerization interface [polypeptide binding]; other site 62928004049 putative path to active site cavity [active] 62928004050 diiron center [ion binding]; other site 62928004051 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 62928004052 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 62928004053 catalytic loop [active] 62928004054 iron binding site [ion binding]; other site 62928004055 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is...; Region: monooxygenase_like; cd06212 62928004056 FAD binding pocket [chemical binding]; other site 62928004057 FAD binding motif [chemical binding]; other site 62928004058 phosphate binding motif [ion binding]; other site 62928004059 beta-alpha-beta structure motif; other site 62928004060 NAD binding pocket [chemical binding]; other site 62928004061 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 62928004062 dimerization interface [polypeptide binding]; other site 62928004063 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 62928004064 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 62928004065 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 62928004066 ring oligomerisation interface [polypeptide binding]; other site 62928004067 ATP/Mg binding site [chemical binding]; other site 62928004068 stacking interactions; other site 62928004069 hinge regions; other site 62928004070 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 62928004071 GAF domain; Region: GAF; pfam01590 62928004072 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 62928004073 Walker A motif; other site 62928004074 ATP binding site [chemical binding]; other site 62928004075 Walker B motif; other site 62928004076 arginine finger; other site 62928004077 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928004078 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928004079 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 62928004080 dimer interface [polypeptide binding]; other site 62928004081 active site 62928004082 metal binding site [ion binding]; metal-binding site 62928004083 glutathione binding site [chemical binding]; other site 62928004084 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 62928004085 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 62928004086 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 62928004087 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; pfam09600 62928004088 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 62928004089 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 62928004090 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 62928004091 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 62928004092 PAS domain; Region: PAS_9; pfam13426 62928004093 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 62928004094 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 62928004095 Walker A motif; other site 62928004096 ATP binding site [chemical binding]; other site 62928004097 Walker B motif; other site 62928004098 arginine finger; other site 62928004099 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928004100 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 62928004101 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 62928004102 [2Fe-2S] cluster binding site [ion binding]; other site 62928004103 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928004104 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 62928004105 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928004106 Walker A/P-loop; other site 62928004107 ATP binding site [chemical binding]; other site 62928004108 Q-loop/lid; other site 62928004109 ABC transporter signature motif; other site 62928004110 Walker B; other site 62928004111 D-loop; other site 62928004112 H-loop/switch region; other site 62928004113 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 62928004114 active site 62928004115 catalytic residues [active] 62928004116 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 62928004117 quinohemoprotein amine dehydrogenase, alpha subunit; Region: QH_alpha; TIGR03908 62928004118 Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; Region: Dehyd-heme_bind; pfam09098 62928004119 Bacterial Ig-like domain (DUF1927); Region: DUF1927; pfam09099 62928004120 Domain of unknown function (DUF1928); Region: DUF1928; pfam09100 62928004121 quinohemoprotein amine dehydrogenase maturation protein; Region: quino_hemo_SAM; TIGR03906 62928004122 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 62928004123 FeS/SAM binding site; other site 62928004124 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 62928004125 Quinohemoprotein amine dehydrogenase, gamma subunit; Region: QH-AmDH_gamma; pfam08992 62928004126 quinohemoprotein amine dehydrogenase, beta subunit; Region: QH_beta; TIGR03907 62928004127 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 62928004128 AMIN domain; Region: AMIN; pfam11741 62928004129 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 62928004130 active site 62928004131 metal binding site [ion binding]; metal-binding site 62928004132 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 62928004133 epoxyqueuosine reductase; Region: TIGR00276 62928004134 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 62928004135 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 62928004136 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_1; cd03326 62928004137 putative active site pocket [active] 62928004138 metal binding site [ion binding]; metal-binding site 62928004139 transcriptional activator TtdR; Provisional; Region: PRK09801 62928004140 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928004141 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 62928004142 putative effector binding pocket; other site 62928004143 putative dimerization interface [polypeptide binding]; other site 62928004144 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 62928004145 SlyX; Region: SlyX; pfam04102 62928004146 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 62928004147 Peptidase family U32; Region: Peptidase_U32; pfam01136 62928004148 Collagenase; Region: DUF3656; pfam12392 62928004149 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 62928004150 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 62928004151 Cache domain; Region: Cache_1; pfam02743 62928004152 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 62928004153 dimerization interface [polypeptide binding]; other site 62928004154 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928004155 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928004156 metal binding site [ion binding]; metal-binding site 62928004157 active site 62928004158 I-site; other site 62928004159 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 62928004160 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 62928004161 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928004162 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 62928004163 active site 62928004164 ATP binding site [chemical binding]; other site 62928004165 substrate binding site [chemical binding]; other site 62928004166 activation loop (A-loop); other site 62928004167 HDOD domain; Region: HDOD; pfam08668 62928004168 GAF domain; Region: GAF; pfam01590 62928004169 Peptidase C13 family; Region: Peptidase_C13; cl02159 62928004170 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 62928004171 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 62928004172 metal binding site [ion binding]; metal-binding site 62928004173 dimer interface [polypeptide binding]; other site 62928004174 Repair protein; Region: Repair_PSII; pfam04536 62928004175 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 62928004176 Repair protein; Region: Repair_PSII; pfam04536 62928004177 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 62928004178 Dodecin; Region: Dodecin; pfam07311 62928004179 TIR domain; Region: TIR_2; pfam13676 62928004180 LCCL domain; Region: LCCL; pfam03815 62928004181 LCCL domain; Region: LCCL; pfam03815 62928004182 chaperone protein DnaJ; Provisional; Region: PRK14292 62928004183 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 62928004184 HSP70 interaction site [polypeptide binding]; other site 62928004185 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 62928004186 Zn binding sites [ion binding]; other site 62928004187 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 62928004188 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 62928004189 XAP5, circadian clock regulator; Region: XAP5; pfam04921 62928004190 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 62928004191 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 62928004192 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928004193 ATP-grasp domain; Region: ATP-grasp; pfam02222 62928004194 Protein of unknown function (DUF342); Region: DUF342; pfam03961 62928004195 Protein of unknown function (DUF330); Region: DUF330; cl01135 62928004196 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 62928004197 mce related protein; Region: MCE; pfam02470 62928004198 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 62928004199 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 62928004200 Walker A/P-loop; other site 62928004201 ATP binding site [chemical binding]; other site 62928004202 Q-loop/lid; other site 62928004203 ABC transporter signature motif; other site 62928004204 Walker B; other site 62928004205 D-loop; other site 62928004206 H-loop/switch region; other site 62928004207 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 62928004208 Permease; Region: Permease; pfam02405 62928004209 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 62928004210 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928004211 Walker A/P-loop; other site 62928004212 ATP binding site [chemical binding]; other site 62928004213 Q-loop/lid; other site 62928004214 ABC transporter signature motif; other site 62928004215 Walker B; other site 62928004216 D-loop; other site 62928004217 H-loop/switch region; other site 62928004218 ABC transporter; Region: ABC_tran_2; pfam12848 62928004219 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 62928004220 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 62928004221 S-adenosylmethionine binding site [chemical binding]; other site 62928004222 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 62928004223 catalytic residues [active] 62928004224 dimer interface [polypeptide binding]; other site 62928004225 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 62928004226 PAS domain; Region: PAS_9; pfam13426 62928004227 putative active site [active] 62928004228 heme pocket [chemical binding]; other site 62928004229 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928004230 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928004231 metal binding site [ion binding]; metal-binding site 62928004232 active site 62928004233 I-site; other site 62928004234 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 62928004235 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 62928004236 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 62928004237 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 62928004238 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 62928004239 FAD binding pocket [chemical binding]; other site 62928004240 FAD binding motif [chemical binding]; other site 62928004241 phosphate binding motif [ion binding]; other site 62928004242 beta-alpha-beta structure motif; other site 62928004243 NAD binding pocket [chemical binding]; other site 62928004244 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 62928004245 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928004246 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 62928004247 putative dimerization interface [polypeptide binding]; other site 62928004248 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 62928004249 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 62928004250 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 62928004251 active site 62928004252 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 62928004253 glycine dehydrogenase; Provisional; Region: PRK05367 62928004254 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 62928004255 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928004256 catalytic residue [active] 62928004257 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 62928004258 tetramer interface [polypeptide binding]; other site 62928004259 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928004260 catalytic residue [active] 62928004261 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 62928004262 lipoyl attachment site [posttranslational modification]; other site 62928004263 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 62928004264 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 62928004265 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 62928004266 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 62928004267 putative substrate translocation pore; other site 62928004268 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 62928004269 Protein phosphatase 2C; Region: PP2C; pfam00481 62928004270 active site 62928004271 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 62928004272 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928004273 active site 62928004274 ATP binding site [chemical binding]; other site 62928004275 substrate binding site [chemical binding]; other site 62928004276 activation loop (A-loop); other site 62928004277 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 62928004278 catalytic core [active] 62928004279 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 62928004280 putative active site [active] 62928004281 putative triphosphate binding site [ion binding]; other site 62928004282 putative metal binding residues [ion binding]; other site 62928004283 The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family; Region: CHAD; smart00880 62928004284 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 62928004285 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 62928004286 metal binding triad; other site 62928004287 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 62928004288 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 62928004289 metal binding triad; other site 62928004290 TIGR02099 family protein; Region: TIGR02099 62928004291 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 62928004292 nitrilase; Region: PLN02798 62928004293 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 62928004294 putative active site [active] 62928004295 catalytic triad [active] 62928004296 dimer interface [polypeptide binding]; other site 62928004297 protease TldD; Provisional; Region: tldD; PRK10735 62928004298 type VI secretion system lysozyme-like protein; Region: VI_zyme; TIGR03357 62928004299 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 62928004300 type VI secretion protein, VC_A0114 family; Region: VI_chp_4; TIGR03353 62928004301 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 62928004302 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 62928004303 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_M15_4; pfam13539 62928004304 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 62928004305 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 62928004306 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 62928004307 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 62928004308 Protein of unknown function (DUF770); Region: DUF770; pfam05591 62928004309 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 62928004310 Protein of unknown function (DUF877); Region: DUF877; pfam05943 62928004311 Protein of unknown function (DUF796); Region: DUF796; pfam05638 62928004312 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 62928004313 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 62928004314 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 62928004315 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 62928004316 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4253 62928004317 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 62928004318 type VI secretion protein, VC_A0110 family; Region: VI_chp_6; TIGR03359 62928004319 Protein of unknown function (DUF1305); Region: DUF1305; pfam06996 62928004320 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 62928004321 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 62928004322 PAAR motif; Region: PAAR_motif; pfam05488 62928004323 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 62928004324 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 62928004325 S-adenosylmethionine binding site [chemical binding]; other site 62928004326 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 62928004327 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 62928004328 PhnA protein; Region: PhnA; pfam03831 62928004329 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG0390 62928004330 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4619 62928004331 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928004332 Walker A/P-loop; other site 62928004333 ATP binding site [chemical binding]; other site 62928004334 Q-loop/lid; other site 62928004335 ABC transporter signature motif; other site 62928004336 Walker B; other site 62928004337 D-loop; other site 62928004338 H-loop/switch region; other site 62928004339 Methyltransferase domain; Region: Methyltransf_23; pfam13489 62928004340 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 62928004341 S-adenosylmethionine binding site [chemical binding]; other site 62928004342 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 62928004343 Methyltransferase domain; Region: Methyltransf_11; pfam08241 62928004344 Cupin; Region: Cupin_6; pfam12852 62928004345 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928004346 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928004347 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928004348 Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Region: PLDc_unchar6; cd09176 62928004349 PLD-like domain; Region: PLDc_2; pfam13091 62928004350 putative homodimer interface [polypeptide binding]; other site 62928004351 putative active site [active] 62928004352 catalytic site [active] 62928004353 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928004354 active site 62928004355 ATP binding site [chemical binding]; other site 62928004356 substrate binding site [chemical binding]; other site 62928004357 activation loop (A-loop); other site 62928004358 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 62928004359 G4 box; other site 62928004360 G5 box; other site 62928004361 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 62928004362 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 62928004363 HflX GTPase family; Region: HflX; cd01878 62928004364 G1 box; other site 62928004365 GTP/Mg2+ binding site [chemical binding]; other site 62928004366 Switch I region; other site 62928004367 G2 box; other site 62928004368 G3 box; other site 62928004369 Switch II region; other site 62928004370 G4 box; other site 62928004371 G5 box; other site 62928004372 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 62928004373 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 62928004374 substrate binding pocket [chemical binding]; other site 62928004375 membrane-bound complex binding site; other site 62928004376 hinge residues; other site 62928004377 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 62928004378 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928004379 catalytic residue [active] 62928004380 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 62928004381 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 62928004382 dimer interface [polypeptide binding]; other site 62928004383 conserved gate region; other site 62928004384 putative PBP binding loops; other site 62928004385 ABC-ATPase subunit interface; other site 62928004386 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 62928004387 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 62928004388 dimer interface [polypeptide binding]; other site 62928004389 conserved gate region; other site 62928004390 putative PBP binding loops; other site 62928004391 ABC-ATPase subunit interface; other site 62928004392 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 62928004393 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 62928004394 substrate binding pocket [chemical binding]; other site 62928004395 membrane-bound complex binding site; other site 62928004396 hinge residues; other site 62928004397 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 62928004398 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928004399 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 62928004400 substrate binding site [chemical binding]; other site 62928004401 dimerization interface [polypeptide binding]; other site 62928004402 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 62928004403 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 62928004404 Walker A/P-loop; other site 62928004405 ATP binding site [chemical binding]; other site 62928004406 Q-loop/lid; other site 62928004407 ABC transporter signature motif; other site 62928004408 Walker B; other site 62928004409 D-loop; other site 62928004410 H-loop/switch region; other site 62928004411 TOBE-like domain; Region: TOBE_3; pfam12857 62928004412 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 62928004413 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 62928004414 dimer interface [polypeptide binding]; other site 62928004415 conserved gate region; other site 62928004416 putative PBP binding loops; other site 62928004417 ABC-ATPase subunit interface; other site 62928004418 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 62928004419 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 62928004420 dimer interface [polypeptide binding]; other site 62928004421 conserved gate region; other site 62928004422 putative PBP binding loops; other site 62928004423 ABC-ATPase subunit interface; other site 62928004424 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 62928004425 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 62928004426 Transglycosylase SLT domain; Region: SLT_2; pfam13406 62928004427 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 62928004428 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928004429 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 62928004430 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 62928004431 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 62928004432 NAD binding site [chemical binding]; other site 62928004433 homodimer interface [polypeptide binding]; other site 62928004434 homotetramer interface [polypeptide binding]; other site 62928004435 active site 62928004436 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 62928004437 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 62928004438 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 62928004439 metal-binding site [ion binding] 62928004440 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 62928004441 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 62928004442 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 62928004443 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 62928004444 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 62928004445 Low-spin heme binding site [chemical binding]; other site 62928004446 Putative water exit pathway; other site 62928004447 Binuclear center (active site) [active] 62928004448 Putative proton exit pathway; other site 62928004449 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 62928004450 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 62928004451 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 62928004452 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 62928004453 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928004454 Cytochrome c; Region: Cytochrom_C; pfam00034 62928004455 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 62928004456 4Fe-4S binding domain; Region: Fer4_5; pfam12801 62928004457 4Fe-4S binding domain; Region: Fer4; pfam00037 62928004458 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 62928004459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 62928004460 FixH; Region: FixH; pfam05751 62928004461 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 62928004462 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 62928004463 Ligand Binding Site [chemical binding]; other site 62928004464 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 62928004465 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 62928004466 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 62928004467 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 62928004468 ligand binding site [chemical binding]; other site 62928004469 flexible hinge region; other site 62928004470 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 62928004471 putative switch regulator; other site 62928004472 non-specific DNA interactions [nucleotide binding]; other site 62928004473 DNA binding site [nucleotide binding] 62928004474 sequence specific DNA binding site [nucleotide binding]; other site 62928004475 putative cAMP binding site [chemical binding]; other site 62928004476 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 62928004477 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 62928004478 FeS/SAM binding site; other site 62928004479 HemN C-terminal domain; Region: HemN_C; pfam06969 62928004480 Family description; Region: DsbD_2; pfam13386 62928004481 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 62928004482 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 62928004483 DNA binding residues [nucleotide binding] 62928004484 dimer interface [polypeptide binding]; other site 62928004485 mercury binding site [ion binding]; other site 62928004486 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 62928004487 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 62928004488 metal-binding site [ion binding] 62928004489 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 62928004490 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 62928004491 metal-binding site [ion binding] 62928004492 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 62928004493 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 62928004494 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 62928004495 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 62928004496 metal-binding site [ion binding] 62928004497 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928004498 PAS domain; Region: PAS_9; pfam13426 62928004499 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928004500 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928004501 metal binding site [ion binding]; metal-binding site 62928004502 active site 62928004503 I-site; other site 62928004504 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 62928004505 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 62928004506 dimer interface [polypeptide binding]; other site 62928004507 substrate binding site [chemical binding]; other site 62928004508 metal binding sites [ion binding]; metal-binding site 62928004509 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 62928004510 Protein of unknown function, DUF482; Region: DUF482; pfam04339 62928004511 NAD synthetase; Provisional; Region: PRK13981 62928004512 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 62928004513 multimer interface [polypeptide binding]; other site 62928004514 active site 62928004515 catalytic triad [active] 62928004516 protein interface 1 [polypeptide binding]; other site 62928004517 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 62928004518 homodimer interface [polypeptide binding]; other site 62928004519 NAD binding pocket [chemical binding]; other site 62928004520 ATP binding pocket [chemical binding]; other site 62928004521 Mg binding site [ion binding]; other site 62928004522 active-site loop [active] 62928004523 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 62928004524 Nitrogen regulatory protein P-II; Region: P-II; smart00938 62928004525 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 62928004526 Smr domain; Region: Smr; pfam01713 62928004527 thioredoxin reductase; Provisional; Region: PRK10262 62928004528 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928004529 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928004530 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 62928004531 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 62928004532 ligand binding site [chemical binding]; other site 62928004533 flexible hinge region; other site 62928004534 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 62928004535 putative switch regulator; other site 62928004536 non-specific DNA interactions [nucleotide binding]; other site 62928004537 DNA binding site [nucleotide binding] 62928004538 sequence specific DNA binding site [nucleotide binding]; other site 62928004539 putative cAMP binding site [chemical binding]; other site 62928004540 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 62928004541 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 62928004542 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 62928004543 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 62928004544 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 62928004545 recombination factor protein RarA; Reviewed; Region: PRK13342 62928004546 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 62928004547 Walker A motif; other site 62928004548 ATP binding site [chemical binding]; other site 62928004549 Walker B motif; other site 62928004550 arginine finger; other site 62928004551 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 62928004552 dipeptidyl carboxypeptidase II; Provisional; Region: PRK10280 62928004553 seryl-tRNA synthetase; Provisional; Region: PRK05431 62928004554 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 62928004555 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 62928004556 dimer interface [polypeptide binding]; other site 62928004557 active site 62928004558 motif 1; other site 62928004559 motif 2; other site 62928004560 motif 3; other site 62928004561 PAS domain; Region: PAS_9; pfam13426 62928004562 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 62928004563 putative active site [active] 62928004564 heme pocket [chemical binding]; other site 62928004565 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 62928004566 dimerization interface [polypeptide binding]; other site 62928004567 Protein of unknown function (DUF972); Region: DUF972; pfam06156 62928004568 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928004569 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928004570 dimer interface [polypeptide binding]; other site 62928004571 putative CheW interface [polypeptide binding]; other site 62928004572 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 62928004573 E3 interaction surface; other site 62928004574 lipoyl attachment site [posttranslational modification]; other site 62928004575 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 62928004576 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 62928004577 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928004578 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 62928004579 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 62928004580 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 62928004581 E3 interaction surface; other site 62928004582 lipoyl attachment site [posttranslational modification]; other site 62928004583 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 62928004584 E3 interaction surface; other site 62928004585 lipoyl attachment site [posttranslational modification]; other site 62928004586 e3 binding domain; Region: E3_binding; pfam02817 62928004587 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 62928004588 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 62928004589 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 62928004590 dimer interface [polypeptide binding]; other site 62928004591 TPP-binding site [chemical binding]; other site 62928004592 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928004593 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_2; cd06335 62928004594 putative ligand binding site [chemical binding]; other site 62928004595 PAS domain S-box; Region: sensory_box; TIGR00229 62928004596 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 62928004597 putative active site [active] 62928004598 heme pocket [chemical binding]; other site 62928004599 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 62928004600 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 62928004601 putative active site [active] 62928004602 heme pocket [chemical binding]; other site 62928004603 PAS domain; Region: PAS_8; pfam13188 62928004604 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 62928004605 dimer interface [polypeptide binding]; other site 62928004606 phosphorylation site [posttranslational modification] 62928004607 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 62928004608 ATP binding site [chemical binding]; other site 62928004609 Mg2+ binding site [ion binding]; other site 62928004610 G-X-G motif; other site 62928004611 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 62928004612 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 62928004613 active site 62928004614 phosphorylation site [posttranslational modification] 62928004615 intermolecular recognition site; other site 62928004616 dimerization interface [polypeptide binding]; other site 62928004617 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 62928004618 DNA binding residues [nucleotide binding] 62928004619 dimerization interface [polypeptide binding]; other site 62928004620 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 62928004621 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 62928004622 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 62928004623 homodimer interface [polypeptide binding]; other site 62928004624 NADP binding site [chemical binding]; other site 62928004625 substrate binding site [chemical binding]; other site 62928004626 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 62928004627 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 62928004628 ATP-grasp domain; Region: ATP-grasp; pfam02222 62928004629 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 62928004630 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 62928004631 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 62928004632 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 62928004633 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 62928004634 catalytic site [active] 62928004635 subunit interface [polypeptide binding]; other site 62928004636 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 62928004637 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 62928004638 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 62928004639 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 62928004640 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 62928004641 ATP-grasp domain; Region: ATP-grasp_4; cl17255 62928004642 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 62928004643 IMP binding site; other site 62928004644 dimer interface [polypeptide binding]; other site 62928004645 interdomain contacts; other site 62928004646 partial ornithine binding site; other site 62928004647 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 62928004648 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 62928004649 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 62928004650 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 62928004651 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 62928004652 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 62928004653 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 62928004654 S-adenosylmethionine binding site [chemical binding]; other site 62928004655 FtsH Extracellular; Region: FtsH_ext; pfam06480 62928004656 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 62928004657 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 62928004658 Walker A motif; other site 62928004659 ATP binding site [chemical binding]; other site 62928004660 Walker B motif; other site 62928004661 arginine finger; other site 62928004662 Peptidase family M41; Region: Peptidase_M41; pfam01434 62928004663 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 62928004664 dihydropteroate synthase; Region: DHPS; TIGR01496 62928004665 substrate binding pocket [chemical binding]; other site 62928004666 dimer interface [polypeptide binding]; other site 62928004667 inhibitor binding site; inhibition site 62928004668 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 62928004669 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 62928004670 active site 62928004671 substrate binding site [chemical binding]; other site 62928004672 metal binding site [ion binding]; metal-binding site 62928004673 PBP superfamily domain; Region: PBP_like_2; cl17296 62928004674 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 62928004675 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 62928004676 dimer interface [polypeptide binding]; other site 62928004677 conserved gate region; other site 62928004678 putative PBP binding loops; other site 62928004679 ABC-ATPase subunit interface; other site 62928004680 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 62928004681 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 62928004682 dimer interface [polypeptide binding]; other site 62928004683 conserved gate region; other site 62928004684 ABC-ATPase subunit interface; other site 62928004685 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 62928004686 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 62928004687 Walker A/P-loop; other site 62928004688 ATP binding site [chemical binding]; other site 62928004689 Q-loop/lid; other site 62928004690 ABC transporter signature motif; other site 62928004691 Walker B; other site 62928004692 D-loop; other site 62928004693 H-loop/switch region; other site 62928004694 triosephosphate isomerase; Provisional; Region: PRK14567 62928004695 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 62928004696 substrate binding site [chemical binding]; other site 62928004697 dimer interface [polypeptide binding]; other site 62928004698 catalytic triad [active] 62928004699 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 62928004700 NADH dehydrogenase subunit B; Validated; Region: PRK06411 62928004701 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 62928004702 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 62928004703 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 62928004704 NADH dehydrogenase subunit D; Validated; Region: PRK06075 62928004705 NADH dehydrogenase subunit E; Validated; Region: PRK07539 62928004706 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 62928004707 putative dimer interface [polypeptide binding]; other site 62928004708 [2Fe-2S] cluster binding site [ion binding]; other site 62928004709 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 62928004710 SLBB domain; Region: SLBB; pfam10531 62928004711 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 62928004712 NADH dehydrogenase subunit G; Validated; Region: PRK09129 62928004713 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 62928004714 catalytic loop [active] 62928004715 iron binding site [ion binding]; other site 62928004716 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 62928004717 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 62928004718 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 62928004719 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 62928004720 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 62928004721 4Fe-4S binding domain; Region: Fer4; pfam00037 62928004722 4Fe-4S binding domain; Region: Fer4; pfam00037 62928004723 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 62928004724 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 62928004725 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 62928004726 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 62928004727 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 62928004728 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 62928004729 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 62928004730 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 62928004731 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 62928004732 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 62928004733 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 62928004734 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 62928004735 dimer interface [polypeptide binding]; other site 62928004736 ADP-ribose binding site [chemical binding]; other site 62928004737 active site 62928004738 nudix motif; other site 62928004739 metal binding site [ion binding]; metal-binding site 62928004740 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 62928004741 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 62928004742 active site 62928004743 dimer interface [polypeptide binding]; other site 62928004744 effector binding site; other site 62928004745 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 62928004746 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 62928004747 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 62928004748 SLBB domain; Region: SLBB; pfam10531 62928004749 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 62928004750 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 62928004751 catalytic loop [active] 62928004752 iron binding site [ion binding]; other site 62928004753 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 62928004754 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 62928004755 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 62928004756 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 62928004757 nickel binding site [ion binding]; other site 62928004758 HDOD domain; Region: HDOD; pfam08668 62928004759 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 62928004760 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 62928004761 putative catalytic site [active] 62928004762 putative metal binding site [ion binding]; other site 62928004763 putative phosphate binding site [ion binding]; other site 62928004764 putative catalytic site [active] 62928004765 putative phosphate binding site [ion binding]; other site 62928004766 putative metal binding site [ion binding]; other site 62928004767 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 62928004768 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 62928004769 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928004770 TAP-like protein; Region: Abhydrolase_4; pfam08386 62928004771 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 62928004772 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 62928004773 homodimer interface [polypeptide binding]; other site 62928004774 substrate-cofactor binding pocket; other site 62928004775 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928004776 catalytic residue [active] 62928004777 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 62928004778 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 62928004779 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 62928004780 heat shock protein 90; Provisional; Region: PRK05218 62928004781 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 62928004782 ATP binding site [chemical binding]; other site 62928004783 Mg2+ binding site [ion binding]; other site 62928004784 G-X-G motif; other site 62928004785 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 62928004786 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 62928004787 putative ion selectivity filter; other site 62928004788 putative pore gating glutamate residue; other site 62928004789 putative H+/Cl- coupling transport residue; other site 62928004790 MarR family; Region: MarR_2; pfam12802 62928004791 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 62928004792 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 62928004793 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928004794 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 62928004795 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 62928004796 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 62928004797 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 62928004798 Walker A motif; other site 62928004799 ATP binding site [chemical binding]; other site 62928004800 Walker B motif; other site 62928004801 arginine finger; other site 62928004802 Cytochrome c; Region: Cytochrom_C; cl11414 62928004803 Cytochrome c553 [Energy production and conversion]; Region: COG2863 62928004804 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 62928004805 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 62928004806 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 62928004807 minor groove reading motif; other site 62928004808 helix-hairpin-helix signature motif; other site 62928004809 substrate binding pocket [chemical binding]; other site 62928004810 active site 62928004811 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 62928004812 electron transport complex RsxE subunit; Provisional; Region: PRK12405 62928004813 electron transport complex, RnfABCDGE type, G subunit; Region: rnfG; TIGR01947 62928004814 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 62928004815 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 62928004816 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 62928004817 SLBB domain; Region: SLBB; pfam10531 62928004818 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 62928004819 ferredoxin; Provisional; Region: PRK08764 62928004820 Putative Fe-S cluster; Region: FeS; pfam04060 62928004821 4Fe-4S binding domain; Region: Fer4; cl02805 62928004822 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 62928004823 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 62928004824 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 62928004825 active site 62928004826 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 62928004827 nudix motif; other site 62928004828 HDOD domain; Region: HDOD; pfam08668 62928004829 Response regulator receiver domain; Region: Response_reg; pfam00072 62928004830 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 62928004831 active site 62928004832 phosphorylation site [posttranslational modification] 62928004833 intermolecular recognition site; other site 62928004834 dimerization interface [polypeptide binding]; other site 62928004835 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928004836 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928004837 metal binding site [ion binding]; metal-binding site 62928004838 active site 62928004839 I-site; other site 62928004840 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928004841 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 62928004842 active site 62928004843 phosphorylation site [posttranslational modification] 62928004844 intermolecular recognition site; other site 62928004845 dimerization interface [polypeptide binding]; other site 62928004846 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928004847 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928004848 active site 62928004849 I-site; other site 62928004850 metal binding site [ion binding]; metal-binding site 62928004851 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 62928004852 Flagellar transcriptional activator (FlhD); Region: FlhD; pfam05247 62928004853 Flagellar transcriptional activator (FlhC); Region: FlhC; pfam05280 62928004854 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 62928004855 flagellar motor stator protein MotA; Region: MotA1; TIGR03818 62928004856 flagellar motor protein MotB; Validated; Region: motB; PRK09041 62928004857 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 62928004858 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928004859 ligand binding site [chemical binding]; other site 62928004860 Response regulator receiver domain; Region: Response_reg; pfam00072 62928004861 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 62928004862 active site 62928004863 phosphorylation site [posttranslational modification] 62928004864 intermolecular recognition site; other site 62928004865 dimerization interface [polypeptide binding]; other site 62928004866 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 62928004867 putative binding surface; other site 62928004868 active site 62928004869 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 62928004870 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 62928004871 ATP binding site [chemical binding]; other site 62928004872 Mg2+ binding site [ion binding]; other site 62928004873 G-X-G motif; other site 62928004874 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 62928004875 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 62928004876 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 62928004877 PAS domain; Region: PAS_9; pfam13426 62928004878 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928004879 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928004880 dimer interface [polypeptide binding]; other site 62928004881 putative CheW interface [polypeptide binding]; other site 62928004882 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 62928004883 PAS domain; Region: PAS_9; pfam13426 62928004884 putative active site [active] 62928004885 heme pocket [chemical binding]; other site 62928004886 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 62928004887 dimerization interface [polypeptide binding]; other site 62928004888 PAS domain; Region: PAS_9; pfam13426 62928004889 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928004890 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928004891 dimer interface [polypeptide binding]; other site 62928004892 putative CheW interface [polypeptide binding]; other site 62928004893 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 62928004894 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 62928004895 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 62928004896 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 62928004897 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 62928004898 active site 62928004899 phosphorylation site [posttranslational modification] 62928004900 intermolecular recognition site; other site 62928004901 dimerization interface [polypeptide binding]; other site 62928004902 CheB methylesterase; Region: CheB_methylest; pfam01339 62928004903 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928004904 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928004905 dimer interface [polypeptide binding]; other site 62928004906 putative CheW interface [polypeptide binding]; other site 62928004907 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 62928004908 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928004909 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 62928004910 active site 62928004911 phosphorylation site [posttranslational modification] 62928004912 intermolecular recognition site; other site 62928004913 dimerization interface [polypeptide binding]; other site 62928004914 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 62928004915 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928004916 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 62928004917 active site 62928004918 phosphorylation site [posttranslational modification] 62928004919 intermolecular recognition site; other site 62928004920 dimerization interface [polypeptide binding]; other site 62928004921 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 62928004922 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 62928004923 active site 62928004924 phosphorylation site [posttranslational modification] 62928004925 intermolecular recognition site; other site 62928004926 dimerization interface [polypeptide binding]; other site 62928004927 chemotaxis regulator CheZ; Provisional; Region: PRK11166 62928004928 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 62928004929 putative binding surface; other site 62928004930 active site 62928004931 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 62928004932 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 62928004933 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 62928004934 ATP binding site [chemical binding]; other site 62928004935 Mg2+ binding site [ion binding]; other site 62928004936 G-X-G motif; other site 62928004937 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 62928004938 Protein of unknown function (DUF3135); Region: DUF3135; pfam11333 62928004939 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 62928004940 putative active site [active] 62928004941 transaldolase; Provisional; Region: PRK03903 62928004942 catalytic residue [active] 62928004943 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 62928004944 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 62928004945 active site 62928004946 superoxide dismutase; Provisional; Region: PRK10543 62928004947 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 62928004948 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 62928004949 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 62928004950 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 62928004951 generic binding surface II; other site 62928004952 generic binding surface I; other site 62928004953 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 62928004954 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 62928004955 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 62928004956 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 62928004957 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 62928004958 Uncharacterized conserved protein [Function unknown]; Region: COG2835 62928004959 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 62928004960 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 62928004961 Ligand binding site; other site 62928004962 oligomer interface; other site 62928004963 adenylate kinase; Reviewed; Region: adk; PRK00279 62928004964 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 62928004965 AMP-binding site [chemical binding]; other site 62928004966 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 62928004967 6-phosphofructokinase; Provisional; Region: PRK14072 62928004968 active site 62928004969 ADP/pyrophosphate binding site [chemical binding]; other site 62928004970 dimerization interface [polypeptide binding]; other site 62928004971 allosteric effector site; other site 62928004972 fructose-1,6-bisphosphate binding site; other site 62928004973 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 62928004974 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 62928004975 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 62928004976 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928004977 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928004978 metal binding site [ion binding]; metal-binding site 62928004979 active site 62928004980 I-site; other site 62928004981 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 62928004982 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 62928004983 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928004984 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 62928004985 DNA binding residues [nucleotide binding] 62928004986 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928004987 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 62928004988 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 62928004989 active site 62928004990 HIGH motif; other site 62928004991 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 62928004992 active site 62928004993 KMSKS motif; other site 62928004994 Domain of unknown function (DUF897); Region: DUF897; pfam05982 62928004995 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 62928004996 Uncharacterized conserved protein [Function unknown]; Region: COG4121 62928004997 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928004998 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 62928004999 Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain; Region: MPP_YhcR_N; cd07412 62928005000 putative active site [active] 62928005001 putative metal binding site [ion binding]; other site 62928005002 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 62928005003 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 62928005004 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 62928005005 generic binding surface I; other site 62928005006 generic binding surface II; other site 62928005007 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 62928005008 putative active site [active] 62928005009 putative catalytic site [active] 62928005010 putative Mg binding site IVb [ion binding]; other site 62928005011 putative phosphate binding site [ion binding]; other site 62928005012 putative DNA binding site [nucleotide binding]; other site 62928005013 putative Mg binding site IVa [ion binding]; other site 62928005014 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 62928005015 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928005016 GAF domain; Region: GAF_2; pfam13185 62928005017 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 62928005018 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 62928005019 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 62928005020 dimer interface [polypeptide binding]; other site 62928005021 putative anticodon binding site; other site 62928005022 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 62928005023 motif 1; other site 62928005024 active site 62928005025 motif 2; other site 62928005026 motif 3; other site 62928005027 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 62928005028 putative ADP-ribose binding site [chemical binding]; other site 62928005029 putative active site [active] 62928005030 Response regulator receiver domain; Region: Response_reg; pfam00072 62928005031 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 62928005032 active site 62928005033 phosphorylation site [posttranslational modification] 62928005034 intermolecular recognition site; other site 62928005035 dimerization interface [polypeptide binding]; other site 62928005036 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928005037 GAF domain; Region: GAF; cl17456 62928005038 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928005039 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928005040 PAS domain; Region: PAS_9; pfam13426 62928005041 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 62928005042 putative active site [active] 62928005043 heme pocket [chemical binding]; other site 62928005044 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928005045 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928005046 metal binding site [ion binding]; metal-binding site 62928005047 active site 62928005048 I-site; other site 62928005049 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 62928005050 Response regulator receiver domain; Region: Response_reg; pfam00072 62928005051 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 62928005052 active site 62928005053 phosphorylation site [posttranslational modification] 62928005054 intermolecular recognition site; other site 62928005055 dimerization interface [polypeptide binding]; other site 62928005056 PAS domain S-box; Region: sensory_box; TIGR00229 62928005057 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 62928005058 putative active site [active] 62928005059 heme pocket [chemical binding]; other site 62928005060 PAS domain S-box; Region: sensory_box; TIGR00229 62928005061 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 62928005062 putative active site [active] 62928005063 heme pocket [chemical binding]; other site 62928005064 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 62928005065 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928005066 putative active site [active] 62928005067 heme pocket [chemical binding]; other site 62928005068 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 62928005069 dimer interface [polypeptide binding]; other site 62928005070 phosphorylation site [posttranslational modification] 62928005071 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 62928005072 ATP binding site [chemical binding]; other site 62928005073 Mg2+ binding site [ion binding]; other site 62928005074 G-X-G motif; other site 62928005075 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 62928005076 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 62928005077 AAA domain; Region: AAA_23; pfam13476 62928005078 AAA domain; Region: AAA_21; pfam13304 62928005079 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928005080 ABC transporter signature motif; other site 62928005081 Walker B; other site 62928005082 D-loop; other site 62928005083 H-loop/switch region; other site 62928005084 peptide chain release factor 2; Validated; Region: prfB; PRK00578 62928005085 This domain is found in peptide chain release factors; Region: PCRF; smart00937 62928005086 RF-1 domain; Region: RF-1; pfam00472 62928005087 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 62928005088 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 62928005089 HIT family signature motif; other site 62928005090 catalytic residue [active] 62928005091 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 62928005092 Sel1 repeat; Region: Sel1; cl02723 62928005093 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928005094 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 62928005095 active site 62928005096 phosphorylation site [posttranslational modification] 62928005097 intermolecular recognition site; other site 62928005098 dimerization interface [polypeptide binding]; other site 62928005099 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 62928005100 DNA binding residues [nucleotide binding] 62928005101 dimerization interface [polypeptide binding]; other site 62928005102 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 62928005103 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 62928005104 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 62928005105 DHH family; Region: DHH; pfam01368 62928005106 DHHA1 domain; Region: DHHA1; pfam02272 62928005107 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 62928005108 hypothetical protein; Provisional; Region: PRK01254 62928005109 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 62928005110 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 62928005111 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 62928005112 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 62928005113 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928005114 FtsX-like permease family; Region: FtsX; pfam02687 62928005115 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 62928005116 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928005117 Walker A/P-loop; other site 62928005118 ATP binding site [chemical binding]; other site 62928005119 Q-loop/lid; other site 62928005120 ABC transporter signature motif; other site 62928005121 Walker B; other site 62928005122 D-loop; other site 62928005123 H-loop/switch region; other site 62928005124 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 62928005125 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 62928005126 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 62928005127 Competence protein; Region: Competence; pfam03772 62928005128 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 62928005129 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 62928005130 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928005131 Uncharacterized conserved protein [Function unknown]; Region: COG2308 62928005132 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 62928005133 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 62928005134 GTPase RsgA; Reviewed; Region: PRK00098 62928005135 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 62928005136 homodimer interface [polypeptide binding]; other site 62928005137 RNA binding site [nucleotide binding]; other site 62928005138 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 62928005139 GTPase/Zn-binding domain interface [polypeptide binding]; other site 62928005140 GTP/Mg2+ binding site [chemical binding]; other site 62928005141 G4 box; other site 62928005142 G5 box; other site 62928005143 G1 box; other site 62928005144 Switch I region; other site 62928005145 G2 box; other site 62928005146 G3 box; other site 62928005147 Switch II region; other site 62928005148 Peptidase family M48; Region: Peptidase_M48; pfam01435 62928005149 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 62928005150 catalytic site [active] 62928005151 putative active site [active] 62928005152 putative substrate binding site [chemical binding]; other site 62928005153 dimer interface [polypeptide binding]; other site 62928005154 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 62928005155 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 62928005156 active site 62928005157 dimer interface [polypeptide binding]; other site 62928005158 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 62928005159 dimer interface [polypeptide binding]; other site 62928005160 active site 62928005161 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 62928005162 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 62928005163 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 62928005164 FMN binding site [chemical binding]; other site 62928005165 active site 62928005166 catalytic residues [active] 62928005167 substrate binding site [chemical binding]; other site 62928005168 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 62928005169 S-adenosylmethionine binding site [chemical binding]; other site 62928005170 hypothetical protein; Provisional; Region: PRK10396 62928005171 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 62928005172 SEC-C motif; Region: SEC-C; pfam02810 62928005173 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 62928005174 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 62928005175 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 62928005176 nucleotide binding site/active site [active] 62928005177 HIT family signature motif; other site 62928005178 catalytic residue [active] 62928005179 ATP adenylyltransferase; Region: ATP_transf; pfam09830 62928005180 S4 domain; Region: S4_2; pfam13275 62928005181 Ion channel; Region: Ion_trans_2; pfam07885 62928005182 TrkA-N domain; Region: TrkA_N; pfam02254 62928005183 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 62928005184 TrkA-N domain; Region: TrkA_N; pfam02254 62928005185 TrkA-C domain; Region: TrkA_C; pfam02080 62928005186 PEP-CTERM motif; Region: VPEP; pfam07589 62928005187 hypothetical protein; Provisional; Region: PRK01842 62928005188 aconitate hydratase; Validated; Region: PRK09277 62928005189 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 62928005190 substrate binding site [chemical binding]; other site 62928005191 ligand binding site [chemical binding]; other site 62928005192 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 62928005193 substrate binding site [chemical binding]; other site 62928005194 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 62928005195 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 62928005196 substrate binding site [chemical binding]; other site 62928005197 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 62928005198 substrate binding site [chemical binding]; other site 62928005199 ligand binding site [chemical binding]; other site 62928005200 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928005201 GAF domain; Region: GAF; pfam01590 62928005202 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928005203 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928005204 metal binding site [ion binding]; metal-binding site 62928005205 active site 62928005206 I-site; other site 62928005207 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 62928005208 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 62928005209 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928005210 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 62928005211 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 62928005212 tetramer interface [polypeptide binding]; other site 62928005213 TPP-binding site [chemical binding]; other site 62928005214 heterodimer interface [polypeptide binding]; other site 62928005215 phosphorylation loop region [posttranslational modification] 62928005216 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 62928005217 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 62928005218 PYR/PP interface [polypeptide binding]; other site 62928005219 dimer interface [polypeptide binding]; other site 62928005220 TPP binding site [chemical binding]; other site 62928005221 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 62928005222 glutathionine S-transferase; Provisional; Region: PRK10542 62928005223 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 62928005224 C-terminal domain interface [polypeptide binding]; other site 62928005225 GSH binding site (G-site) [chemical binding]; other site 62928005226 dimer interface [polypeptide binding]; other site 62928005227 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 62928005228 dimer interface [polypeptide binding]; other site 62928005229 substrate binding pocket (H-site) [chemical binding]; other site 62928005230 N-terminal domain interface [polypeptide binding]; other site 62928005231 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 62928005232 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 62928005233 putative substrate translocation pore; other site 62928005234 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928005235 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928005236 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 62928005237 dimerization interface [polypeptide binding]; other site 62928005238 substrate binding pocket [chemical binding]; other site 62928005239 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 62928005240 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 62928005241 putative active site [active] 62928005242 heme pocket [chemical binding]; other site 62928005243 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 62928005244 putative active site [active] 62928005245 heme pocket [chemical binding]; other site 62928005246 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 62928005247 PAS domain; Region: PAS_9; pfam13426 62928005248 putative active site [active] 62928005249 heme pocket [chemical binding]; other site 62928005250 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928005251 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928005252 metal binding site [ion binding]; metal-binding site 62928005253 active site 62928005254 I-site; other site 62928005255 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 62928005256 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 62928005257 malate dehydrogenase; Provisional; Region: PRK05442 62928005258 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 62928005259 NAD(P) binding site [chemical binding]; other site 62928005260 dimer interface [polypeptide binding]; other site 62928005261 malate binding site [chemical binding]; other site 62928005262 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 62928005263 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928005264 DNA-binding site [nucleotide binding]; DNA binding site 62928005265 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 62928005266 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 62928005267 Iron-sulfur protein interface; other site 62928005268 proximal quinone binding site [chemical binding]; other site 62928005269 SdhD (CybS) interface [polypeptide binding]; other site 62928005270 proximal heme binding site [chemical binding]; other site 62928005271 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 62928005272 SdhC subunit interface [polypeptide binding]; other site 62928005273 proximal heme binding site [chemical binding]; other site 62928005274 cardiolipin binding site; other site 62928005275 Iron-sulfur protein interface; other site 62928005276 proximal quinone binding site [chemical binding]; other site 62928005277 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 62928005278 L-aspartate oxidase; Provisional; Region: PRK06175 62928005279 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 62928005280 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 62928005281 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 62928005282 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 62928005283 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 62928005284 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 62928005285 dimer interface [polypeptide binding]; other site 62928005286 active site 62928005287 citrylCoA binding site [chemical binding]; other site 62928005288 NADH binding [chemical binding]; other site 62928005289 cationic pore residues; other site 62928005290 oxalacetate/citrate binding site [chemical binding]; other site 62928005291 coenzyme A binding site [chemical binding]; other site 62928005292 catalytic triad [active] 62928005293 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 62928005294 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 62928005295 TPP-binding site [chemical binding]; other site 62928005296 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 62928005297 dimer interface [polypeptide binding]; other site 62928005298 PYR/PP interface [polypeptide binding]; other site 62928005299 TPP binding site [chemical binding]; other site 62928005300 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 62928005301 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 62928005302 E3 interaction surface; other site 62928005303 lipoyl attachment site [posttranslational modification]; other site 62928005304 e3 binding domain; Region: E3_binding; pfam02817 62928005305 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 62928005306 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 62928005307 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928005308 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928005309 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 62928005310 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 62928005311 Predicted ATPase [General function prediction only]; Region: COG1485 62928005312 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 62928005313 DEAD/DEAH box helicase; Region: DEAD; pfam00270 62928005314 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 62928005315 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 62928005316 Walker A motif; other site 62928005317 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 62928005318 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 62928005319 dimer interface [polypeptide binding]; other site 62928005320 putative functional site; other site 62928005321 putative MPT binding site; other site 62928005322 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 62928005323 MoaE interaction surface [polypeptide binding]; other site 62928005324 MoeB interaction surface [polypeptide binding]; other site 62928005325 thiocarboxylated glycine; other site 62928005326 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 62928005327 MoaE homodimer interface [polypeptide binding]; other site 62928005328 MoaD interaction [polypeptide binding]; other site 62928005329 active site residues [active] 62928005330 Phasin protein; Region: Phasin_2; pfam09361 62928005331 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 62928005332 Clp amino terminal domain; Region: Clp_N; pfam02861 62928005333 Clp amino terminal domain; Region: Clp_N; pfam02861 62928005334 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 62928005335 Walker A motif; other site 62928005336 ATP binding site [chemical binding]; other site 62928005337 Walker B motif; other site 62928005338 arginine finger; other site 62928005339 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 62928005340 Walker A motif; other site 62928005341 ATP binding site [chemical binding]; other site 62928005342 Walker B motif; other site 62928005343 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 62928005344 MASE1; Region: MASE1; pfam05231 62928005345 CHASE domain; Region: CHASE; pfam03924 62928005346 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928005347 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928005348 metal binding site [ion binding]; metal-binding site 62928005349 active site 62928005350 I-site; other site 62928005351 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 62928005352 SurA N-terminal domain; Region: SurA_N_3; cl07813 62928005353 periplasmic folding chaperone; Provisional; Region: PRK10788 62928005354 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 62928005355 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 62928005356 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 62928005357 NAD binding site [chemical binding]; other site 62928005358 homotetramer interface [polypeptide binding]; other site 62928005359 homodimer interface [polypeptide binding]; other site 62928005360 substrate binding site [chemical binding]; other site 62928005361 active site 62928005362 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 62928005363 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_18; cd08505 62928005364 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 62928005365 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 62928005366 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 62928005367 dimer interface [polypeptide binding]; other site 62928005368 conserved gate region; other site 62928005369 putative PBP binding loops; other site 62928005370 ABC-ATPase subunit interface; other site 62928005371 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 62928005372 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 62928005373 dimer interface [polypeptide binding]; other site 62928005374 conserved gate region; other site 62928005375 putative PBP binding loops; other site 62928005376 ABC-ATPase subunit interface; other site 62928005377 hypothetical protein; Validated; Region: PRK00029 62928005378 Uncharacterized conserved protein [Function unknown]; Region: COG0397 62928005379 NnrU protein; Region: NnrU; pfam07298 62928005380 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 62928005381 SmpB-tmRNA interface; other site 62928005382 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 62928005383 putative coenzyme Q binding site [chemical binding]; other site 62928005384 hypothetical protein; Validated; Region: PRK01777 62928005385 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 62928005386 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 62928005387 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 62928005388 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 62928005389 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 62928005390 active site 62928005391 GMP synthase; Reviewed; Region: guaA; PRK00074 62928005392 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 62928005393 AMP/PPi binding site [chemical binding]; other site 62928005394 candidate oxyanion hole; other site 62928005395 catalytic triad [active] 62928005396 potential glutamine specificity residues [chemical binding]; other site 62928005397 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 62928005398 ATP Binding subdomain [chemical binding]; other site 62928005399 Ligand Binding sites [chemical binding]; other site 62928005400 Dimerization subdomain; other site 62928005401 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928005402 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928005403 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 62928005404 dimerization interface [polypeptide binding]; other site 62928005405 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 62928005406 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928005407 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 62928005408 active site 62928005409 phosphorylation site [posttranslational modification] 62928005410 intermolecular recognition site; other site 62928005411 dimerization interface [polypeptide binding]; other site 62928005412 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928005413 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928005414 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 62928005415 dimer interface [polypeptide binding]; other site 62928005416 phosphorylation site [posttranslational modification] 62928005417 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 62928005418 ATP binding site [chemical binding]; other site 62928005419 Mg2+ binding site [ion binding]; other site 62928005420 G-X-G motif; other site 62928005421 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 62928005422 PAS fold; Region: PAS_4; pfam08448 62928005423 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 62928005424 PAS fold; Region: PAS_3; pfam08447 62928005425 putative active site [active] 62928005426 heme pocket [chemical binding]; other site 62928005427 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 62928005428 dimer interface [polypeptide binding]; other site 62928005429 phosphorylation site [posttranslational modification] 62928005430 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 62928005431 ATP binding site [chemical binding]; other site 62928005432 Mg2+ binding site [ion binding]; other site 62928005433 G-X-G motif; other site 62928005434 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 62928005435 nucleoside/Zn binding site; other site 62928005436 dimer interface [polypeptide binding]; other site 62928005437 catalytic motif [active] 62928005438 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 62928005439 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 62928005440 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 62928005441 NRDE protein; Region: NRDE; cl01315 62928005442 Aminomethyltransferase folate-binding domain; Region: GCV_T; pfam01571 62928005443 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 62928005444 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 62928005445 YceG-like family; Region: YceG; pfam02618 62928005446 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 62928005447 dimerization interface [polypeptide binding]; other site 62928005448 thymidylate kinase; Validated; Region: tmk; PRK00698 62928005449 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 62928005450 TMP-binding site; other site 62928005451 ATP-binding site [chemical binding]; other site 62928005452 DNA polymerase III subunit delta'; Validated; Region: PRK06964 62928005453 DNA polymerase III subunit delta'; Validated; Region: PRK08485 62928005454 PilZ domain; Region: PilZ; cl01260 62928005455 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 62928005456 active site 62928005457 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 62928005458 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 62928005459 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 62928005460 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 62928005461 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 62928005462 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 62928005463 putative active site [active] 62928005464 Zn binding site [ion binding]; other site 62928005465 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 62928005466 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 62928005467 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 62928005468 Uncharacterized conserved protein [Function unknown]; Region: COG2308 62928005469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 62928005470 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 62928005471 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 62928005472 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 62928005473 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 62928005474 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 62928005475 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 62928005476 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 62928005477 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 62928005478 metal binding site [ion binding]; metal-binding site 62928005479 putative dimer interface [polypeptide binding]; other site 62928005480 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 62928005481 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928005482 FtsX-like permease family; Region: FtsX; pfam02687 62928005483 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 62928005484 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 62928005485 FeS/SAM binding site; other site 62928005486 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 62928005487 AAA domain; Region: AAA_32; pfam13654 62928005488 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 62928005489 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 62928005490 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 62928005491 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 62928005492 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928005493 homodimer interface [polypeptide binding]; other site 62928005494 catalytic residue [active] 62928005495 excinuclease ABC subunit B; Provisional; Region: PRK05298 62928005496 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 62928005497 ATP binding site [chemical binding]; other site 62928005498 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 62928005499 nucleotide binding region [chemical binding]; other site 62928005500 ATP-binding site [chemical binding]; other site 62928005501 Ultra-violet resistance protein B; Region: UvrB; pfam12344 62928005502 UvrB/uvrC motif; Region: UVR; pfam02151 62928005503 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 62928005504 Low molecular weight phosphatase family; Region: LMWPc; cd00115 62928005505 active site 62928005506 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 62928005507 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 62928005508 homodimer interface [polypeptide binding]; other site 62928005509 oligonucleotide binding site [chemical binding]; other site 62928005510 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 62928005511 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 62928005512 active site 62928005513 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 62928005514 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 62928005515 motif II; other site 62928005516 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 62928005517 iron-sulfur cluster [ion binding]; other site 62928005518 [2Fe-2S] cluster binding site [ion binding]; other site 62928005519 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 62928005520 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 62928005521 tandem repeat interface [polypeptide binding]; other site 62928005522 oligomer interface [polypeptide binding]; other site 62928005523 active site residues [active] 62928005524 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 62928005525 putative SAM binding site [chemical binding]; other site 62928005526 homodimer interface [polypeptide binding]; other site 62928005527 Maf-like protein; Region: Maf; pfam02545 62928005528 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 62928005529 active site 62928005530 dimer interface [polypeptide binding]; other site 62928005531 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 62928005532 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 62928005533 putative phosphate acyltransferase; Provisional; Region: PRK05331 62928005534 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 62928005535 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 62928005536 dimer interface [polypeptide binding]; other site 62928005537 active site 62928005538 CoA binding pocket [chemical binding]; other site 62928005539 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 62928005540 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 62928005541 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 62928005542 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928005543 NAD(P) binding site [chemical binding]; other site 62928005544 active site 62928005545 acyl carrier protein; Provisional; Region: acpP; PRK00982 62928005546 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 62928005547 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 62928005548 dimer interface [polypeptide binding]; other site 62928005549 active site 62928005550 L-aspartate oxidase; Provisional; Region: PRK09077 62928005551 L-aspartate oxidase; Provisional; Region: PRK06175 62928005552 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 62928005553 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 62928005554 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928005555 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 62928005556 DNA binding residues [nucleotide binding] 62928005557 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 62928005558 anti-sigma E factor; Provisional; Region: rseB; PRK09455 62928005559 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 62928005560 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 62928005561 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 62928005562 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928005563 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 62928005564 protein binding site [polypeptide binding]; other site 62928005565 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 62928005566 protein binding site [polypeptide binding]; other site 62928005567 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 62928005568 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928005569 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928005570 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 62928005571 putative effector binding pocket; other site 62928005572 dimerization interface [polypeptide binding]; other site 62928005573 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 62928005574 GTP-binding protein LepA; Provisional; Region: PRK05433 62928005575 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 62928005576 G1 box; other site 62928005577 putative GEF interaction site [polypeptide binding]; other site 62928005578 GTP/Mg2+ binding site [chemical binding]; other site 62928005579 Switch I region; other site 62928005580 G2 box; other site 62928005581 G3 box; other site 62928005582 Switch II region; other site 62928005583 G4 box; other site 62928005584 G5 box; other site 62928005585 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 62928005586 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 62928005587 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 62928005588 signal peptidase I; Provisional; Region: PRK10861 62928005589 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 62928005590 Catalytic site [active] 62928005591 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 62928005592 ribonuclease III; Reviewed; Region: rnc; PRK00102 62928005593 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 62928005594 dimerization interface [polypeptide binding]; other site 62928005595 active site 62928005596 metal binding site [ion binding]; metal-binding site 62928005597 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 62928005598 dsRNA binding site [nucleotide binding]; other site 62928005599 GTPase Era; Reviewed; Region: era; PRK00089 62928005600 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 62928005601 G1 box; other site 62928005602 GTP/Mg2+ binding site [chemical binding]; other site 62928005603 Switch I region; other site 62928005604 G2 box; other site 62928005605 Switch II region; other site 62928005606 G3 box; other site 62928005607 G4 box; other site 62928005608 G5 box; other site 62928005609 KH domain; Region: KH_2; pfam07650 62928005610 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 62928005611 Recombination protein O N terminal; Region: RecO_N; pfam11967 62928005612 Recombination protein O C terminal; Region: RecO_C; pfam02565 62928005613 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 62928005614 active site 62928005615 hydrophilic channel; other site 62928005616 dimerization interface [polypeptide binding]; other site 62928005617 catalytic residues [active] 62928005618 active site lid [active] 62928005619 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 62928005620 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 62928005621 beta-hexosaminidase; Provisional; Region: PRK05337 62928005622 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 62928005623 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 62928005624 GIY-YIG motif/motif A; other site 62928005625 active site 62928005626 catalytic site [active] 62928005627 putative DNA binding site [nucleotide binding]; other site 62928005628 metal binding site [ion binding]; metal-binding site 62928005629 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 62928005630 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 62928005631 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 62928005632 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 62928005633 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 62928005634 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 62928005635 Autotransporter beta-domain; Region: Autotransporter; pfam03797 62928005636 cell division topological specificity factor MinE; Provisional; Region: PRK13989 62928005637 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 62928005638 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 62928005639 Switch I; other site 62928005640 Switch II; other site 62928005641 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 62928005642 Septum formation inhibitor [Cell division and chromosome partitioning]; Region: MinC; COG0850 62928005643 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 62928005644 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 62928005645 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 62928005646 dimerization interface [polypeptide binding]; other site 62928005647 domain crossover interface; other site 62928005648 redox-dependent activation switch; other site 62928005649 ArsC family; Region: ArsC; pfam03960 62928005650 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 62928005651 putative catalytic residues [active] 62928005652 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 62928005653 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 62928005654 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 62928005655 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 62928005656 RNA binding site [nucleotide binding]; other site 62928005657 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 62928005658 active site 62928005659 phosphate binding residues; other site 62928005660 catalytic residues [active] 62928005661 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 62928005662 CoA binding domain; Region: CoA_binding_2; pfam13380 62928005663 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 62928005664 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 62928005665 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 62928005666 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 62928005667 PAS domain; Region: PAS_9; pfam13426 62928005668 PAS fold; Region: PAS; pfam00989 62928005669 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 62928005670 putative active site [active] 62928005671 heme pocket [chemical binding]; other site 62928005672 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 62928005673 dimer interface [polypeptide binding]; other site 62928005674 phosphorylation site [posttranslational modification] 62928005675 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 62928005676 ATP binding site [chemical binding]; other site 62928005677 Mg2+ binding site [ion binding]; other site 62928005678 G-X-G motif; other site 62928005679 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 62928005680 S-adenosylmethionine binding site [chemical binding]; other site 62928005681 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 62928005682 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 62928005683 active site residue [active] 62928005684 selenophosphate synthetase; Provisional; Region: PRK00943 62928005685 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 62928005686 dimerization interface [polypeptide binding]; other site 62928005687 putative ATP binding site [chemical binding]; other site 62928005688 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 62928005689 active site 62928005690 catalytic triad [active] 62928005691 oxyanion hole [active] 62928005692 switch loop; other site 62928005693 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 62928005694 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928005695 Walker A/P-loop; other site 62928005696 ATP binding site [chemical binding]; other site 62928005697 Q-loop/lid; other site 62928005698 ABC transporter signature motif; other site 62928005699 Walker B; other site 62928005700 D-loop; other site 62928005701 H-loop/switch region; other site 62928005702 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 62928005703 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 62928005704 motif II; other site 62928005705 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 62928005706 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 62928005707 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 62928005708 PAS domain S-box; Region: sensory_box; TIGR00229 62928005709 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 62928005710 putative active site [active] 62928005711 heme pocket [chemical binding]; other site 62928005712 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928005713 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928005714 metal binding site [ion binding]; metal-binding site 62928005715 active site 62928005716 I-site; other site 62928005717 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 62928005718 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 62928005719 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 62928005720 oligomer interface [polypeptide binding]; other site 62928005721 metal binding site [ion binding]; metal-binding site 62928005722 metal binding site [ion binding]; metal-binding site 62928005723 putative Cl binding site [ion binding]; other site 62928005724 basic sphincter; other site 62928005725 hydrophobic gate; other site 62928005726 periplasmic entrance; other site 62928005727 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 62928005728 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 62928005729 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 62928005730 ATP binding site [chemical binding]; other site 62928005731 putative Mg++ binding site [ion binding]; other site 62928005732 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 62928005733 nucleotide binding region [chemical binding]; other site 62928005734 ATP-binding site [chemical binding]; other site 62928005735 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 62928005736 SprA-related family; Region: SprA-related; pfam12118 62928005737 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 62928005738 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 62928005739 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 62928005740 FeS/SAM binding site; other site 62928005741 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 62928005742 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 62928005743 ligand binding site [chemical binding]; other site 62928005744 flexible hinge region; other site 62928005745 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 62928005746 putative switch regulator; other site 62928005747 non-specific DNA interactions [nucleotide binding]; other site 62928005748 DNA binding site [nucleotide binding] 62928005749 sequence specific DNA binding site [nucleotide binding]; other site 62928005750 putative cAMP binding site [chemical binding]; other site 62928005751 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 62928005752 AMMECR1; Region: AMMECR1; pfam01871 62928005753 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 62928005754 putative ligand binding pocket/active site [active] 62928005755 putative metal binding site [ion binding]; other site 62928005756 Predicted membrane protein [Function unknown]; Region: COG3174 62928005757 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 62928005758 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 62928005759 substrate binding site; other site 62928005760 dimer interface; other site 62928005761 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 62928005762 homotrimer interaction site [polypeptide binding]; other site 62928005763 zinc binding site [ion binding]; other site 62928005764 CDP-binding sites; other site 62928005765 Protein required for attachment to host cells; Region: Host_attach; pfam10116 62928005766 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 62928005767 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 62928005768 EamA-like transporter family; Region: EamA; pfam00892 62928005769 EamA-like transporter family; Region: EamA; pfam00892 62928005770 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 62928005771 Transglycosylase; Region: Transgly; pfam00912 62928005772 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 62928005773 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 62928005774 HD domain; Region: HD_4; pfam13328 62928005775 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 62928005776 synthetase active site [active] 62928005777 NTP binding site [chemical binding]; other site 62928005778 metal binding site [ion binding]; metal-binding site 62928005779 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 62928005780 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 62928005781 polyphosphate kinase; Provisional; Region: PRK05443 62928005782 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 62928005783 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 62928005784 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 62928005785 putative active site [active] 62928005786 catalytic site [active] 62928005787 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 62928005788 putative domain interface [polypeptide binding]; other site 62928005789 putative active site [active] 62928005790 catalytic site [active] 62928005791 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 62928005792 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 62928005793 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 62928005794 Permease; Region: Permease; pfam02405 62928005795 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928005796 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 62928005797 Walker A/P-loop; other site 62928005798 ATP binding site [chemical binding]; other site 62928005799 Q-loop/lid; other site 62928005800 ABC transporter signature motif; other site 62928005801 Walker B; other site 62928005802 D-loop; other site 62928005803 H-loop/switch region; other site 62928005804 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 62928005805 mce related protein; Region: MCE; pfam02470 62928005806 Protein of unknown function (DUF330); Region: DUF330; cl01135 62928005807 acyl-CoA synthetase; Validated; Region: PRK08162 62928005808 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 62928005809 acyl-activating enzyme (AAE) consensus motif; other site 62928005810 putative active site [active] 62928005811 AMP binding site [chemical binding]; other site 62928005812 putative CoA binding site [chemical binding]; other site 62928005813 enoyl-CoA hydratase; Validated; Region: PRK08139 62928005814 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928005815 substrate binding site [chemical binding]; other site 62928005816 oxyanion hole (OAH) forming residues; other site 62928005817 trimer interface [polypeptide binding]; other site 62928005818 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 62928005819 active site 62928005820 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928005821 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928005822 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 62928005823 Ligand binding site [chemical binding]; other site 62928005824 Electron transfer flavoprotein domain; Region: ETF; pfam01012 62928005825 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 62928005826 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 62928005827 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 62928005828 Predicted membrane protein [Function unknown]; Region: COG3235 62928005829 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 62928005830 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 62928005831 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 62928005832 active site 62928005833 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 62928005834 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 62928005835 BolA-like protein; Region: BolA; pfam01722 62928005836 YciI-like protein; Reviewed; Region: PRK11370 62928005837 intracellular septation protein A; Reviewed; Region: PRK00259 62928005838 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 62928005839 apolar tunnel; other site 62928005840 heme binding site [chemical binding]; other site 62928005841 dimerization interface [polypeptide binding]; other site 62928005842 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928005843 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 62928005844 dimerization interface [polypeptide binding]; other site 62928005845 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 62928005846 dimer interface [polypeptide binding]; other site 62928005847 phosphorylation site [posttranslational modification] 62928005848 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 62928005849 ATP binding site [chemical binding]; other site 62928005850 Mg2+ binding site [ion binding]; other site 62928005851 G-X-G motif; other site 62928005852 osmolarity response regulator; Provisional; Region: ompR; PRK09468 62928005853 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 62928005854 active site 62928005855 phosphorylation site [posttranslational modification] 62928005856 intermolecular recognition site; other site 62928005857 dimerization interface [polypeptide binding]; other site 62928005858 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 62928005859 DNA binding site [nucleotide binding] 62928005860 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 62928005861 Glycoprotease family; Region: Peptidase_M22; pfam00814 62928005862 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 62928005863 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928005864 Coenzyme A binding pocket [chemical binding]; other site 62928005865 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 62928005866 Fe-S cluster binding site [ion binding]; other site 62928005867 active site 62928005868 lysophospholipid transporter LplT; Provisional; Region: PRK11195 62928005869 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 62928005870 putative substrate translocation pore; other site 62928005871 LysR transcriptional regulator; Provisional; Region: rbcR; CHL00180 62928005872 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928005873 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 62928005874 putative dimerization interface [polypeptide binding]; other site 62928005875 DNA repair protein RadA; Provisional; Region: PRK11823 62928005876 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 62928005877 Walker A motif/ATP binding site; other site 62928005878 ATP binding site [chemical binding]; other site 62928005879 Walker B motif; other site 62928005880 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 62928005881 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 62928005882 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 62928005883 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 62928005884 active site 62928005885 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 62928005886 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 62928005887 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 62928005888 putative active site [active] 62928005889 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 62928005890 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 62928005891 putative active site [active] 62928005892 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 62928005893 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 62928005894 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 62928005895 glycogen branching enzyme; Provisional; Region: PRK12313 62928005896 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 62928005897 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 62928005898 active site 62928005899 catalytic site [active] 62928005900 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 62928005901 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 62928005902 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 62928005903 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 62928005904 active site 62928005905 homodimer interface [polypeptide binding]; other site 62928005906 catalytic site [active] 62928005907 acceptor binding site [chemical binding]; other site 62928005908 trehalose synthase; Region: treS_nterm; TIGR02456 62928005909 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 62928005910 active site 62928005911 catalytic site [active] 62928005912 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 62928005913 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 62928005914 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 62928005915 short chain dehydrogenase; Provisional; Region: PRK06701 62928005916 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 62928005917 NAD binding site [chemical binding]; other site 62928005918 metal binding site [ion binding]; metal-binding site 62928005919 active site 62928005920 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 62928005921 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 62928005922 dimerization interface [polypeptide binding]; other site 62928005923 PRC-barrel domain; Region: PRC; pfam05239 62928005924 short chain dehydrogenase; Provisional; Region: PRK07109 62928005925 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 62928005926 putative NAD(P) binding site [chemical binding]; other site 62928005927 active site 62928005928 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 62928005929 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 62928005930 putative DNA binding site [nucleotide binding]; other site 62928005931 putative homodimer interface [polypeptide binding]; other site 62928005932 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 62928005933 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 62928005934 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 62928005935 active site 62928005936 DNA binding site [nucleotide binding] 62928005937 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 62928005938 DNA binding site [nucleotide binding] 62928005939 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 62928005940 nucleotide binding site [chemical binding]; other site 62928005941 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 62928005942 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 62928005943 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 62928005944 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 62928005945 ATP-grasp domain; Region: ATP-grasp_4; cl17255 62928005946 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 62928005947 putative active site [active] 62928005948 FOG: CBS domain [General function prediction only]; Region: COG0517 62928005949 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 62928005950 BON domain; Region: BON; pfam04972 62928005951 BON domain; Region: BON; pfam04972 62928005952 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 62928005953 putative active site [active] 62928005954 catalytic site [active] 62928005955 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 62928005956 PLD-like domain; Region: PLDc_2; pfam13091 62928005957 putative active site [active] 62928005958 catalytic site [active] 62928005959 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 62928005960 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 62928005961 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 62928005962 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 62928005963 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 62928005964 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 62928005965 D-pathway; other site 62928005966 Putative ubiquinol binding site [chemical binding]; other site 62928005967 Low-spin heme (heme b) binding site [chemical binding]; other site 62928005968 Putative water exit pathway; other site 62928005969 Binuclear center (heme o3/CuB) [ion binding]; other site 62928005970 K-pathway; other site 62928005971 Putative proton exit pathway; other site 62928005972 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; pfam09678 62928005973 short chain dehydrogenase; Provisional; Region: PRK06181 62928005974 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 62928005975 putative NAD(P) binding site [chemical binding]; other site 62928005976 active site 62928005977 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928005978 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928005979 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928005980 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 62928005981 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 62928005982 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928005983 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 62928005984 protein binding site [polypeptide binding]; other site 62928005985 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 62928005986 BON domain; Region: BON; pfam04972 62928005987 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 62928005988 Anabaena sensory rhodopsin transducer; Region: ASRT; pfam07100 62928005989 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 62928005990 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 62928005991 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 62928005992 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 62928005993 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 62928005994 dimerization interface [polypeptide binding]; other site 62928005995 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928005996 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 62928005997 DNA binding residues [nucleotide binding] 62928005998 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 62928005999 amidase catalytic site [active] 62928006000 Zn binding residues [ion binding]; other site 62928006001 substrate binding site [chemical binding]; other site 62928006002 Bacterial SH3 domain; Region: SH3_3; cl17532 62928006003 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 62928006004 ChaB; Region: ChaB; pfam06150 62928006005 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 62928006006 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 62928006007 putative catalytic site [active] 62928006008 putative metal binding site [ion binding]; other site 62928006009 putative phosphate binding site [ion binding]; other site 62928006010 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_1; cd09140 62928006011 putative active site [active] 62928006012 catalytic site [active] 62928006013 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_2; cd09143 62928006014 PLD-like domain; Region: PLDc_2; pfam13091 62928006015 putative active site [active] 62928006016 catalytic site [active] 62928006017 Uncharacterized conserved protein [Function unknown]; Region: COG0398 62928006018 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 62928006019 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 62928006020 Ferritin-like domain; Region: Ferritin; pfam00210 62928006021 dinuclear metal binding motif [ion binding]; other site 62928006022 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928006023 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 62928006024 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 62928006025 active site 62928006026 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 62928006027 active site 62928006028 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; Region: CE4_u10; cd11374 62928006029 putative active site [active] 62928006030 putative Zn binding site [ion binding]; other site 62928006031 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928006032 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 62928006033 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 62928006034 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 62928006035 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 62928006036 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 62928006037 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 62928006038 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 62928006039 Mechanosensitive ion channel; Region: MS_channel; pfam00924 62928006040 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 62928006041 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 62928006042 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 62928006043 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 62928006044 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 62928006045 active site 62928006046 catalytic site [active] 62928006047 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 62928006048 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 62928006049 active site 62928006050 DNA binding site [nucleotide binding] 62928006051 Int/Topo IB signature motif; other site 62928006052 catalytic residues [active] 62928006053 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 62928006054 glycogen branching enzyme; Provisional; Region: PRK12313 62928006055 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 62928006056 active site 62928006057 catalytic site [active] 62928006058 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 62928006059 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 62928006060 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 62928006061 ligand binding site; other site 62928006062 oligomer interface; other site 62928006063 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 62928006064 dimer interface [polypeptide binding]; other site 62928006065 N-terminal domain interface [polypeptide binding]; other site 62928006066 sulfate 1 binding site; other site 62928006067 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 62928006068 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 62928006069 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 62928006070 catalytic site [active] 62928006071 active site 62928006072 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 62928006073 putative bifunctional 4-alpha-glucanotransferase/malto-oligosyltrehalose synthase; Provisional; Region: PRK14507 62928006074 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 62928006075 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 62928006076 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 62928006077 active site 62928006078 catalytic site [active] 62928006079 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 62928006080 Glucokinase; Region: Glucokinase; pfam02685 62928006081 glucokinase, proteobacterial type; Region: glk; TIGR00749 62928006082 glycogen synthase; Provisional; Region: glgA; PRK00654 62928006083 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 62928006084 ADP-binding pocket [chemical binding]; other site 62928006085 homodimer interface [polypeptide binding]; other site 62928006086 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 62928006087 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 62928006088 NAD binding site [chemical binding]; other site 62928006089 putative substrate binding site 2 [chemical binding]; other site 62928006090 putative substrate binding site 1 [chemical binding]; other site 62928006091 active site 62928006092 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928006093 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 62928006094 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 62928006095 active site 62928006096 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 62928006097 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 62928006098 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 62928006099 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 62928006100 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 62928006101 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 62928006102 putative active site [active] 62928006103 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 62928006104 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 62928006105 active site 62928006106 motif I; other site 62928006107 motif II; other site 62928006108 short chain dehydrogenase; Provisional; Region: PRK07454 62928006109 classical (c) SDRs; Region: SDR_c; cd05233 62928006110 NAD(P) binding site [chemical binding]; other site 62928006111 active site 62928006112 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 62928006113 D-inositol-3-phosphate glycosyltransferase; Region: mycothiol_MshA; TIGR03449 62928006114 putative ADP-binding pocket [chemical binding]; other site 62928006115 Predicted membrane protein [Function unknown]; Region: COG2323 62928006116 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928006117 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 62928006118 active site 62928006119 phosphorylation site [posttranslational modification] 62928006120 intermolecular recognition site; other site 62928006121 dimerization interface [polypeptide binding]; other site 62928006122 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 62928006123 Walker A motif; other site 62928006124 ATP binding site [chemical binding]; other site 62928006125 Walker B motif; other site 62928006126 arginine finger; other site 62928006127 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928006128 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 62928006129 PAS domain; Region: PAS_9; pfam13426 62928006130 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 62928006131 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 62928006132 putative active site [active] 62928006133 heme pocket [chemical binding]; other site 62928006134 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 62928006135 dimer interface [polypeptide binding]; other site 62928006136 phosphorylation site [posttranslational modification] 62928006137 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 62928006138 ATP binding site [chemical binding]; other site 62928006139 Mg2+ binding site [ion binding]; other site 62928006140 G-X-G motif; other site 62928006141 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 62928006142 Response regulator receiver domain; Region: Response_reg; pfam00072 62928006143 active site 62928006144 phosphorylation site [posttranslational modification] 62928006145 intermolecular recognition site; other site 62928006146 dimerization interface [polypeptide binding]; other site 62928006147 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 62928006148 BON domain; Region: BON; pfam04972 62928006149 PRC-barrel domain; Region: PRC; pfam05239 62928006150 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928006151 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 62928006152 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928006153 Walker A/P-loop; other site 62928006154 ATP binding site [chemical binding]; other site 62928006155 Q-loop/lid; other site 62928006156 ABC transporter signature motif; other site 62928006157 Walker B; other site 62928006158 D-loop; other site 62928006159 H-loop/switch region; other site 62928006160 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928006161 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 62928006162 active site 62928006163 phosphorylation site [posttranslational modification] 62928006164 intermolecular recognition site; other site 62928006165 dimerization interface [polypeptide binding]; other site 62928006166 MgtC family; Region: MgtC; pfam02308 62928006167 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 62928006168 Competence-damaged protein; Region: CinA; pfam02464 62928006169 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 62928006170 NADH(P)-binding; Region: NAD_binding_10; pfam13460 62928006171 putative NAD(P) binding site [chemical binding]; other site 62928006172 active site 62928006173 DoxX-like family; Region: DoxX_3; pfam13781 62928006174 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 62928006175 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 62928006176 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 62928006177 FAD binding pocket [chemical binding]; other site 62928006178 conserved FAD binding motif [chemical binding]; other site 62928006179 phosphate binding motif [ion binding]; other site 62928006180 beta-alpha-beta structure motif; other site 62928006181 NAD binding pocket [chemical binding]; other site 62928006182 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 62928006183 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 62928006184 catalytic loop [active] 62928006185 iron binding site [ion binding]; other site 62928006186 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 62928006187 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 62928006188 N-terminal plug; other site 62928006189 ligand-binding site [chemical binding]; other site 62928006190 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 62928006191 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 62928006192 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 62928006193 endonuclease III; Region: ENDO3c; smart00478 62928006194 minor groove reading motif; other site 62928006195 helix-hairpin-helix signature motif; other site 62928006196 substrate binding pocket [chemical binding]; other site 62928006197 active site 62928006198 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 62928006199 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928006200 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 62928006201 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928006202 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_Chlorocatechol; cd08446 62928006203 dimerization interface [polypeptide binding]; other site 62928006204 putative substrate binding pocket [chemical binding]; other site 62928006205 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 62928006206 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 62928006207 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 62928006208 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 62928006209 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 62928006210 Ligand Binding Site [chemical binding]; other site 62928006211 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928006212 dimer interface [polypeptide binding]; other site 62928006213 putative CheW interface [polypeptide binding]; other site 62928006214 Activator of aromatic catabolism; Region: XylR_N; pfam06505 62928006215 V4R domain; Region: V4R; pfam02830 62928006216 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 62928006217 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 62928006218 Walker A motif; other site 62928006219 ATP binding site [chemical binding]; other site 62928006220 Walker B motif; other site 62928006221 arginine finger; other site 62928006222 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928006223 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 62928006224 catalytic loop [active] 62928006225 iron binding site [ion binding]; other site 62928006226 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 62928006227 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 62928006228 tetramer interface [polypeptide binding]; other site 62928006229 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 62928006230 tetramer interface [polypeptide binding]; other site 62928006231 active site 62928006232 Fe binding site [ion binding]; other site 62928006233 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 62928006234 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 62928006235 dinuclear metal binding motif [ion binding]; other site 62928006236 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 62928006237 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 62928006238 dimerization interface [polypeptide binding]; other site 62928006239 putative path to active site cavity [active] 62928006240 diiron center [ion binding]; other site 62928006241 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 62928006242 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 62928006243 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 62928006244 catalytic loop [active] 62928006245 iron binding site [ion binding]; other site 62928006246 Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H...; Region: phenol_2-monooxygenase_like; cd06211 62928006247 FAD binding pocket [chemical binding]; other site 62928006248 FAD binding motif [chemical binding]; other site 62928006249 phosphate binding motif [ion binding]; other site 62928006250 beta-alpha-beta structure motif; other site 62928006251 NAD binding pocket [chemical binding]; other site 62928006252 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 62928006253 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 62928006254 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 62928006255 NAD binding site [chemical binding]; other site 62928006256 catalytic residues [active] 62928006257 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 62928006258 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 62928006259 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 62928006260 active site 1 [active] 62928006261 dimer interface [polypeptide binding]; other site 62928006262 hexamer interface [polypeptide binding]; other site 62928006263 active site 2 [active] 62928006264 acetaldehyde dehydrogenase; Validated; Region: PRK08300 62928006265 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 62928006266 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 62928006267 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 62928006268 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 62928006269 active site 62928006270 catalytic residues [active] 62928006271 metal binding site [ion binding]; metal-binding site 62928006272 DmpG-like communication domain; Region: DmpG_comm; pfam07836 62928006273 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 62928006274 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 62928006275 active site 62928006276 metal binding site [ion binding]; metal-binding site 62928006277 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 62928006278 active site 62928006279 metal binding site [ion binding]; metal-binding site 62928006280 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 62928006281 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928006282 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928006283 active site 62928006284 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 62928006285 active site 1 [active] 62928006286 dimer interface [polypeptide binding]; other site 62928006287 hexamer interface [polypeptide binding]; other site 62928006288 active site 2 [active] 62928006289 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 62928006290 active site 1 [active] 62928006291 dimer interface [polypeptide binding]; other site 62928006292 hexamer interface [polypeptide binding]; other site 62928006293 active site 2 [active] 62928006294 LabA_like proteins; Region: LabA_like; cd06167 62928006295 putative metal binding site [ion binding]; other site 62928006296 Uncharacterized conserved protein [Function unknown]; Region: COG1432 62928006297 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 62928006298 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 62928006299 active site 62928006300 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 62928006301 active site 62928006302 DNA binding site [nucleotide binding] 62928006303 Int/Topo IB signature motif; other site 62928006304 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 62928006305 Helix-turn-helix domain; Region: HTH_39; pfam14090 62928006306 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 62928006307 Clp protease; Region: CLP_protease; pfam00574 62928006308 oligomer interface [polypeptide binding]; other site 62928006309 active site residues [active] 62928006310 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 62928006311 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 62928006312 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 62928006313 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 62928006314 substrate binding site; other site 62928006315 tetramer interface; other site 62928006316 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 62928006317 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 62928006318 NADP binding site [chemical binding]; other site 62928006319 active site 62928006320 putative substrate binding site [chemical binding]; other site 62928006321 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 62928006322 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 62928006323 NAD binding site [chemical binding]; other site 62928006324 substrate binding site [chemical binding]; other site 62928006325 homodimer interface [polypeptide binding]; other site 62928006326 active site 62928006327 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 62928006328 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 62928006329 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 62928006330 dimerization interface [polypeptide binding]; other site 62928006331 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928006332 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928006333 metal binding site [ion binding]; metal-binding site 62928006334 active site 62928006335 I-site; other site 62928006336 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 62928006337 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 62928006338 FtsX-like permease family; Region: FtsX; pfam02687 62928006339 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 62928006340 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928006341 Walker A/P-loop; other site 62928006342 ATP binding site [chemical binding]; other site 62928006343 Q-loop/lid; other site 62928006344 ABC transporter signature motif; other site 62928006345 Walker B; other site 62928006346 D-loop; other site 62928006347 H-loop/switch region; other site 62928006348 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 62928006349 active site lid residues [active] 62928006350 substrate binding pocket [chemical binding]; other site 62928006351 catalytic residues [active] 62928006352 substrate-Mg2+ binding site; other site 62928006353 aspartate-rich region 1; other site 62928006354 aspartate-rich region 2; other site 62928006355 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 62928006356 active site lid residues [active] 62928006357 substrate binding pocket [chemical binding]; other site 62928006358 catalytic residues [active] 62928006359 substrate-Mg2+ binding site; other site 62928006360 aspartate-rich region 1; other site 62928006361 aspartate-rich region 2; other site 62928006362 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928006363 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 62928006364 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 62928006365 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 62928006366 putative active site [active] 62928006367 Zn binding site [ion binding]; other site 62928006368 hypothetical protein; Validated; Region: PRK02101 62928006369 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 62928006370 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 62928006371 inhibitor-cofactor binding pocket; inhibition site 62928006372 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928006373 catalytic residue [active] 62928006374 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 62928006375 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 62928006376 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928006377 catalytic residue [active] 62928006378 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 62928006379 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 62928006380 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 62928006381 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 62928006382 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 62928006383 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 62928006384 AAA domain; Region: AAA_26; pfam13500 62928006385 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 62928006386 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 62928006387 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 62928006388 Predicted integral membrane protein [Function unknown]; Region: COG5615 62928006389 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 62928006390 RNA/DNA hybrid binding site [nucleotide binding]; other site 62928006391 active site 62928006392 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 62928006393 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 62928006394 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 62928006395 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 62928006396 active site 62928006397 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 62928006398 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 62928006399 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 62928006400 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 62928006401 trimer interface [polypeptide binding]; other site 62928006402 active site 62928006403 UDP-GlcNAc binding site [chemical binding]; other site 62928006404 lipid binding site [chemical binding]; lipid-binding site 62928006405 periplasmic chaperone; Provisional; Region: PRK10780 62928006406 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 62928006407 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 62928006408 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 62928006409 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 62928006410 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 62928006411 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 62928006412 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 62928006413 Surface antigen; Region: Bac_surface_Ag; pfam01103 62928006414 zinc metallopeptidase RseP; Provisional; Region: PRK10779 62928006415 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 62928006416 active site 62928006417 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 62928006418 protein binding site [polypeptide binding]; other site 62928006419 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 62928006420 protein binding site [polypeptide binding]; other site 62928006421 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 62928006422 putative substrate binding region [chemical binding]; other site 62928006423 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 62928006424 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 62928006425 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 62928006426 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 62928006427 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 62928006428 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 62928006429 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 62928006430 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 62928006431 catalytic residue [active] 62928006432 putative FPP diphosphate binding site; other site 62928006433 putative FPP binding hydrophobic cleft; other site 62928006434 dimer interface [polypeptide binding]; other site 62928006435 putative IPP diphosphate binding site; other site 62928006436 ribosome recycling factor; Reviewed; Region: frr; PRK00083 62928006437 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 62928006438 hinge region; other site 62928006439 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 62928006440 putative nucleotide binding site [chemical binding]; other site 62928006441 uridine monophosphate binding site [chemical binding]; other site 62928006442 homohexameric interface [polypeptide binding]; other site 62928006443 elongation factor Ts; Provisional; Region: tsf; PRK09377 62928006444 UBA/TS-N domain; Region: UBA; pfam00627 62928006445 Elongation factor TS; Region: EF_TS; pfam00889 62928006446 Elongation factor TS; Region: EF_TS; pfam00889 62928006447 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 62928006448 rRNA interaction site [nucleotide binding]; other site 62928006449 S8 interaction site; other site 62928006450 putative laminin-1 binding site; other site 62928006451 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 62928006452 active site 62928006453 PII uridylyl-transferase; Provisional; Region: PRK03059 62928006454 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 62928006455 metal binding triad; other site 62928006456 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 62928006457 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928006458 Zn2+ binding site [ion binding]; other site 62928006459 Mg2+ binding site [ion binding]; other site 62928006460 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 62928006461 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 62928006462 hypothetical protein; Provisional; Region: PRK05208 62928006463 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 62928006464 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928006465 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928006466 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 62928006467 active site 62928006468 phosphorylation site [posttranslational modification] 62928006469 intermolecular recognition site; other site 62928006470 dimerization interface [polypeptide binding]; other site 62928006471 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 62928006472 Walker A motif; other site 62928006473 ATP binding site [chemical binding]; other site 62928006474 Walker B motif; other site 62928006475 arginine finger; other site 62928006476 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928006477 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 62928006478 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 62928006479 dimer interface [polypeptide binding]; other site 62928006480 phosphorylation site [posttranslational modification] 62928006481 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 62928006482 ATP binding site [chemical binding]; other site 62928006483 Mg2+ binding site [ion binding]; other site 62928006484 G-X-G motif; other site 62928006485 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 62928006486 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 62928006487 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 62928006488 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 62928006489 hydroxyglutarate oxidase; Provisional; Region: PRK11728 62928006490 Predicted dehydrogenase [General function prediction only]; Region: COG0579 62928006491 succinic semialdehyde dehydrogenase; Region: PLN02278 62928006492 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 62928006493 tetramerization interface [polypeptide binding]; other site 62928006494 NAD(P) binding site [chemical binding]; other site 62928006495 catalytic residues [active] 62928006496 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 62928006497 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 62928006498 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 62928006499 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 62928006500 Ligand binding site [chemical binding]; other site 62928006501 Electron transfer flavoprotein domain; Region: ETF; pfam01012 62928006502 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 62928006503 CoA-transferase family III; Region: CoA_transf_3; pfam02515 62928006504 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 62928006505 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 62928006506 FAD binding site [chemical binding]; other site 62928006507 substrate binding pocket [chemical binding]; other site 62928006508 catalytic base [active] 62928006509 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 62928006510 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928006511 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 62928006512 dimerization interface [polypeptide binding]; other site 62928006513 substrate binding pocket [chemical binding]; other site 62928006514 Peptidase family M54, also called archaemetzincins or archaelysins; Region: Peptidase_M54; cl17349 62928006515 enoyl-CoA hydratase-isomerase; Provisional; Region: PRK09674 62928006516 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928006517 substrate binding site [chemical binding]; other site 62928006518 oxyanion hole (OAH) forming residues; other site 62928006519 trimer interface [polypeptide binding]; other site 62928006520 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 62928006521 homotrimer interaction site [polypeptide binding]; other site 62928006522 putative active site [active] 62928006523 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 62928006524 active site 62928006525 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 62928006526 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 62928006527 FAD binding site [chemical binding]; other site 62928006528 substrate binding pocket [chemical binding]; other site 62928006529 catalytic base [active] 62928006530 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 62928006531 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 62928006532 active site 62928006533 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928006534 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 62928006535 substrate binding site [chemical binding]; other site 62928006536 oxyanion hole (OAH) forming residues; other site 62928006537 trimer interface [polypeptide binding]; other site 62928006538 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 62928006539 classical (c) SDRs; Region: SDR_c; cd05233 62928006540 NAD(P) binding site [chemical binding]; other site 62928006541 active site 62928006542 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 62928006543 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928006544 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928006545 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 62928006546 active site 62928006547 FMN binding site [chemical binding]; other site 62928006548 substrate binding site [chemical binding]; other site 62928006549 homotetramer interface [polypeptide binding]; other site 62928006550 catalytic residue [active] 62928006551 MarR family; Region: MarR_2; cl17246 62928006552 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 62928006553 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928006554 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006555 short chain dehydrogenase; Provisional; Region: PRK08265 62928006556 classical (c) SDRs; Region: SDR_c; cd05233 62928006557 NAD(P) binding site [chemical binding]; other site 62928006558 active site 62928006559 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 62928006560 Protein of unknown function (DUF808); Region: DUF808; pfam05661 62928006561 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 62928006562 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 62928006563 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 62928006564 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 62928006565 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 62928006566 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 62928006567 active site 62928006568 dimer interface [polypeptide binding]; other site 62928006569 non-prolyl cis peptide bond; other site 62928006570 insertion regions; other site 62928006571 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006572 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928006573 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006574 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 62928006575 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 62928006576 molybdopterin cofactor binding site; other site 62928006577 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 62928006578 The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_CT_Thiosulfate-R-like; cd02778 62928006579 putative molybdopterin cofactor binding site; other site 62928006580 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 62928006581 4Fe-4S binding domain; Region: Fer4; cl02805 62928006582 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006583 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928006584 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006585 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 62928006586 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 62928006587 Protein export membrane protein; Region: SecD_SecF; cl14618 62928006588 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 62928006589 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 62928006590 short chain dehydrogenase; Provisional; Region: PRK06172 62928006591 classical (c) SDRs; Region: SDR_c; cd05233 62928006592 NAD(P) binding site [chemical binding]; other site 62928006593 active site 62928006594 indole acetimide hydrolase; Validated; Region: PRK07488 62928006595 Amidase; Region: Amidase; cl11426 62928006596 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 62928006597 Amidase; Region: Amidase; pfam01425 62928006598 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 62928006599 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 62928006600 Ligand Binding Site [chemical binding]; other site 62928006601 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 62928006602 putative metal binding site [ion binding]; other site 62928006603 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 62928006604 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 62928006605 catalytic loop [active] 62928006606 iron binding site [ion binding]; other site 62928006607 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 62928006608 FAD binding pocket [chemical binding]; other site 62928006609 conserved FAD binding motif [chemical binding]; other site 62928006610 phosphate binding motif [ion binding]; other site 62928006611 beta-alpha-beta structure motif; other site 62928006612 NAD binding pocket [chemical binding]; other site 62928006613 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 62928006614 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 62928006615 iron-sulfur cluster [ion binding]; other site 62928006616 [2Fe-2S] cluster binding site [ion binding]; other site 62928006617 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 62928006618 alpha subunit interface [polypeptide binding]; other site 62928006619 active site 62928006620 substrate binding site [chemical binding]; other site 62928006621 Fe binding site [ion binding]; other site 62928006622 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 62928006623 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006624 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928006625 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006626 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928006627 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928006628 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 62928006629 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 62928006630 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 62928006631 active site 62928006632 Fe binding site [ion binding]; other site 62928006633 Lipocalin-like domain; Region: Lipocalin_5; pfam13924 62928006634 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 62928006635 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 62928006636 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl17414 62928006637 DNA-binding site [nucleotide binding]; DNA binding site 62928006638 DNA-binding transcriptional regulator CsiR; Provisional; Region: PRK11534 62928006639 FCD domain; Region: FCD; pfam07729 62928006640 Cupin domain; Region: Cupin_2; pfam07883 62928006641 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 62928006642 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 62928006643 NAD(P) binding site [chemical binding]; other site 62928006644 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 62928006645 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 62928006646 active site 62928006647 catalytic residues [active] 62928006648 metal binding site [ion binding]; metal-binding site 62928006649 DmpG-like communication domain; Region: DmpG_comm; pfam07836 62928006650 acetaldehyde dehydrogenase; Validated; Region: PRK08300 62928006651 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 62928006652 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 62928006653 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 62928006654 Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate; Region: MhpB_like; cd07365 62928006655 putative active site [active] 62928006656 Fe(II) binding site [ion binding]; other site 62928006657 putative dimer interface [polypeptide binding]; other site 62928006658 putative tetramer interface [polypeptide binding]; other site 62928006659 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 62928006660 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 62928006661 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 62928006662 iron-sulfur cluster [ion binding]; other site 62928006663 [2Fe-2S] cluster binding site [ion binding]; other site 62928006664 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 62928006665 alpha subunit interface [polypeptide binding]; other site 62928006666 active site 62928006667 substrate binding site [chemical binding]; other site 62928006668 Fe binding site [ion binding]; other site 62928006669 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 62928006670 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]; Region: COG4231 62928006671 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 62928006672 PYR/PP interface [polypeptide binding]; other site 62928006673 dimer interface [polypeptide binding]; other site 62928006674 TPP binding site [chemical binding]; other site 62928006675 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 62928006676 TPP-binding site; other site 62928006677 putative indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK08312 62928006678 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 62928006679 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 62928006680 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 62928006681 FMN-binding pocket [chemical binding]; other site 62928006682 flavin binding motif; other site 62928006683 phosphate binding motif [ion binding]; other site 62928006684 beta-alpha-beta structure motif; other site 62928006685 NAD binding pocket [chemical binding]; other site 62928006686 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 62928006687 catalytic loop [active] 62928006688 iron binding site [ion binding]; other site 62928006689 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 62928006690 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 62928006691 iron-sulfur cluster [ion binding]; other site 62928006692 [2Fe-2S] cluster binding site [ion binding]; other site 62928006693 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 62928006694 putative alpha subunit interface [polypeptide binding]; other site 62928006695 putative active site [active] 62928006696 putative substrate binding site [chemical binding]; other site 62928006697 Fe binding site [ion binding]; other site 62928006698 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 62928006699 inter-subunit interface; other site 62928006700 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 62928006701 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_DitJ_like; cd05934 62928006702 acyl-activating enzyme (AAE) consensus motif; other site 62928006703 putative AMP binding site [chemical binding]; other site 62928006704 putative active site [active] 62928006705 putative CoA binding site [chemical binding]; other site 62928006706 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 62928006707 active site 62928006708 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 62928006709 DUF35 OB-fold domain; Region: DUF35; pfam01796 62928006710 short chain dehydrogenase; Validated; Region: PRK08264 62928006711 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928006712 NAD(P) binding site [chemical binding]; other site 62928006713 active site 62928006714 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 62928006715 short chain dehydrogenase; Provisional; Region: PRK07577 62928006716 classical (c) SDRs; Region: SDR_c; cd05233 62928006717 NAD(P) binding site [chemical binding]; other site 62928006718 active site 62928006719 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928006720 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 62928006721 putative ligand binding site [chemical binding]; other site 62928006722 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928006723 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928006724 TM-ABC transporter signature motif; other site 62928006725 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928006726 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928006727 TM-ABC transporter signature motif; other site 62928006728 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928006729 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928006730 Walker A/P-loop; other site 62928006731 ATP binding site [chemical binding]; other site 62928006732 Q-loop/lid; other site 62928006733 ABC transporter signature motif; other site 62928006734 Walker B; other site 62928006735 D-loop; other site 62928006736 H-loop/switch region; other site 62928006737 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928006738 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928006739 Walker A/P-loop; other site 62928006740 ATP binding site [chemical binding]; other site 62928006741 Q-loop/lid; other site 62928006742 ABC transporter signature motif; other site 62928006743 Walker B; other site 62928006744 D-loop; other site 62928006745 H-loop/switch region; other site 62928006746 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 62928006747 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 62928006748 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 62928006749 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 62928006750 intersubunit interface [polypeptide binding]; other site 62928006751 active site 62928006752 Zn2+ binding site [ion binding]; other site 62928006753 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928006754 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 62928006755 acyl-activating enzyme (AAE) consensus motif; other site 62928006756 AMP binding site [chemical binding]; other site 62928006757 active site 62928006758 CoA binding site [chemical binding]; other site 62928006759 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 62928006760 MarR family; Region: MarR; pfam01047 62928006761 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 62928006762 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 62928006763 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 62928006764 G1 box; other site 62928006765 putative GEF interaction site [polypeptide binding]; other site 62928006766 GTP/Mg2+ binding site [chemical binding]; other site 62928006767 Switch I region; other site 62928006768 G2 box; other site 62928006769 G3 box; other site 62928006770 Switch II region; other site 62928006771 G4 box; other site 62928006772 G5 box; other site 62928006773 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 62928006774 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 62928006775 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 62928006776 active site 62928006777 tetramer interface; other site 62928006778 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 62928006779 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 62928006780 nucleotide binding pocket [chemical binding]; other site 62928006781 K-X-D-G motif; other site 62928006782 catalytic site [active] 62928006783 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 62928006784 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 62928006785 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 62928006786 Dimer interface [polypeptide binding]; other site 62928006787 BRCT sequence motif; other site 62928006788 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 62928006789 FtsZ protein binding site [polypeptide binding]; other site 62928006790 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 62928006791 AAA domain; Region: AAA_23; pfam13476 62928006792 Walker A/P-loop; other site 62928006793 ATP binding site [chemical binding]; other site 62928006794 Q-loop/lid; other site 62928006795 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 62928006796 Q-loop/lid; other site 62928006797 ABC transporter signature motif; other site 62928006798 Walker B; other site 62928006799 D-loop; other site 62928006800 H-loop/switch region; other site 62928006801 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 62928006802 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 62928006803 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928006804 homodimer interface [polypeptide binding]; other site 62928006805 catalytic residue [active] 62928006806 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 62928006807 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 62928006808 trimer interface [polypeptide binding]; other site 62928006809 active site 62928006810 substrate binding site [chemical binding]; other site 62928006811 CoA binding site [chemical binding]; other site 62928006812 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 62928006813 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 62928006814 Walker A motif; other site 62928006815 ATP binding site [chemical binding]; other site 62928006816 Walker B motif; other site 62928006817 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 62928006818 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 62928006819 metal binding site [ion binding]; metal-binding site 62928006820 dimer interface [polypeptide binding]; other site 62928006821 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 62928006822 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 62928006823 S-adenosylmethionine binding site [chemical binding]; other site 62928006824 Response regulator receiver domain; Region: Response_reg; pfam00072 62928006825 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 62928006826 active site 62928006827 phosphorylation site [posttranslational modification] 62928006828 intermolecular recognition site; other site 62928006829 dimerization interface [polypeptide binding]; other site 62928006830 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 62928006831 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 62928006832 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 62928006833 catalytic loop [active] 62928006834 iron binding site [ion binding]; other site 62928006835 chaperone protein HscA; Provisional; Region: hscA; PRK05183 62928006836 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 62928006837 nucleotide binding site [chemical binding]; other site 62928006838 putative NEF/HSP70 interaction site [polypeptide binding]; other site 62928006839 SBD interface [polypeptide binding]; other site 62928006840 co-chaperone HscB; Provisional; Region: hscB; PRK03578 62928006841 DnaJ domain; Region: DnaJ; pfam00226 62928006842 HSP70 interaction site [polypeptide binding]; other site 62928006843 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 62928006844 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 62928006845 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 62928006846 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 62928006847 trimerization site [polypeptide binding]; other site 62928006848 active site 62928006849 cysteine desulfurase; Provisional; Region: PRK14012 62928006850 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 62928006851 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928006852 catalytic residue [active] 62928006853 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 62928006854 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 62928006855 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928006856 catalytic residue [active] 62928006857 Predicted transcriptional regulator [Transcription]; Region: COG1959 62928006858 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 62928006859 serine O-acetyltransferase; Region: cysE; TIGR01172 62928006860 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 62928006861 trimer interface [polypeptide binding]; other site 62928006862 active site 62928006863 substrate binding site [chemical binding]; other site 62928006864 CoA binding site [chemical binding]; other site 62928006865 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 62928006866 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 62928006867 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 62928006868 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 62928006869 active site 62928006870 dimerization interface [polypeptide binding]; other site 62928006871 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 62928006872 putative hydrophobic ligand binding site [chemical binding]; other site 62928006873 protein interface [polypeptide binding]; other site 62928006874 gate; other site 62928006875 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 62928006876 Plasmid encoded toxin Txe; Region: Plasmid_Txe; pfam06769 62928006877 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 62928006878 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4453 62928006879 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 62928006880 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 62928006881 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 62928006882 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 62928006883 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 62928006884 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 62928006885 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 62928006886 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 62928006887 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 62928006888 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 62928006889 Methyltransferase domain; Region: Methyltransf_26; pfam13659 62928006890 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 62928006891 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 62928006892 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 62928006893 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 62928006894 DnaJ central domain; Region: DnaJ_CXXCXGXG; pfam00684 62928006895 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 62928006896 Zn binding sites [ion binding]; other site 62928006897 Uncharacterized conserved protein [Function unknown]; Region: COG1479 62928006898 Protein of unknown function DUF262; Region: DUF262; pfam03235 62928006899 Protein of unknown function DUF262; Region: DUF262; pfam03235 62928006900 Uncharacterized conserved protein [Function unknown]; Region: COG1479 62928006901 Protein of unknown function DUF262; Region: DUF262; pfam03235 62928006902 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 62928006903 MPN+ (JAMM) motif; other site 62928006904 Zinc-binding site [ion binding]; other site 62928006905 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 62928006906 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 62928006907 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 62928006908 Transposase [DNA replication, recombination, and repair]; Region: COG5433 62928006909 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 62928006910 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 62928006911 active site 62928006912 DNA binding site [nucleotide binding] 62928006913 Int/Topo IB signature motif; other site 62928006914 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 62928006915 MutS domain I; Region: MutS_I; pfam01624 62928006916 MutS domain II; Region: MutS_II; pfam05188 62928006917 MutS domain III; Region: MutS_III; pfam05192 62928006918 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 62928006919 Walker A/P-loop; other site 62928006920 ATP binding site [chemical binding]; other site 62928006921 Q-loop/lid; other site 62928006922 ABC transporter signature motif; other site 62928006923 Walker B; other site 62928006924 D-loop; other site 62928006925 H-loop/switch region; other site 62928006926 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 62928006927 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 62928006928 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 62928006929 active site 62928006930 catalytic site [active] 62928006931 substrate binding site [chemical binding]; other site 62928006932 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 62928006933 RNA/DNA hybrid binding site [nucleotide binding]; other site 62928006934 active site 62928006935 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 62928006936 Response regulator receiver domain; Region: Response_reg; pfam00072 62928006937 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 62928006938 active site 62928006939 phosphorylation site [posttranslational modification] 62928006940 intermolecular recognition site; other site 62928006941 dimerization interface [polypeptide binding]; other site 62928006942 Response regulator receiver domain; Region: Response_reg; pfam00072 62928006943 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 62928006944 active site 62928006945 phosphorylation site [posttranslational modification] 62928006946 intermolecular recognition site; other site 62928006947 dimerization interface [polypeptide binding]; other site 62928006948 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928006949 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928006950 metal binding site [ion binding]; metal-binding site 62928006951 active site 62928006952 I-site; other site 62928006953 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 62928006954 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 62928006955 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928006956 catalytic residue [active] 62928006957 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 62928006958 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 62928006959 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 62928006960 Walker A/P-loop; other site 62928006961 ATP binding site [chemical binding]; other site 62928006962 Q-loop/lid; other site 62928006963 ABC transporter signature motif; other site 62928006964 Walker B; other site 62928006965 D-loop; other site 62928006966 H-loop/switch region; other site 62928006967 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 62928006968 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 62928006969 Walker A/P-loop; other site 62928006970 ATP binding site [chemical binding]; other site 62928006971 Q-loop/lid; other site 62928006972 ABC transporter signature motif; other site 62928006973 Walker B; other site 62928006974 D-loop; other site 62928006975 H-loop/switch region; other site 62928006976 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 62928006977 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 62928006978 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 62928006979 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 62928006980 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 62928006981 catalytic triad [active] 62928006982 LexA repressor; Validated; Region: PRK00215 62928006983 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 62928006984 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 62928006985 Catalytic site [active] 62928006986 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 62928006987 putative efflux protein, MATE family; Region: matE; TIGR00797 62928006988 cation binding site [ion binding]; other site 62928006989 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 62928006990 ArsC family; Region: ArsC; pfam03960 62928006991 catalytic residues [active] 62928006992 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 62928006993 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 62928006994 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 62928006995 protein binding site [polypeptide binding]; other site 62928006996 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 62928006997 Found in ATP-dependent protease La (LON); Region: LON; smart00464 62928006998 Found in ATP-dependent protease La (LON); Region: LON; smart00464 62928006999 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 62928007000 Walker A motif; other site 62928007001 ATP binding site [chemical binding]; other site 62928007002 Walker B motif; other site 62928007003 arginine finger; other site 62928007004 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 62928007005 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 62928007006 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 62928007007 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 62928007008 Walker A motif; other site 62928007009 ATP binding site [chemical binding]; other site 62928007010 Walker B motif; other site 62928007011 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 62928007012 Clp protease; Region: CLP_protease; pfam00574 62928007013 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 62928007014 oligomer interface [polypeptide binding]; other site 62928007015 active site residues [active] 62928007016 trigger factor; Provisional; Region: tig; PRK01490 62928007017 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 62928007018 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 62928007019 PrkA family serine protein kinase; Provisional; Region: PRK15455 62928007020 AAA ATPase domain; Region: AAA_16; pfam13191 62928007021 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 62928007022 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 62928007023 hypothetical protein; Provisional; Region: PRK05325 62928007024 SpoVR family protein; Provisional; Region: PRK11767 62928007025 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 62928007026 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 62928007027 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 62928007028 putative ATP binding site [chemical binding]; other site 62928007029 putative substrate binding site [chemical binding]; other site 62928007030 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 62928007031 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928007032 Zn2+ binding site [ion binding]; other site 62928007033 Mg2+ binding site [ion binding]; other site 62928007034 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 62928007035 EamA-like transporter family; Region: EamA; pfam00892 62928007036 EamA-like transporter family; Region: EamA; pfam00892 62928007037 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 62928007038 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 62928007039 dimerization interface [polypeptide binding]; other site 62928007040 active site 62928007041 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 62928007042 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 62928007043 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928007044 catalytic residue [active] 62928007045 homoserine dehydrogenase; Provisional; Region: PRK06349 62928007046 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 62928007047 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 62928007048 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 62928007049 aminotransferase AlaT; Validated; Region: PRK09265 62928007050 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 62928007051 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928007052 homodimer interface [polypeptide binding]; other site 62928007053 catalytic residue [active] 62928007054 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 62928007055 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 62928007056 putative substrate translocation pore; other site 62928007057 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928007058 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 62928007059 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 62928007060 Substrate binding site; other site 62928007061 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 62928007062 transcriptional regulator EpsA; Region: EpsA; TIGR03020 62928007063 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 62928007064 DNA binding residues [nucleotide binding] 62928007065 dimerization interface [polypeptide binding]; other site 62928007066 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 62928007067 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 62928007068 Secretin and TonB N terminus short domain; Region: STN; smart00965 62928007069 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 62928007070 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 62928007071 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 62928007072 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 62928007073 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 62928007074 Walker A motif; other site 62928007075 ATP binding site [chemical binding]; other site 62928007076 Walker B motif; other site 62928007077 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 62928007078 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 62928007079 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 62928007080 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 62928007081 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 62928007082 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 62928007083 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 62928007084 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 62928007085 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 62928007086 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928007087 catalytic residue [active] 62928007088 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 62928007089 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 62928007090 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 62928007091 inhibitor-cofactor binding pocket; inhibition site 62928007092 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928007093 catalytic residue [active] 62928007094 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 62928007095 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 62928007096 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 62928007097 RNase E interface [polypeptide binding]; other site 62928007098 trimer interface [polypeptide binding]; other site 62928007099 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 62928007100 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 62928007101 RNase E interface [polypeptide binding]; other site 62928007102 trimer interface [polypeptide binding]; other site 62928007103 active site 62928007104 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 62928007105 putative nucleic acid binding region [nucleotide binding]; other site 62928007106 G-X-X-G motif; other site 62928007107 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 62928007108 RNA binding site [nucleotide binding]; other site 62928007109 domain interface; other site 62928007110 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 62928007111 16S/18S rRNA binding site [nucleotide binding]; other site 62928007112 S13e-L30e interaction site [polypeptide binding]; other site 62928007113 25S rRNA binding site [nucleotide binding]; other site 62928007114 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 62928007115 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 62928007116 RNA binding site [nucleotide binding]; other site 62928007117 active site 62928007118 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 62928007119 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 62928007120 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 62928007121 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 62928007122 translation initiation factor IF-2; Region: IF-2; TIGR00487 62928007123 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 62928007124 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 62928007125 G1 box; other site 62928007126 putative GEF interaction site [polypeptide binding]; other site 62928007127 GTP/Mg2+ binding site [chemical binding]; other site 62928007128 Switch I region; other site 62928007129 G2 box; other site 62928007130 G3 box; other site 62928007131 Switch II region; other site 62928007132 G4 box; other site 62928007133 G5 box; other site 62928007134 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 62928007135 Translation-initiation factor 2; Region: IF-2; pfam11987 62928007136 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 62928007137 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 62928007138 NusA N-terminal domain; Region: NusA_N; pfam08529 62928007139 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 62928007140 RNA binding site [nucleotide binding]; other site 62928007141 homodimer interface [polypeptide binding]; other site 62928007142 NusA-like KH domain; Region: KH_5; pfam13184 62928007143 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 62928007144 G-X-X-G motif; other site 62928007145 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 62928007146 ribosome maturation protein RimP; Reviewed; Region: PRK00092 62928007147 Sm and related proteins; Region: Sm_like; cl00259 62928007148 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 62928007149 putative oligomer interface [polypeptide binding]; other site 62928007150 putative RNA binding site [nucleotide binding]; other site 62928007151 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 62928007152 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 62928007153 RNA binding surface [nucleotide binding]; other site 62928007154 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 62928007155 probable active site [active] 62928007156 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 62928007157 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 62928007158 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 62928007159 Peptidase family M50; Region: Peptidase_M50; pfam02163 62928007160 active site 62928007161 putative substrate binding region [chemical binding]; other site 62928007162 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 62928007163 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 62928007164 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 62928007165 active site 62928007166 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 62928007167 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 62928007168 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 62928007169 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 62928007170 aldehyde dehydrogenase family 7 member; Region: PLN02315 62928007171 NAD(P) binding site [chemical binding]; other site 62928007172 catalytic residues [active] 62928007173 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 62928007174 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 62928007175 GTP/Mg2+ binding site [chemical binding]; other site 62928007176 G4 box; other site 62928007177 G5 box; other site 62928007178 G1 box; other site 62928007179 Switch I region; other site 62928007180 G2 box; other site 62928007181 G3 box; other site 62928007182 Switch II region; other site 62928007183 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 62928007184 DNA-binding site [nucleotide binding]; DNA binding site 62928007185 RNA-binding motif; other site 62928007186 DEAD-like helicases superfamily; Region: DEXDc; smart00487 62928007187 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 62928007188 ATP binding site [chemical binding]; other site 62928007189 Mg++ binding site [ion binding]; other site 62928007190 motif III; other site 62928007191 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 62928007192 nucleotide binding region [chemical binding]; other site 62928007193 ATP-binding site [chemical binding]; other site 62928007194 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 62928007195 putative RNA binding site [nucleotide binding]; other site 62928007196 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 62928007197 active site 62928007198 catalytic triad [active] 62928007199 oxyanion hole [active] 62928007200 serine/threonine protein kinase; Provisional; Region: PRK11768 62928007201 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 62928007202 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 62928007203 YaeQ protein; Region: YaeQ; pfam07152 62928007204 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928007205 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928007206 metal binding site [ion binding]; metal-binding site 62928007207 active site 62928007208 I-site; other site 62928007209 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK07533 62928007210 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 62928007211 NAD binding site [chemical binding]; other site 62928007212 homotetramer interface [polypeptide binding]; other site 62928007213 homodimer interface [polypeptide binding]; other site 62928007214 substrate binding site [chemical binding]; other site 62928007215 active site 62928007216 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 62928007217 Walker A motif; other site 62928007218 ATP binding site [chemical binding]; other site 62928007219 Walker B motif; other site 62928007220 arginine finger; other site 62928007221 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 62928007222 GTP cyclohydrolase I; Provisional; Region: PLN03044 62928007223 active site 62928007224 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 62928007225 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 62928007226 Phosphate transporter family; Region: PHO4; pfam01384 62928007227 Phosphate transporter family; Region: PHO4; cl00396 62928007228 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 62928007229 homodimer interface [polypeptide binding]; other site 62928007230 chemical substrate binding site [chemical binding]; other site 62928007231 oligomer interface [polypeptide binding]; other site 62928007232 metal binding site [ion binding]; metal-binding site 62928007233 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 62928007234 Methyltransferase domain; Region: Methyltransf_26; pfam13659 62928007235 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 62928007236 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 62928007237 trimer interface [polypeptide binding]; other site 62928007238 putative metal binding site [ion binding]; other site 62928007239 Protein of unknown function (DUF541); Region: SIMPL; cl01077 62928007240 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 62928007241 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 62928007242 NlpC/P60 family; Region: NLPC_P60; pfam00877 62928007243 FOG: CBS domain [General function prediction only]; Region: COG0517 62928007244 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 62928007245 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 62928007246 Septum formation initiator; Region: DivIC; cl17659 62928007247 enolase; Provisional; Region: eno; PRK00077 62928007248 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 62928007249 dimer interface [polypeptide binding]; other site 62928007250 metal binding site [ion binding]; metal-binding site 62928007251 substrate binding pocket [chemical binding]; other site 62928007252 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 62928007253 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 62928007254 CTP synthetase; Validated; Region: pyrG; PRK05380 62928007255 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 62928007256 Catalytic site [active] 62928007257 active site 62928007258 UTP binding site [chemical binding]; other site 62928007259 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 62928007260 active site 62928007261 putative oxyanion hole; other site 62928007262 catalytic triad [active] 62928007263 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 62928007264 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 62928007265 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 62928007266 acyl-activating enzyme (AAE) consensus motif; other site 62928007267 putative AMP binding site [chemical binding]; other site 62928007268 putative active site [active] 62928007269 putative CoA binding site [chemical binding]; other site 62928007270 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 62928007271 active site 62928007272 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 62928007273 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928007274 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 62928007275 Protein of unknown function, DUF481; Region: DUF481; pfam04338 62928007276 Protein of unknown function (DUF461); Region: DUF461; pfam04314 62928007277 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 62928007278 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928007279 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 62928007280 N-terminal plug; other site 62928007281 ligand-binding site [chemical binding]; other site 62928007282 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 62928007283 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 62928007284 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 62928007285 dimerization interface [polypeptide binding]; other site 62928007286 ATP binding site [chemical binding]; other site 62928007287 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 62928007288 dimerization interface [polypeptide binding]; other site 62928007289 ATP binding site [chemical binding]; other site 62928007290 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 62928007291 putative active site [active] 62928007292 catalytic triad [active] 62928007293 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 62928007294 active site 62928007295 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 62928007296 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 62928007297 Ligand binding site; other site 62928007298 Putative Catalytic site; other site 62928007299 DXD motif; other site 62928007300 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 62928007301 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 62928007302 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 62928007303 active site 62928007304 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 62928007305 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 62928007306 Peptidase family M23; Region: Peptidase_M23; pfam01551 62928007307 phosphoenolpyruvate synthase; Validated; Region: PRK06464 62928007308 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 62928007309 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 62928007310 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 62928007311 PEP synthetase regulatory protein; Provisional; Region: PRK05339 62928007312 Protein of unknown function (DUF2863); Region: DUF2863; pfam11062 62928007313 methionine sulfoxide reductase B; Provisional; Region: PRK00222 62928007314 SelR domain; Region: SelR; pfam01641 62928007315 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 62928007316 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 62928007317 dimerization interface [polypeptide binding]; other site 62928007318 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928007319 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928007320 dimer interface [polypeptide binding]; other site 62928007321 putative CheW interface [polypeptide binding]; other site 62928007322 beta-ketothiolase; Provisional; Region: PRK09051 62928007323 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928007324 dimer interface [polypeptide binding]; other site 62928007325 active site 62928007326 CobD/CbiB family protein; Provisional; Region: PRK07630 62928007327 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 62928007328 putative active site [active] 62928007329 putative CoA binding site [chemical binding]; other site 62928007330 nudix motif; other site 62928007331 metal binding site [ion binding]; metal-binding site 62928007332 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 62928007333 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 62928007334 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 62928007335 Type II transport protein GspH; Region: GspH; pfam12019 62928007336 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 62928007337 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 62928007338 catalytic motif [active] 62928007339 Catalytic residue [active] 62928007340 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 62928007341 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 62928007342 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 62928007343 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 62928007344 argininosuccinate synthase; Provisional; Region: PRK13820 62928007345 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 62928007346 ANP binding site [chemical binding]; other site 62928007347 Substrate Binding Site II [chemical binding]; other site 62928007348 Substrate Binding Site I [chemical binding]; other site 62928007349 ornithine carbamoyltransferase; Provisional; Region: PRK00779 62928007350 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 62928007351 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 62928007352 acetylornithine aminotransferase; Provisional; Region: PRK02627 62928007353 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 62928007354 inhibitor-cofactor binding pocket; inhibition site 62928007355 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928007356 catalytic residue [active] 62928007357 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 62928007358 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 62928007359 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 62928007360 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 62928007361 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 62928007362 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 62928007363 homodimer interface [polypeptide binding]; other site 62928007364 substrate-cofactor binding pocket; other site 62928007365 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928007366 catalytic residue [active] 62928007367 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928007368 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928007369 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928007370 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 62928007371 HI0933-like protein; Region: HI0933_like; pfam03486 62928007372 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 62928007373 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 62928007374 putative active site [active] 62928007375 putative metal binding site [ion binding]; other site 62928007376 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 62928007377 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 62928007378 catalytic triad [active] 62928007379 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 62928007380 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 62928007381 putative active site [active] 62928007382 PhoH-like protein; Region: PhoH; pfam02562 62928007383 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 62928007384 PAS domain; Region: PAS_9; pfam13426 62928007385 putative active site [active] 62928007386 heme pocket [chemical binding]; other site 62928007387 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928007388 dimer interface [polypeptide binding]; other site 62928007389 putative CheW interface [polypeptide binding]; other site 62928007390 GAF domain; Region: GAF_2; pfam13185 62928007391 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928007392 Zn2+ binding site [ion binding]; other site 62928007393 Mg2+ binding site [ion binding]; other site 62928007394 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 62928007395 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 62928007396 ligand binding site [chemical binding]; other site 62928007397 flexible hinge region; other site 62928007398 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 62928007399 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 62928007400 metal binding triad; other site 62928007401 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 62928007402 active site 62928007403 catalytic site [active] 62928007404 substrate binding site [chemical binding]; other site 62928007405 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 62928007406 NlpC/P60 family; Region: NLPC_P60; pfam00877 62928007407 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 62928007408 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 62928007409 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 62928007410 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 62928007411 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 62928007412 dimer interface [polypeptide binding]; other site 62928007413 conserved gate region; other site 62928007414 putative PBP binding loops; other site 62928007415 ABC-ATPase subunit interface; other site 62928007416 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 62928007417 dimer interface [polypeptide binding]; other site 62928007418 conserved gate region; other site 62928007419 putative PBP binding loops; other site 62928007420 ABC-ATPase subunit interface; other site 62928007421 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 62928007422 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 62928007423 Walker A/P-loop; other site 62928007424 ATP binding site [chemical binding]; other site 62928007425 Q-loop/lid; other site 62928007426 ABC transporter signature motif; other site 62928007427 Walker B; other site 62928007428 D-loop; other site 62928007429 H-loop/switch region; other site 62928007430 TOBE domain; Region: TOBE_2; pfam08402 62928007431 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 62928007432 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 62928007433 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 62928007434 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 62928007435 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 62928007436 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 62928007437 quinone interaction residues [chemical binding]; other site 62928007438 active site 62928007439 catalytic residues [active] 62928007440 FMN binding site [chemical binding]; other site 62928007441 substrate binding site [chemical binding]; other site 62928007442 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 62928007443 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2; pfam00111 62928007444 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 62928007445 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 62928007446 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 62928007447 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 62928007448 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 62928007449 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 62928007450 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 62928007451 XdhC Rossmann domain; Region: XdhC_C; pfam13478 62928007452 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 62928007453 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 62928007454 Walker A/P-loop; other site 62928007455 ATP binding site [chemical binding]; other site 62928007456 Q-loop/lid; other site 62928007457 ABC transporter signature motif; other site 62928007458 Walker B; other site 62928007459 D-loop; other site 62928007460 H-loop/switch region; other site 62928007461 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 62928007462 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928007463 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 62928007464 TM-ABC transporter signature motif; other site 62928007465 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 62928007466 TM-ABC transporter signature motif; other site 62928007467 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 62928007468 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 62928007469 N-terminal plug; other site 62928007470 ligand-binding site [chemical binding]; other site 62928007471 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 62928007472 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 62928007473 cobalt transport protein CbiM; Validated; Region: PRK06265 62928007474 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 62928007475 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 62928007476 Walker A/P-loop; other site 62928007477 ATP binding site [chemical binding]; other site 62928007478 Q-loop/lid; other site 62928007479 ABC transporter signature motif; other site 62928007480 Walker B; other site 62928007481 D-loop; other site 62928007482 H-loop/switch region; other site 62928007483 guanine deaminase; Provisional; Region: PRK09228 62928007484 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 62928007485 active site 62928007486 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 62928007487 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 62928007488 putative active site [active] 62928007489 heme pocket [chemical binding]; other site 62928007490 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928007491 metal binding site [ion binding]; metal-binding site 62928007492 active site 62928007493 I-site; other site 62928007494 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 62928007495 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 62928007496 active site 62928007497 metal binding site [ion binding]; metal-binding site 62928007498 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 62928007499 PAS domain S-box; Region: sensory_box; TIGR00229 62928007500 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 62928007501 putative active site [active] 62928007502 heme pocket [chemical binding]; other site 62928007503 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 62928007504 PAS domain; Region: PAS_9; pfam13426 62928007505 putative active site [active] 62928007506 heme pocket [chemical binding]; other site 62928007507 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928007508 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928007509 metal binding site [ion binding]; metal-binding site 62928007510 active site 62928007511 I-site; other site 62928007512 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 62928007513 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 62928007514 substrate binding pocket [chemical binding]; other site 62928007515 membrane-bound complex binding site; other site 62928007516 hinge residues; other site 62928007517 Domain of Unknown Function with PDB structure (DUF3862); Region: DUF3862; pfam12978 62928007518 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 62928007519 NTP_transferases catalyze the transfer of nucleotides onto phosphosugars; Region: NTP_transferase; cd04181 62928007520 active site 62928007521 Substrate binding site; other site 62928007522 Mg++ binding site; other site 62928007523 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 62928007524 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 62928007525 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 62928007526 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 62928007527 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 62928007528 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 62928007529 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 62928007530 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928007531 Endoglucanase [Carbohydrate transport and metabolism]; Region: BglC; COG2730 62928007532 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 62928007533 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 62928007534 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 62928007535 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 62928007536 Acyltransferase family; Region: Acyl_transf_3; pfam01757 62928007537 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 62928007538 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 62928007539 chain length determinant protein EpsF; Region: EpsF; TIGR03017 62928007540 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 62928007541 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 62928007542 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 62928007543 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 62928007544 exopolysaccharide biosynthesis operon protein EpsL; Region: EpsL; TIGR03014 62928007545 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 62928007546 Bacterial sugar transferase; Region: Bac_transf; pfam02397 62928007547 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 62928007548 Fe-S cluster binding site [ion binding]; other site 62928007549 active site 62928007550 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 62928007551 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 62928007552 NAD(P) binding site [chemical binding]; other site 62928007553 catalytic residues [active] 62928007554 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 62928007555 putative metal binding site [ion binding]; other site 62928007556 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 62928007557 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 62928007558 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 62928007559 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 62928007560 Cytochrome c; Region: Cytochrom_C; pfam00034 62928007561 Methylamine dehydrogenase, L chain; Region: Me-amine-dh_L; cl03812 62928007562 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 62928007563 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 62928007564 Methylamine utilisation protein MauE; Region: MauE; pfam07291 62928007565 methylamine dehydrogenase (amicyanin) heavy chain; Region: TTQ_MADH_Hv; TIGR02658 62928007566 Helix-turn-helix domain; Region: HTH_18; pfam12833 62928007567 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928007568 Transcriptional regulators [Transcription]; Region: FadR; COG2186 62928007569 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928007570 DNA-binding site [nucleotide binding]; DNA binding site 62928007571 FCD domain; Region: FCD; pfam07729 62928007572 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 62928007573 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 62928007574 substrate binding pocket [chemical binding]; other site 62928007575 membrane-bound complex binding site; other site 62928007576 hinge residues; other site 62928007577 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 62928007578 dimer interface [polypeptide binding]; other site 62928007579 conserved gate region; other site 62928007580 putative PBP binding loops; other site 62928007581 ABC-ATPase subunit interface; other site 62928007582 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 62928007583 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 62928007584 dimer interface [polypeptide binding]; other site 62928007585 conserved gate region; other site 62928007586 putative PBP binding loops; other site 62928007587 ABC-ATPase subunit interface; other site 62928007588 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 62928007589 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 62928007590 Walker A/P-loop; other site 62928007591 ATP binding site [chemical binding]; other site 62928007592 Q-loop/lid; other site 62928007593 ABC transporter signature motif; other site 62928007594 Walker B; other site 62928007595 D-loop; other site 62928007596 H-loop/switch region; other site 62928007597 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 62928007598 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 62928007599 putative C-terminal domain interface [polypeptide binding]; other site 62928007600 putative GSH binding site (G-site) [chemical binding]; other site 62928007601 putative dimer interface [polypeptide binding]; other site 62928007602 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 62928007603 dimer interface [polypeptide binding]; other site 62928007604 N-terminal domain interface [polypeptide binding]; other site 62928007605 putative substrate binding pocket (H-site) [chemical binding]; other site 62928007606 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 62928007607 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 62928007608 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 62928007609 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 62928007610 dimerization interface [polypeptide binding]; other site 62928007611 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928007612 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928007613 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928007614 dimer interface [polypeptide binding]; other site 62928007615 putative CheW interface [polypeptide binding]; other site 62928007616 HDOD domain; Region: HDOD; pfam08668 62928007617 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 62928007618 potassium uptake protein; Region: kup; TIGR00794 62928007619 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 62928007620 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 62928007621 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 62928007622 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 62928007623 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 62928007624 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 62928007625 Peptidase C26; Region: Peptidase_C26; pfam07722 62928007626 catalytic triad [active] 62928007627 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 62928007628 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 62928007629 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 62928007630 NADPH bind site [chemical binding]; other site 62928007631 putative FMN binding site [chemical binding]; other site 62928007632 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 62928007633 putative FMN binding site [chemical binding]; other site 62928007634 NADPH bind site [chemical binding]; other site 62928007635 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 62928007636 active site residue [active] 62928007637 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 62928007638 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 62928007639 flavodoxin FldA; Validated; Region: PRK09267 62928007640 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 62928007641 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 62928007642 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 62928007643 catalytic residues [active] 62928007644 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 62928007645 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 62928007646 DctM-like transporters; Region: DctM; pfam06808 62928007647 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 62928007648 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 62928007649 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928007650 Zn2+ binding site [ion binding]; other site 62928007651 Mg2+ binding site [ion binding]; other site 62928007652 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 62928007653 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928007654 Zn2+ binding site [ion binding]; other site 62928007655 Mg2+ binding site [ion binding]; other site 62928007656 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 62928007657 MgtC family; Region: MgtC; pfam02308 62928007658 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 62928007659 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 62928007660 putative active site [active] 62928007661 putative dimer interface [polypeptide binding]; other site 62928007662 TfoX N-terminal domain; Region: TfoX_N; pfam04993 62928007663 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 62928007664 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 62928007665 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 62928007666 DNA binding site [nucleotide binding] 62928007667 active site 62928007668 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 62928007669 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 62928007670 putative active site [active] 62928007671 Zn binding site [ion binding]; other site 62928007672 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928007673 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 62928007674 aromatic arch; other site 62928007675 DCoH dimer interaction site [polypeptide binding]; other site 62928007676 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 62928007677 DCoH tetramer interaction site [polypeptide binding]; other site 62928007678 substrate binding site [chemical binding]; other site 62928007679 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 62928007680 active site 62928007681 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 62928007682 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 62928007683 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 62928007684 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 62928007685 Walker A motif; other site 62928007686 ATP binding site [chemical binding]; other site 62928007687 Walker B motif; other site 62928007688 Fic family protein [Function unknown]; Region: COG3177 62928007689 Fic/DOC family; Region: Fic; pfam02661 62928007690 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 62928007691 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928007692 putative substrate translocation pore; other site 62928007693 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 62928007694 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928007695 DNA binding residues [nucleotide binding] 62928007696 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 62928007697 active site 62928007698 catalytic residues [active] 62928007699 DNA binding site [nucleotide binding] 62928007700 Int/Topo IB signature motif; other site 62928007701 DEAD-like helicases superfamily; Region: DEXDc; smart00487 62928007702 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 62928007703 ATP binding site [chemical binding]; other site 62928007704 putative Mg++ binding site [ion binding]; other site 62928007705 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 62928007706 nucleotide binding region [chemical binding]; other site 62928007707 ATP-binding site [chemical binding]; other site 62928007708 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 62928007709 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 62928007710 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 62928007711 Ca binding site [ion binding]; other site 62928007712 active site 62928007713 catalytic site [active] 62928007714 Endoglucanase [Carbohydrate transport and metabolism]; Region: BglC; COG2730 62928007715 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 62928007716 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 62928007717 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 62928007718 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 62928007719 Glucokinase; Region: Glucokinase; pfam02685 62928007720 glucokinase, proteobacterial type; Region: glk; TIGR00749 62928007721 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 62928007722 Protein tyrosine/serine phosphatase [Signal transduction mechanisms]; Region: COG2365 62928007723 Putative phosphatase (DUF442); Region: DUF442; cl17385 62928007724 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 62928007725 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928007726 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928007727 Walker A/P-loop; other site 62928007728 ATP binding site [chemical binding]; other site 62928007729 Q-loop/lid; other site 62928007730 ABC transporter signature motif; other site 62928007731 Walker B; other site 62928007732 D-loop; other site 62928007733 H-loop/switch region; other site 62928007734 Glycosyltransferase family 29 (sialyltransferase); Region: Glyco_transf_29; pfam00777 62928007735 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 62928007736 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 62928007737 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 62928007738 putative active site [active] 62928007739 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 62928007740 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928007741 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928007742 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 62928007743 putative ADP-binding pocket [chemical binding]; other site 62928007744 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 62928007745 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 62928007746 putative active site [active] 62928007747 putative metal binding site [ion binding]; other site 62928007748 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 62928007749 putative hydrophobic ligand binding site [chemical binding]; other site 62928007750 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 62928007751 dimerization interface [polypeptide binding]; other site 62928007752 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928007753 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928007754 metal binding site [ion binding]; metal-binding site 62928007755 active site 62928007756 I-site; other site 62928007757 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 62928007758 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928007759 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 62928007760 substrate binding site [chemical binding]; other site 62928007761 dimerization interface [polypeptide binding]; other site 62928007762 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 62928007763 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 62928007764 Walker A motif; other site 62928007765 ATP binding site [chemical binding]; other site 62928007766 Walker B motif; other site 62928007767 arginine finger; other site 62928007768 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 62928007769 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 62928007770 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 62928007771 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 62928007772 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 62928007773 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 62928007774 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928007775 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928007776 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 62928007777 Protein export membrane protein; Region: SecD_SecF; cl14618 62928007778 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 62928007779 Protein export membrane protein; Region: SecD_SecF; cl14618 62928007780 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 62928007781 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 62928007782 carboxy-terminal protease; Provisional; Region: PRK11186 62928007783 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 62928007784 protein binding site [polypeptide binding]; other site 62928007785 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 62928007786 Catalytic dyad [active] 62928007787 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 62928007788 Cytochrome C' Region: Cytochrom_C_2; pfam01322 62928007789 Dienelactone hydrolase family; Region: DLH; pfam01738 62928007790 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 62928007791 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 62928007792 Cytochrome c; Region: Cytochrom_C; cl11414 62928007793 Cytochrome c; Region: Cytochrom_C; cl11414 62928007794 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 62928007795 catalytic triad [active] 62928007796 Protein of unknown function (DUF1501); Region: DUF1501; pfam07394 62928007797 Protein of unknown function (DUF1549); Region: PSCyt2; pfam07583 62928007798 Protein of unknown function (DUF1553); Region: PSD1; pfam07587 62928007799 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 62928007800 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 62928007801 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 62928007802 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 62928007803 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 62928007804 Domain of unknown function (DUF2703); Region: DUF2703; pfam10865 62928007805 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 62928007806 Low molecular weight phosphatase family; Region: LMWPc; cd00115 62928007807 active site 62928007808 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 62928007809 putative DNA binding site [nucleotide binding]; other site 62928007810 putative Zn2+ binding site [ion binding]; other site 62928007811 Low molecular weight phosphatase family; Region: LMWPc; cl00105 62928007812 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 62928007813 active site 62928007814 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 62928007815 Sodium Bile acid symporter family; Region: SBF; cl17470 62928007816 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 62928007817 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 62928007818 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 62928007819 P loop; other site 62928007820 Nucleotide binding site [chemical binding]; other site 62928007821 DTAP/Switch II; other site 62928007822 Switch I; other site 62928007823 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 62928007824 DTAP/Switch II; other site 62928007825 Switch I; other site 62928007826 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 62928007827 Amidase; Region: Amidase; cl11426 62928007828 Helix-turn-helix domain; Region: HTH_18; pfam12833 62928007829 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928007830 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 62928007831 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 62928007832 active site 1 [active] 62928007833 dimer interface [polypeptide binding]; other site 62928007834 hexamer interface [polypeptide binding]; other site 62928007835 active site 2 [active] 62928007836 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928007837 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 62928007838 dimerization interface [polypeptide binding]; other site 62928007839 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 62928007840 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 62928007841 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 62928007842 PAS domain; Region: PAS_9; pfam13426 62928007843 putative active site [active] 62928007844 heme pocket [chemical binding]; other site 62928007845 PAS fold; Region: PAS_4; pfam08448 62928007846 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928007847 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 62928007848 dimer interface [polypeptide binding]; other site 62928007849 phosphorylation site [posttranslational modification] 62928007850 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 62928007851 ATP binding site [chemical binding]; other site 62928007852 Mg2+ binding site [ion binding]; other site 62928007853 G-X-G motif; other site 62928007854 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928007855 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 62928007856 active site 62928007857 phosphorylation site [posttranslational modification] 62928007858 intermolecular recognition site; other site 62928007859 dimerization interface [polypeptide binding]; other site 62928007860 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 62928007861 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 62928007862 substrate binding pocket [chemical binding]; other site 62928007863 membrane-bound complex binding site; other site 62928007864 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 62928007865 oligomerisation interface [polypeptide binding]; other site 62928007866 mobile loop; other site 62928007867 roof hairpin; other site 62928007868 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 62928007869 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 62928007870 ring oligomerisation interface [polypeptide binding]; other site 62928007871 ATP/Mg binding site [chemical binding]; other site 62928007872 stacking interactions; other site 62928007873 hinge regions; other site 62928007874 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928007875 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928007876 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 62928007877 dimerization interface [polypeptide binding]; other site 62928007878 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 62928007879 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928007880 NAD(P) binding site [chemical binding]; other site 62928007881 active site 62928007882 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 62928007883 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 62928007884 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928007885 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 62928007886 DNA binding residues [nucleotide binding] 62928007887 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 62928007888 FecR protein; Region: FecR; pfam04773 62928007889 Secretin and TonB N terminus short domain; Region: STN; smart00965 62928007890 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928007891 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 62928007892 N-terminal plug; other site 62928007893 ligand-binding site [chemical binding]; other site 62928007894 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 62928007895 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 62928007896 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 62928007897 active site residue [active] 62928007898 Protein of unknown function, DUF479; Region: DUF479; cl01203 62928007899 Fructosamine kinase; Region: Fructosamin_kin; pfam03881 62928007900 Phosphotransferase enzyme family; Region: APH; pfam01636 62928007901 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 62928007902 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 62928007903 Ligand binding site; other site 62928007904 Putative Catalytic site; other site 62928007905 DXD motif; other site 62928007906 Predicted membrane protein [Function unknown]; Region: COG2246 62928007907 GtrA-like protein; Region: GtrA; pfam04138 62928007908 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 62928007909 FMN-binding domain; Region: FMN_bind; pfam04205 62928007910 ApbE family; Region: ApbE; pfam02424 62928007911 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 62928007912 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 62928007913 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 62928007914 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 62928007915 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 62928007916 substrate binding pocket [chemical binding]; other site 62928007917 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 62928007918 membrane-bound complex binding site; other site 62928007919 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 62928007920 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 62928007921 Walker A/P-loop; other site 62928007922 ATP binding site [chemical binding]; other site 62928007923 Q-loop/lid; other site 62928007924 ABC transporter signature motif; other site 62928007925 Walker B; other site 62928007926 D-loop; other site 62928007927 H-loop/switch region; other site 62928007928 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 62928007929 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 62928007930 ABC-ATPase subunit interface; other site 62928007931 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 62928007932 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 62928007933 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928007934 acyl-activating enzyme (AAE) consensus motif; other site 62928007935 AMP binding site [chemical binding]; other site 62928007936 active site 62928007937 CoA binding site [chemical binding]; other site 62928007938 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928007939 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 62928007940 EAL domain; Region: EAL; pfam00563 62928007941 Serine hydrolase; Region: Ser_hydrolase; pfam06821 62928007942 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 62928007943 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 62928007944 dimer interface [polypeptide binding]; other site 62928007945 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928007946 catalytic residue [active] 62928007947 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928007948 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 62928007949 N-terminal plug; other site 62928007950 ligand-binding site [chemical binding]; other site 62928007951 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 62928007952 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 62928007953 dimerization interface [polypeptide binding]; other site 62928007954 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 62928007955 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 62928007956 dimer interface [polypeptide binding]; other site 62928007957 phosphorylation site [posttranslational modification] 62928007958 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 62928007959 ATP binding site [chemical binding]; other site 62928007960 Mg2+ binding site [ion binding]; other site 62928007961 G-X-G motif; other site 62928007962 Response regulator receiver domain; Region: Response_reg; pfam00072 62928007963 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 62928007964 active site 62928007965 phosphorylation site [posttranslational modification] 62928007966 intermolecular recognition site; other site 62928007967 dimerization interface [polypeptide binding]; other site 62928007968 Response regulator receiver domain; Region: Response_reg; pfam00072 62928007969 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 62928007970 active site 62928007971 phosphorylation site [posttranslational modification] 62928007972 intermolecular recognition site; other site 62928007973 dimerization interface [polypeptide binding]; other site 62928007974 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 62928007975 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928007976 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 62928007977 active site 62928007978 phosphorylation site [posttranslational modification] 62928007979 intermolecular recognition site; other site 62928007980 dimerization interface [polypeptide binding]; other site 62928007981 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928007982 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928007983 metal binding site [ion binding]; metal-binding site 62928007984 active site 62928007985 I-site; other site 62928007986 OsmC-like protein; Region: OsmC; cl00767 62928007987 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 62928007988 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 62928007989 dimer interface [polypeptide binding]; other site 62928007990 PYR/PP interface [polypeptide binding]; other site 62928007991 TPP binding site [chemical binding]; other site 62928007992 substrate binding site [chemical binding]; other site 62928007993 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 62928007994 TPP-binding site [chemical binding]; other site 62928007995 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 62928007996 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 62928007997 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 62928007998 putative DNA binding site [nucleotide binding]; other site 62928007999 putative Zn2+ binding site [ion binding]; other site 62928008000 AsnC family; Region: AsnC_trans_reg; pfam01037 62928008001 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 62928008002 GAF domain; Region: GAF_2; pfam13185 62928008003 PAS domain; Region: PAS_9; pfam13426 62928008004 PAS domain; Region: PAS_9; pfam13426 62928008005 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008006 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008007 metal binding site [ion binding]; metal-binding site 62928008008 active site 62928008009 I-site; other site 62928008010 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 62928008011 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 62928008012 Na binding site [ion binding]; other site 62928008013 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 62928008014 active site 62928008015 catalytic site [active] 62928008016 substrate binding site [chemical binding]; other site 62928008017 Response regulator receiver domain; Region: Response_reg; pfam00072 62928008018 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 62928008019 active site 62928008020 phosphorylation site [posttranslational modification] 62928008021 intermolecular recognition site; other site 62928008022 dimerization interface [polypeptide binding]; other site 62928008023 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 62928008024 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928008025 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 62928008026 dimer interface [polypeptide binding]; other site 62928008027 phosphorylation site [posttranslational modification] 62928008028 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 62928008029 ATP binding site [chemical binding]; other site 62928008030 Mg2+ binding site [ion binding]; other site 62928008031 G-X-G motif; other site 62928008032 acetyl-CoA synthetase; Provisional; Region: PRK00174 62928008033 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 62928008034 active site 62928008035 CoA binding site [chemical binding]; other site 62928008036 acyl-activating enzyme (AAE) consensus motif; other site 62928008037 AMP binding site [chemical binding]; other site 62928008038 acetate binding site [chemical binding]; other site 62928008039 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 62928008040 Fumarase C-terminus; Region: Fumerase_C; pfam05683 62928008041 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; cl15837 62928008042 NnrS protein; Region: NnrS; pfam05940 62928008043 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 62928008044 erythrose-4-phosphate dehydrogenase; Region: E4PD_g-proteo; TIGR01532 62928008045 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 62928008046 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008047 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 62928008048 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 62928008049 substrate binding pocket [chemical binding]; other site 62928008050 dimerization interface [polypeptide binding]; other site 62928008051 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3435 62928008052 Cupin domain; Region: Cupin_2; pfam07883 62928008053 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 62928008054 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 62928008055 salicylate hydroxylase; Provisional; Region: PRK08163 62928008056 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928008057 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 62928008058 maleylacetoacetate isomerase; Region: maiA; TIGR01262 62928008059 C-terminal domain interface [polypeptide binding]; other site 62928008060 GSH binding site (G-site) [chemical binding]; other site 62928008061 putative dimer interface [polypeptide binding]; other site 62928008062 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 62928008063 dimer interface [polypeptide binding]; other site 62928008064 N-terminal domain interface [polypeptide binding]; other site 62928008065 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 62928008066 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 62928008067 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 62928008068 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 62928008069 DctM-like transporters; Region: DctM; pfam06808 62928008070 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 62928008071 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 62928008072 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 62928008073 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 62928008074 active site 1 [active] 62928008075 dimer interface [polypeptide binding]; other site 62928008076 hexamer interface [polypeptide binding]; other site 62928008077 active site 2 [active] 62928008078 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 62928008079 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 62928008080 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 62928008081 active site 62928008082 catalytic residues [active] 62928008083 metal binding site [ion binding]; metal-binding site 62928008084 DmpG-like communication domain; Region: DmpG_comm; pfam07836 62928008085 acetaldehyde dehydrogenase; Validated; Region: PRK08300 62928008086 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 62928008087 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 62928008088 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 62928008089 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928008090 NAD(P) binding site [chemical binding]; other site 62928008091 active site 62928008092 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 62928008093 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 62928008094 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 62928008095 NAD binding site [chemical binding]; other site 62928008096 catalytic residues [active] 62928008097 Domain of unknown function (DUF336); Region: DUF336; pfam03928 62928008098 DNA-binding transcriptional regulator CsiR; Provisional; Region: PRK11534 62928008099 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928008100 DNA-binding site [nucleotide binding]; DNA binding site 62928008101 FCD domain; Region: FCD; pfam07729 62928008102 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 62928008103 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 62928008104 tetramer interface [polypeptide binding]; other site 62928008105 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 62928008106 tetramer interface [polypeptide binding]; other site 62928008107 active site 62928008108 Fe binding site [ion binding]; other site 62928008109 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 62928008110 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 62928008111 catalytic loop [active] 62928008112 iron binding site [ion binding]; other site 62928008113 Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H...; Region: phenol_2-monooxygenase_like; cd06211 62928008114 FAD binding pocket [chemical binding]; other site 62928008115 FAD binding motif [chemical binding]; other site 62928008116 phosphate binding motif [ion binding]; other site 62928008117 beta-alpha-beta structure motif; other site 62928008118 NAD binding pocket [chemical binding]; other site 62928008119 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 62928008120 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 62928008121 dimerization interface [polypeptide binding]; other site 62928008122 putative path to active site cavity [active] 62928008123 diiron center [ion binding]; other site 62928008124 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 62928008125 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 62928008126 dimerization interface [polypeptide binding]; other site 62928008127 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 62928008128 Activator of aromatic catabolism; Region: XylR_N; pfam06505 62928008129 V4R domain; Region: V4R; pfam02830 62928008130 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 62928008131 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 62928008132 Walker A motif; other site 62928008133 ATP binding site [chemical binding]; other site 62928008134 Walker B motif; other site 62928008135 arginine finger; other site 62928008136 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928008137 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 62928008138 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928008139 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 62928008140 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928008141 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928008142 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 62928008143 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 62928008144 active site 62928008145 phosphorylation site [posttranslational modification] 62928008146 intermolecular recognition site; other site 62928008147 dimerization interface [polypeptide binding]; other site 62928008148 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928008149 Zn2+ binding site [ion binding]; other site 62928008150 Mg2+ binding site [ion binding]; other site 62928008151 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 62928008152 PAS domain; Region: PAS_9; pfam13426 62928008153 putative active site [active] 62928008154 heme pocket [chemical binding]; other site 62928008155 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 62928008156 PAS fold; Region: PAS_3; pfam08447 62928008157 putative active site [active] 62928008158 heme pocket [chemical binding]; other site 62928008159 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 62928008160 PAS fold; Region: PAS_3; pfam08447 62928008161 putative active site [active] 62928008162 heme pocket [chemical binding]; other site 62928008163 PAS domain; Region: PAS_9; pfam13426 62928008164 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 62928008165 putative active site [active] 62928008166 heme pocket [chemical binding]; other site 62928008167 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928008168 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 62928008169 dimer interface [polypeptide binding]; other site 62928008170 phosphorylation site [posttranslational modification] 62928008171 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 62928008172 ATP binding site [chemical binding]; other site 62928008173 Mg2+ binding site [ion binding]; other site 62928008174 G-X-G motif; other site 62928008175 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928008176 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 62928008177 active site 62928008178 phosphorylation site [posttranslational modification] 62928008179 intermolecular recognition site; other site 62928008180 dimerization interface [polypeptide binding]; other site 62928008181 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928008182 NAD(P) binding site [chemical binding]; other site 62928008183 active site 62928008184 Yqey-like protein; Region: YqeY; cl17540 62928008185 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 62928008186 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928008187 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 62928008188 active site 62928008189 phosphorylation site [posttranslational modification] 62928008190 intermolecular recognition site; other site 62928008191 dimerization interface [polypeptide binding]; other site 62928008192 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 62928008193 putative active site [active] 62928008194 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928008195 heme pocket [chemical binding]; other site 62928008196 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 62928008197 dimer interface [polypeptide binding]; other site 62928008198 phosphorylation site [posttranslational modification] 62928008199 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 62928008200 ATP binding site [chemical binding]; other site 62928008201 Mg2+ binding site [ion binding]; other site 62928008202 G-X-G motif; other site 62928008203 PAS domain S-box; Region: sensory_box; TIGR00229 62928008204 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 62928008205 putative active site [active] 62928008206 heme pocket [chemical binding]; other site 62928008207 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 62928008208 PAS fold; Region: PAS_3; pfam08447 62928008209 putative active site [active] 62928008210 heme pocket [chemical binding]; other site 62928008211 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 62928008212 dimer interface [polypeptide binding]; other site 62928008213 phosphorylation site [posttranslational modification] 62928008214 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 62928008215 ATP binding site [chemical binding]; other site 62928008216 Mg2+ binding site [ion binding]; other site 62928008217 G-X-G motif; other site 62928008218 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928008219 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 62928008220 DNA binding residues [nucleotide binding] 62928008221 dimerization interface [polypeptide binding]; other site 62928008222 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 62928008223 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928008224 DNA-binding site [nucleotide binding]; DNA binding site 62928008225 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 62928008226 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928008227 homodimer interface [polypeptide binding]; other site 62928008228 catalytic residue [active] 62928008229 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 62928008230 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928008231 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 62928008232 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 62928008233 phosphate binding site [ion binding]; other site 62928008234 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 62928008235 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 62928008236 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 62928008237 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 62928008238 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 62928008239 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 62928008240 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 62928008241 NAD(P) binding site [chemical binding]; other site 62928008242 catalytic residues [active] 62928008243 acetolactate synthase catalytic subunit; Validated; Region: PRK08327 62928008244 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 62928008245 PYR/PP interface [polypeptide binding]; other site 62928008246 dimer interface [polypeptide binding]; other site 62928008247 TPP binding site [chemical binding]; other site 62928008248 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 62928008249 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 62928008250 TPP-binding site [chemical binding]; other site 62928008251 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 62928008252 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008253 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 62928008254 substrate binding pocket [chemical binding]; other site 62928008255 dimerization interface [polypeptide binding]; other site 62928008256 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 62928008257 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 62928008258 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 62928008259 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 62928008260 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928008261 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 62928008262 putative substrate translocation pore; other site 62928008263 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928008264 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 62928008265 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928008266 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928008267 HPP family; Region: HPP; pfam04982 62928008268 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 62928008269 PAS domain; Region: PAS_9; pfam13426 62928008270 putative active site [active] 62928008271 heme pocket [chemical binding]; other site 62928008272 PAS domain; Region: PAS_9; pfam13426 62928008273 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 62928008274 putative active site [active] 62928008275 heme pocket [chemical binding]; other site 62928008276 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 62928008277 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 62928008278 putative active site [active] 62928008279 heme pocket [chemical binding]; other site 62928008280 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 62928008281 putative active site [active] 62928008282 heme pocket [chemical binding]; other site 62928008283 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 62928008284 dimer interface [polypeptide binding]; other site 62928008285 phosphorylation site [posttranslational modification] 62928008286 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 62928008287 ATP binding site [chemical binding]; other site 62928008288 Mg2+ binding site [ion binding]; other site 62928008289 G-X-G motif; other site 62928008290 Response regulator receiver domain; Region: Response_reg; pfam00072 62928008291 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 62928008292 active site 62928008293 phosphorylation site [posttranslational modification] 62928008294 intermolecular recognition site; other site 62928008295 dimerization interface [polypeptide binding]; other site 62928008296 Response regulator receiver domain; Region: Response_reg; pfam00072 62928008297 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 62928008298 active site 62928008299 phosphorylation site [posttranslational modification] 62928008300 intermolecular recognition site; other site 62928008301 dimerization interface [polypeptide binding]; other site 62928008302 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 62928008303 putative binding surface; other site 62928008304 active site 62928008305 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 62928008306 catalytic core [active] 62928008307 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 62928008308 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 62928008309 active site 62928008310 phosphorylation site [posttranslational modification] 62928008311 intermolecular recognition site; other site 62928008312 dimerization interface [polypeptide binding]; other site 62928008313 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928008314 Zn2+ binding site [ion binding]; other site 62928008315 Mg2+ binding site [ion binding]; other site 62928008316 KTSC domain; Region: KTSC; pfam13619 62928008317 phosphoenolpyruvate synthase; Validated; Region: PRK06241 62928008318 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 62928008319 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 62928008320 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928008321 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928008322 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 62928008323 transmembrane helices; other site 62928008324 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 62928008325 TrkA-C domain; Region: TrkA_C; pfam02080 62928008326 TrkA-C domain; Region: TrkA_C; pfam02080 62928008327 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 62928008328 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 62928008329 catalytic residues [active] 62928008330 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 62928008331 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 62928008332 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 62928008333 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 62928008334 Ligand binding site [chemical binding]; other site 62928008335 Electron transfer flavoprotein domain; Region: ETF; pfam01012 62928008336 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 62928008337 putative active site [active] 62928008338 putative catalytic site [active] 62928008339 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 62928008340 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 62928008341 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 62928008342 active site 62928008343 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 62928008344 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 62928008345 active site 62928008346 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 62928008347 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 62928008348 NAD binding site [chemical binding]; other site 62928008349 homodimer interface [polypeptide binding]; other site 62928008350 homotetramer interface [polypeptide binding]; other site 62928008351 active site 62928008352 putative acyltransferase; Provisional; Region: PRK05790 62928008353 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928008354 dimer interface [polypeptide binding]; other site 62928008355 active site 62928008356 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 62928008357 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928008358 substrate binding site [chemical binding]; other site 62928008359 oxyanion hole (OAH) forming residues; other site 62928008360 trimer interface [polypeptide binding]; other site 62928008361 feruloyl-CoA synthase; Reviewed; Region: PRK08180 62928008362 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 62928008363 acyl-activating enzyme (AAE) consensus motif; other site 62928008364 putative AMP binding site [chemical binding]; other site 62928008365 putative active site [active] 62928008366 putative CoA binding site [chemical binding]; other site 62928008367 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928008368 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 62928008369 putative ligand binding site [chemical binding]; other site 62928008370 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928008371 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928008372 Walker A/P-loop; other site 62928008373 ATP binding site [chemical binding]; other site 62928008374 Q-loop/lid; other site 62928008375 ABC transporter signature motif; other site 62928008376 Walker B; other site 62928008377 D-loop; other site 62928008378 H-loop/switch region; other site 62928008379 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928008380 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928008381 TM-ABC transporter signature motif; other site 62928008382 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928008383 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928008384 Walker A/P-loop; other site 62928008385 ATP binding site [chemical binding]; other site 62928008386 Q-loop/lid; other site 62928008387 ABC transporter signature motif; other site 62928008388 Walker B; other site 62928008389 D-loop; other site 62928008390 H-loop/switch region; other site 62928008391 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928008392 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928008393 TM-ABC transporter signature motif; other site 62928008394 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928008395 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928008396 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928008397 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928008398 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 62928008399 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 62928008400 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 62928008401 B12 binding domain; Region: B12-binding; pfam02310 62928008402 B12 binding site [chemical binding]; other site 62928008403 Radical SAM superfamily; Region: Radical_SAM; pfam04055 62928008404 Ring hydroxylating alpha subunit (catalytic domain); Region: Ring_hydroxyl_A; pfam00848 62928008405 hydrophobic ligand binding site; other site 62928008406 Secretin and TonB N terminus short domain; Region: STN; smart00965 62928008407 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 62928008408 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 62928008409 N-terminal plug; other site 62928008410 ligand-binding site [chemical binding]; other site 62928008411 fec operon regulator FecR; Reviewed; Region: PRK09774 62928008412 FecR protein; Region: FecR; pfam04773 62928008413 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 62928008414 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928008415 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 62928008416 DNA binding residues [nucleotide binding] 62928008417 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 62928008418 [2Fe-2S] cluster binding site [ion binding]; other site 62928008419 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 62928008420 inter-subunit interface; other site 62928008421 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 62928008422 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 62928008423 iron-sulfur cluster [ion binding]; other site 62928008424 [2Fe-2S] cluster binding site [ion binding]; other site 62928008425 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 62928008426 putative alpha subunit interface [polypeptide binding]; other site 62928008427 putative active site [active] 62928008428 putative substrate binding site [chemical binding]; other site 62928008429 Fe binding site [ion binding]; other site 62928008430 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 62928008431 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 62928008432 catalytic loop [active] 62928008433 iron binding site [ion binding]; other site 62928008434 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 62928008435 FAD binding pocket [chemical binding]; other site 62928008436 FAD binding motif [chemical binding]; other site 62928008437 phosphate binding motif [ion binding]; other site 62928008438 beta-alpha-beta structure motif; other site 62928008439 NAD binding pocket [chemical binding]; other site 62928008440 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 62928008441 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008442 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 62928008443 substrate binding pocket [chemical binding]; other site 62928008444 dimerization interface [polypeptide binding]; other site 62928008445 DctM-like transporters; Region: DctM; pfam06808 62928008446 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 62928008447 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 62928008448 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 62928008449 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 62928008450 The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase; Region: PCA_45_Doxase_B_like_1; cd07949 62928008451 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 62928008452 putative active site [active] 62928008453 Fe(II) binding site [ion binding]; other site 62928008454 putative dimer interface [polypeptide binding]; other site 62928008455 putative tetramer interface [polypeptide binding]; other site 62928008456 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB); Region: LigA_like_1; cd07925 62928008457 putative dimer interface [polypeptide binding]; other site 62928008458 putative tetramer interface [polypeptide binding]; other site 62928008459 putative active site [active] 62928008460 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928008461 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008462 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 62928008463 substrate binding pocket [chemical binding]; other site 62928008464 dimerization interface [polypeptide binding]; other site 62928008465 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 62928008466 GIY-YIG motif/motif A; other site 62928008467 putative active site [active] 62928008468 putative metal binding site [ion binding]; other site 62928008469 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 62928008470 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928008471 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 62928008472 Cytochrome P450; Region: p450; cl12078 62928008473 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 62928008474 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 62928008475 catalytic loop [active] 62928008476 iron binding site [ion binding]; other site 62928008477 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 62928008478 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928008479 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928008480 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 62928008481 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 62928008482 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 62928008483 catalytic triad [active] 62928008484 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 62928008485 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 62928008486 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 62928008487 Membrane transport protein; Region: Mem_trans; cl09117 62928008488 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 62928008489 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 62928008490 active site 62928008491 catalytic tetrad [active] 62928008492 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 62928008493 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 62928008494 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 62928008495 Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate; Region: PCA_45_Dioxygenase_B; cd07364 62928008496 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 62928008497 active site 62928008498 Fe(II) binding site [ion binding]; other site 62928008499 dimer interface [polypeptide binding]; other site 62928008500 tetramer interface [polypeptide binding]; other site 62928008501 The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit; Region: PCA_45_Doxase_A; cd07924 62928008502 tetramer interface [polypeptide binding]; other site 62928008503 dimer interface [polypeptide binding]; other site 62928008504 active site 62928008505 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 62928008506 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 62928008507 active site 62928008508 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 62928008509 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 62928008510 NAD binding site [chemical binding]; other site 62928008511 Domain of unknown function (DUF1932); Region: DUF1932; pfam09130 62928008512 hypothetical protein; Provisional; Region: PRK09262 62928008513 Amidohydrolase; Region: Amidohydro_2; pfam04909 62928008514 benzoate transport; Region: 2A0115; TIGR00895 62928008515 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 62928008516 putative substrate translocation pore; other site 62928008517 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 62928008518 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 62928008519 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 62928008520 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 62928008521 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 62928008522 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008523 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 62928008524 putative dimerization interface [polypeptide binding]; other site 62928008525 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 62928008526 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 62928008527 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 62928008528 dimerization interface [polypeptide binding]; other site 62928008529 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928008530 dimer interface [polypeptide binding]; other site 62928008531 putative CheW interface [polypeptide binding]; other site 62928008532 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 62928008533 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 62928008534 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 62928008535 Predicted permeases [General function prediction only]; Region: COG0679 62928008536 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 62928008537 EamA-like transporter family; Region: EamA; pfam00892 62928008538 EamA-like transporter family; Region: EamA; pfam00892 62928008539 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 62928008540 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 62928008541 ATP binding site [chemical binding]; other site 62928008542 Walker B motif; other site 62928008543 Outer membrane efflux protein; Region: OEP; pfam02321 62928008544 Outer membrane efflux protein; Region: OEP; pfam02321 62928008545 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928008546 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928008547 VCBS repeat; Region: VCBS_repeat; TIGR01965 62928008548 VCBS repeat; Region: VCBS_repeat; TIGR01965 62928008549 VCBS repeat; Region: VCBS_repeat; TIGR01965 62928008550 VCBS repeat; Region: VCBS_repeat; TIGR01965 62928008551 Calx-beta domain; Region: Calx-beta; cl02522 62928008552 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 62928008553 Ca2+ binding site [ion binding]; other site 62928008554 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 62928008555 Ca2+ binding site [ion binding]; other site 62928008556 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 62928008557 Ca2+ binding site [ion binding]; other site 62928008558 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 62928008559 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928008560 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928008561 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 62928008562 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 62928008563 active site 62928008564 active site 62928008565 putative substrate binding region [chemical binding]; other site 62928008566 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928008567 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 62928008568 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 62928008569 BON domain; Region: BON; pfam04972 62928008570 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 62928008571 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 62928008572 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 62928008573 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 62928008574 RNA polymerase factor sigma-70; Validated; Region: PRK09047 62928008575 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928008576 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 62928008577 DNA binding residues [nucleotide binding] 62928008578 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 62928008579 TIR domain; Region: TIR_2; pfam13676 62928008580 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928008581 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008582 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 62928008583 putative effector binding pocket; other site 62928008584 putative dimerization interface [polypeptide binding]; other site 62928008585 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928008586 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928008587 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928008588 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 62928008589 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 62928008590 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 62928008591 protoporphyrinogen oxidase; Reviewed; Region: PRK11883 62928008592 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928008593 Cupin domain; Region: Cupin_2; cl17218 62928008594 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 62928008595 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928008596 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928008597 PAS fold; Region: PAS_3; pfam08447 62928008598 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 62928008599 dimer interface [polypeptide binding]; other site 62928008600 phosphorylation site [posttranslational modification] 62928008601 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 62928008602 ATP binding site [chemical binding]; other site 62928008603 Mg2+ binding site [ion binding]; other site 62928008604 G-X-G motif; other site 62928008605 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 62928008606 active site 62928008607 phosphorylation site [posttranslational modification] 62928008608 intermolecular recognition site; other site 62928008609 dimerization interface [polypeptide binding]; other site 62928008610 Response regulator receiver domain; Region: Response_reg; pfam00072 62928008611 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 62928008612 active site 62928008613 phosphorylation site [posttranslational modification] 62928008614 intermolecular recognition site; other site 62928008615 dimerization interface [polypeptide binding]; other site 62928008616 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 62928008617 dihydrodipicolinate reductase; Provisional; Region: PRK00048 62928008618 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 62928008619 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 62928008620 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 62928008621 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 62928008622 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 62928008623 ferric uptake regulator; Provisional; Region: fur; PRK09462 62928008624 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 62928008625 metal binding site 2 [ion binding]; metal-binding site 62928008626 putative DNA binding helix; other site 62928008627 metal binding site 1 [ion binding]; metal-binding site 62928008628 dimer interface [polypeptide binding]; other site 62928008629 structural Zn2+ binding site [ion binding]; other site 62928008630 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 62928008631 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 62928008632 Walker A/P-loop; other site 62928008633 ATP binding site [chemical binding]; other site 62928008634 Q-loop/lid; other site 62928008635 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 62928008636 ABC transporter signature motif; other site 62928008637 Walker B; other site 62928008638 D-loop; other site 62928008639 H-loop/switch region; other site 62928008640 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 62928008641 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 62928008642 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 62928008643 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 62928008644 ferrochelatase; Reviewed; Region: hemH; PRK00035 62928008645 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 62928008646 C-terminal domain interface [polypeptide binding]; other site 62928008647 active site 62928008648 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 62928008649 active site 62928008650 N-terminal domain interface [polypeptide binding]; other site 62928008651 Membrane protein of unknown function; Region: DUF360; pfam04020 62928008652 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 62928008653 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928008654 active site 62928008655 ATP binding site [chemical binding]; other site 62928008656 substrate binding site [chemical binding]; other site 62928008657 activation loop (A-loop); other site 62928008658 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 62928008659 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 62928008660 ligand binding site [chemical binding]; other site 62928008661 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 62928008662 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 62928008663 active site 62928008664 putative substrate binding pocket [chemical binding]; other site 62928008665 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928008666 ligand binding site [chemical binding]; other site 62928008667 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 62928008668 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 62928008669 S-adenosylmethionine binding site [chemical binding]; other site 62928008670 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 62928008671 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928008672 TIR domain; Region: TIR_2; pfam13676 62928008673 TPR repeat; Region: TPR_11; pfam13414 62928008674 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 62928008675 TPR motif; other site 62928008676 binding surface 62928008677 Cupin domain; Region: Cupin_2; cl17218 62928008678 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928008679 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928008680 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 62928008681 putative effector binding pocket; other site 62928008682 dimerization interface [polypeptide binding]; other site 62928008683 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 62928008684 iron-sulfur cluster [ion binding]; other site 62928008685 [2Fe-2S] cluster binding site [ion binding]; other site 62928008686 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 62928008687 rRNA binding site [nucleotide binding]; other site 62928008688 predicted 30S ribosome binding site; other site 62928008689 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 62928008690 DNA-binding site [nucleotide binding]; DNA binding site 62928008691 RNA-binding motif; other site 62928008692 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 62928008693 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 62928008694 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 62928008695 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 62928008696 aldolase II superfamily protein; Provisional; Region: PRK07044 62928008697 intersubunit interface [polypeptide binding]; other site 62928008698 active site 62928008699 Zn2+ binding site [ion binding]; other site 62928008700 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 62928008701 putative active site [active] 62928008702 putative catalytic site [active] 62928008703 putative Mg binding site IVb [ion binding]; other site 62928008704 putative phosphate binding site [ion binding]; other site 62928008705 putative DNA binding site [nucleotide binding]; other site 62928008706 putative Mg binding site IVa [ion binding]; other site 62928008707 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 62928008708 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 62928008709 N-terminal plug; other site 62928008710 ligand-binding site [chemical binding]; other site 62928008711 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 62928008712 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 62928008713 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928008714 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928008715 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008716 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008717 metal binding site [ion binding]; metal-binding site 62928008718 active site 62928008719 I-site; other site 62928008720 Uncharacterized conserved protein [Function unknown]; Region: COG3791 62928008721 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 62928008722 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 62928008723 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 62928008724 motif II; other site 62928008725 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg6; cd04781 62928008726 DNA binding residues [nucleotide binding] 62928008727 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928008728 putative dimer interface [polypeptide binding]; other site 62928008729 putative metal binding residues [ion binding]; other site 62928008730 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928008731 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 62928008732 S-adenosylmethionine binding site [chemical binding]; other site 62928008733 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 62928008734 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008735 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008736 metal binding site [ion binding]; metal-binding site 62928008737 active site 62928008738 I-site; other site 62928008739 SMI1 / KNR4 family; Region: SMI1_KNR4; smart00860 62928008740 Transposase domain (DUF772); Region: DUF772; pfam05598 62928008741 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 62928008742 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 62928008743 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 62928008744 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 62928008745 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 62928008746 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 62928008747 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 62928008748 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 62928008749 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 62928008750 S-adenosylmethionine binding site [chemical binding]; other site 62928008751 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 62928008752 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 62928008753 motif II; other site 62928008754 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 62928008755 putative ADP-ribose binding site [chemical binding]; other site 62928008756 putative active site [active] 62928008757 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 62928008758 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 62928008759 Walker A motif; other site 62928008760 ATP binding site [chemical binding]; other site 62928008761 Walker B motif; other site 62928008762 arginine finger; other site 62928008763 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 62928008764 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 62928008765 Walker A motif; other site 62928008766 ATP binding site [chemical binding]; other site 62928008767 Walker B motif; other site 62928008768 arginine finger; other site 62928008769 WYL domain; Region: WYL; pfam13280 62928008770 This entry represents the putative helicase A859L; Region: T5orf172; smart00974 62928008771 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 62928008772 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 62928008773 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 62928008774 enterobactin exporter EntS; Provisional; Region: PRK10489 62928008775 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 62928008776 putative substrate translocation pore; other site 62928008777 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008778 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008779 metal binding site [ion binding]; metal-binding site 62928008780 active site 62928008781 I-site; other site 62928008782 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 62928008783 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 62928008784 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 62928008785 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_8; cd07246 62928008786 putative dimer interface [polypeptide binding]; other site 62928008787 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928008788 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 62928008789 hypothetical protein; Provisional; Region: PRK02237 62928008790 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 62928008791 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 62928008792 FAD binding pocket [chemical binding]; other site 62928008793 FAD binding motif [chemical binding]; other site 62928008794 phosphate binding motif [ion binding]; other site 62928008795 beta-alpha-beta structure motif; other site 62928008796 NAD binding pocket [chemical binding]; other site 62928008797 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 62928008798 catalytic residues [active] 62928008799 Electron transfer DM13; Region: DM13; pfam10517 62928008800 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 62928008801 substrate binding site [chemical binding]; other site 62928008802 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 62928008803 HSP70 interaction site [polypeptide binding]; other site 62928008804 Uncharacterized conserved protein [Function unknown]; Region: COG1432 62928008805 LabA_like proteins; Region: LabA_like; cd06167 62928008806 putative metal binding site [ion binding]; other site 62928008807 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 62928008808 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 62928008809 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 62928008810 dimer interface [polypeptide binding]; other site 62928008811 decamer (pentamer of dimers) interface [polypeptide binding]; other site 62928008812 catalytic triad [active] 62928008813 YceI-like domain; Region: YceI; pfam04264 62928008814 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 62928008815 dimerization interface [polypeptide binding]; other site 62928008816 putative DNA binding site [nucleotide binding]; other site 62928008817 putative Zn2+ binding site [ion binding]; other site 62928008818 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 62928008819 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 62928008820 FMN binding site [chemical binding]; other site 62928008821 active site 62928008822 substrate binding site [chemical binding]; other site 62928008823 catalytic residue [active] 62928008824 Cytochrome c [Energy production and conversion]; Region: COG3258 62928008825 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928008826 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 62928008827 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 62928008828 active site 62928008829 phosphorylation site [posttranslational modification] 62928008830 intermolecular recognition site; other site 62928008831 dimerization interface [polypeptide binding]; other site 62928008832 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 62928008833 dimerization interface [polypeptide binding]; other site 62928008834 DNA binding residues [nucleotide binding] 62928008835 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 62928008836 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 62928008837 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 62928008838 dimer interface [polypeptide binding]; other site 62928008839 phosphorylation site [posttranslational modification] 62928008840 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 62928008841 ATP binding site [chemical binding]; other site 62928008842 Mg2+ binding site [ion binding]; other site 62928008843 G-X-G motif; other site 62928008844 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 62928008845 dimer interface [polypeptide binding]; other site 62928008846 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 62928008847 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 62928008848 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 62928008849 inhibitor-cofactor binding pocket; inhibition site 62928008850 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928008851 catalytic residue [active] 62928008852 Methyltransferase domain; Region: Methyltransf_23; pfam13489 62928008853 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 62928008854 S-adenosylmethionine binding site [chemical binding]; other site 62928008855 GtrA-like protein; Region: GtrA; pfam04138 62928008856 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 62928008857 active site 62928008858 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 62928008859 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 62928008860 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 62928008861 putative trimer interface [polypeptide binding]; other site 62928008862 putative CoA binding site [chemical binding]; other site 62928008863 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 62928008864 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 62928008865 Ligand binding site; other site 62928008866 Putative Catalytic site; other site 62928008867 DXD motif; other site 62928008868 WbqC-like protein family; Region: WbqC; pfam08889 62928008869 Restriction endonuclease [Defense mechanisms]; Region: COG3587 62928008870 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 62928008871 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008872 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008873 metal binding site [ion binding]; metal-binding site 62928008874 active site 62928008875 I-site; other site 62928008876 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 62928008877 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 62928008878 CreA protein; Region: CreA; pfam05981 62928008879 ProQ/FINO family; Region: ProQ; smart00945 62928008880 tellurium resistance terB-like protein; Region: terB_like; cd07177 62928008881 metal binding site [ion binding]; metal-binding site 62928008882 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 62928008883 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008884 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008885 metal binding site [ion binding]; metal-binding site 62928008886 active site 62928008887 I-site; other site 62928008888 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008889 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008890 metal binding site [ion binding]; metal-binding site 62928008891 active site 62928008892 I-site; other site 62928008893 flagellin; Provisional; Region: PRK12806 62928008894 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 62928008895 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 62928008896 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 62928008897 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 62928008898 inhibitor-cofactor binding pocket; inhibition site 62928008899 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928008900 catalytic residue [active] 62928008901 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 62928008902 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 62928008903 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 62928008904 active site 62928008905 cytidylyltransferase; Region: cytidylyltransferase; cd02170 62928008906 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 62928008907 active site 62928008908 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 62928008909 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 62928008910 tetramer interface [polypeptide binding]; other site 62928008911 active site 62928008912 Mg2+/Mn2+ binding site [ion binding]; other site 62928008913 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 62928008914 phosphonopyruvate decarboxylase; Region: Ppyr-DeCO2ase; TIGR03297 62928008915 PYR/PP interface [polypeptide binding]; other site 62928008916 dimer interface [polypeptide binding]; other site 62928008917 TPP binding site [chemical binding]; other site 62928008918 Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as...; Region: TPP_PpyrDC; cd03371 62928008919 TPP-binding site; other site 62928008920 Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP); Region: HEPD; cd08182 62928008921 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 62928008922 putative active site [active] 62928008923 metal binding site [ion binding]; metal-binding site 62928008924 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 62928008925 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 62928008926 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 62928008927 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 62928008928 active site 62928008929 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 62928008930 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 62928008931 binding surface 62928008932 Tetratricopeptide repeat; Region: TPR_16; pfam13432 62928008933 TPR motif; other site 62928008934 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 62928008935 TPR motif; other site 62928008936 binding surface 62928008937 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 62928008938 flagellin; Provisional; Region: PRK12806 62928008939 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 62928008940 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 62928008941 FlaG protein; Region: FlaG; pfam03646 62928008942 flagellar capping protein; Reviewed; Region: fliD; PRK08032 62928008943 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 62928008944 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 62928008945 flagellar protein FliS; Validated; Region: fliS; PRK05685 62928008946 Flagellar protein FliT; Region: FliT; pfam05400 62928008947 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 62928008948 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 62928008949 Flagellar regulator YcgR; Region: YcgR; pfam07317 62928008950 PilZ domain; Region: PilZ; pfam07238 62928008951 MASE1; Region: MASE1; pfam05231 62928008952 PAS domain S-box; Region: sensory_box; TIGR00229 62928008953 PAS domain S-box; Region: sensory_box; TIGR00229 62928008954 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 62928008955 putative active site [active] 62928008956 heme pocket [chemical binding]; other site 62928008957 PAS domain S-box; Region: sensory_box; TIGR00229 62928008958 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 62928008959 putative active site [active] 62928008960 heme pocket [chemical binding]; other site 62928008961 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928008962 PAS fold; Region: PAS_4; pfam08448 62928008963 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 62928008964 putative active site [active] 62928008965 heme pocket [chemical binding]; other site 62928008966 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 62928008967 PAS domain; Region: PAS_9; pfam13426 62928008968 putative active site [active] 62928008969 heme pocket [chemical binding]; other site 62928008970 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928008971 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928008972 metal binding site [ion binding]; metal-binding site 62928008973 active site 62928008974 I-site; other site 62928008975 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 62928008976 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928008977 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 62928008978 active site 62928008979 phosphorylation site [posttranslational modification] 62928008980 intermolecular recognition site; other site 62928008981 dimerization interface [polypeptide binding]; other site 62928008982 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 62928008983 Walker A motif; other site 62928008984 ATP binding site [chemical binding]; other site 62928008985 Walker B motif; other site 62928008986 arginine finger; other site 62928008987 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928008988 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928008989 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 62928008990 dimer interface [polypeptide binding]; other site 62928008991 phosphorylation site [posttranslational modification] 62928008992 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 62928008993 ATP binding site [chemical binding]; other site 62928008994 Mg2+ binding site [ion binding]; other site 62928008995 G-X-G motif; other site 62928008996 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 62928008997 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 62928008998 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 62928008999 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 62928009000 MgtE intracellular N domain; Region: MgtE_N; cl15244 62928009001 FliG C-terminal domain; Region: FliG_C; pfam01706 62928009002 flagellar assembly protein H; Validated; Region: fliH; PRK05687 62928009003 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 62928009004 Flagellar assembly protein FliH; Region: FliH; pfam02108 62928009005 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 62928009006 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 62928009007 Walker A motif/ATP binding site; other site 62928009008 Walker B motif; other site 62928009009 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 62928009010 Flagellar FliJ protein; Region: FliJ; pfam02050 62928009011 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 62928009012 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 62928009013 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 62928009014 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 62928009015 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 62928009016 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 62928009017 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 62928009018 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 62928009019 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 62928009020 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 62928009021 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 62928009022 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 62928009023 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 62928009024 flagellar rod assembly protein/muramidase FlgJ; Provisional; Region: flgJ; PRK12713 62928009025 Rod binding protein; Region: Rod-binding; cl01626 62928009026 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 62928009027 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 62928009028 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 62928009029 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 62928009030 Flagellar L-ring protein; Region: FlgH; pfam02107 62928009031 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12694 62928009032 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 62928009033 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 62928009034 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 62928009035 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 62928009036 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 62928009037 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 62928009038 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 62928009039 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 62928009040 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 62928009041 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 62928009042 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 62928009043 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 62928009044 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 62928009045 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 62928009046 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 62928009047 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 62928009048 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 62928009049 FlgN protein; Region: FlgN; pfam05130 62928009050 LTXXQ motif family protein; Region: LTXXQ; pfam07813 62928009051 osmolarity response regulator; Provisional; Region: ompR; PRK09468 62928009052 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 62928009053 active site 62928009054 phosphorylation site [posttranslational modification] 62928009055 intermolecular recognition site; other site 62928009056 dimerization interface [polypeptide binding]; other site 62928009057 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 62928009058 DNA binding site [nucleotide binding] 62928009059 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 62928009060 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 62928009061 dimer interface [polypeptide binding]; other site 62928009062 phosphorylation site [posttranslational modification] 62928009063 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 62928009064 ATP binding site [chemical binding]; other site 62928009065 Mg2+ binding site [ion binding]; other site 62928009066 G-X-G motif; other site 62928009067 Phasin protein; Region: Phasin_2; cl11491 62928009068 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 62928009069 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 62928009070 putative active site [active] 62928009071 heme pocket [chemical binding]; other site 62928009072 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 62928009073 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 62928009074 putative active site [active] 62928009075 heme pocket [chemical binding]; other site 62928009076 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 62928009077 Histidine kinase; Region: HisKA_3; pfam07730 62928009078 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 62928009079 ATP binding site [chemical binding]; other site 62928009080 Mg2+ binding site [ion binding]; other site 62928009081 G-X-G motif; other site 62928009082 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928009083 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 62928009084 active site 62928009085 phosphorylation site [posttranslational modification] 62928009086 intermolecular recognition site; other site 62928009087 dimerization interface [polypeptide binding]; other site 62928009088 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 62928009089 DNA binding residues [nucleotide binding] 62928009090 dimerization interface [polypeptide binding]; other site 62928009091 glycerol-3-phosphate dehydrogenase; Provisional; Region: PRK13369 62928009092 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 62928009093 glycerol kinase; Provisional; Region: glpK; PRK00047 62928009094 N- and C-terminal domain interface [polypeptide binding]; other site 62928009095 active site 62928009096 MgATP binding site [chemical binding]; other site 62928009097 catalytic site [active] 62928009098 metal binding site [ion binding]; metal-binding site 62928009099 glycerol binding site [chemical binding]; other site 62928009100 homotetramer interface [polypeptide binding]; other site 62928009101 homodimer interface [polypeptide binding]; other site 62928009102 FBP binding site [chemical binding]; other site 62928009103 protein IIAGlc interface [polypeptide binding]; other site 62928009104 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 62928009105 EamA-like transporter family; Region: EamA; pfam00892 62928009106 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 62928009107 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 62928009108 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 62928009109 active site residue [active] 62928009110 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 62928009111 active site residue [active] 62928009112 glutamate racemase; Provisional; Region: PRK00865 62928009113 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 62928009114 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 62928009115 active site 62928009116 HIGH motif; other site 62928009117 dimer interface [polypeptide binding]; other site 62928009118 KMSKS motif; other site 62928009119 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 62928009120 RNA binding surface [nucleotide binding]; other site 62928009121 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 62928009122 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 62928009123 Peptidase family M23; Region: Peptidase_M23; pfam01551 62928009124 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 62928009125 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 62928009126 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 62928009127 23S rRNA interface [nucleotide binding]; other site 62928009128 L3 interface [polypeptide binding]; other site 62928009129 OsmC-like protein; Region: OsmC; cl00767 62928009130 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 62928009131 diiron binding motif [ion binding]; other site 62928009132 CNP1-like family; Region: CNP1; pfam08750 62928009133 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 62928009134 putative active site [active] 62928009135 Ap4A binding site [chemical binding]; other site 62928009136 nudix motif; other site 62928009137 putative metal binding site [ion binding]; other site 62928009138 prolyl-tRNA synthetase; Provisional; Region: PRK09194 62928009139 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 62928009140 dimer interface [polypeptide binding]; other site 62928009141 motif 1; other site 62928009142 active site 62928009143 motif 2; other site 62928009144 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 62928009145 putative deacylase active site [active] 62928009146 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 62928009147 active site 62928009148 motif 3; other site 62928009149 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 62928009150 anticodon binding site; other site 62928009151 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 62928009152 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 62928009153 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928009154 catalytic residue [active] 62928009155 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 62928009156 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928009157 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 62928009158 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 62928009159 dimer interface [polypeptide binding]; other site 62928009160 phosphorylation site [posttranslational modification] 62928009161 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 62928009162 ATP binding site [chemical binding]; other site 62928009163 Mg2+ binding site [ion binding]; other site 62928009164 G-X-G motif; other site 62928009165 response regulator GlrR; Provisional; Region: PRK15115 62928009166 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 62928009167 active site 62928009168 phosphorylation site [posttranslational modification] 62928009169 intermolecular recognition site; other site 62928009170 dimerization interface [polypeptide binding]; other site 62928009171 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 62928009172 Walker A motif; other site 62928009173 ATP binding site [chemical binding]; other site 62928009174 Walker B motif; other site 62928009175 arginine finger; other site 62928009176 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 62928009177 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 62928009178 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 62928009179 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 62928009180 nudix motif; other site 62928009181 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 62928009182 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 62928009183 homodimer interface [polypeptide binding]; other site 62928009184 substrate-cofactor binding pocket; other site 62928009185 catalytic residue [active] 62928009186 Zinc-finger domain; Region: zf-CHCC; cl01821 62928009187 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 62928009188 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 62928009189 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 62928009190 active site 62928009191 substrate binding site [chemical binding]; other site 62928009192 metal binding site [ion binding]; metal-binding site 62928009193 HDOD domain; Region: HDOD; pfam08668 62928009194 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 62928009195 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 62928009196 motif 1; other site 62928009197 active site 62928009198 motif 2; other site 62928009199 motif 3; other site 62928009200 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 62928009201 DHHA1 domain; Region: DHHA1; pfam02272 62928009202 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 62928009203 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 62928009204 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 62928009205 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 62928009206 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 62928009207 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 62928009208 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 62928009209 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928009210 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 62928009211 Walker A/P-loop; other site 62928009212 ATP binding site [chemical binding]; other site 62928009213 Q-loop/lid; other site 62928009214 ABC transporter signature motif; other site 62928009215 Walker B; other site 62928009216 D-loop; other site 62928009217 H-loop/switch region; other site 62928009218 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 62928009219 active site 62928009220 DNA polymerase IV; Validated; Region: PRK02406 62928009221 DNA binding site [nucleotide binding] 62928009222 RmuC family; Region: RmuC; pfam02646 62928009223 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 62928009224 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 62928009225 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 62928009226 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 62928009227 TMAO/DMSO reductase; Reviewed; Region: PRK05363 62928009228 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 62928009229 Moco binding site; other site 62928009230 metal coordination site [ion binding]; other site 62928009231 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 62928009232 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 62928009233 MPT binding site; other site 62928009234 trimer interface [polypeptide binding]; other site 62928009235 hypothetical protein; Provisional; Region: PRK05255 62928009236 peptidase PmbA; Provisional; Region: PRK11040 62928009237 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 62928009238 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 62928009239 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 62928009240 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 62928009241 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 62928009242 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 62928009243 catalytic core [active] 62928009244 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 62928009245 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 62928009246 dimer interface [polypeptide binding]; other site 62928009247 phosphorylation site [posttranslational modification] 62928009248 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 62928009249 ATP binding site [chemical binding]; other site 62928009250 Mg2+ binding site [ion binding]; other site 62928009251 G-X-G motif; other site 62928009252 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 62928009253 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 62928009254 active site 62928009255 phosphorylation site [posttranslational modification] 62928009256 intermolecular recognition site; other site 62928009257 dimerization interface [polypeptide binding]; other site 62928009258 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 62928009259 DNA binding site [nucleotide binding] 62928009260 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 62928009261 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 62928009262 dimer interface [polypeptide binding]; other site 62928009263 active site 62928009264 glycine-pyridoxal phosphate binding site [chemical binding]; other site 62928009265 folate binding site [chemical binding]; other site 62928009266 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 62928009267 ATP cone domain; Region: ATP-cone; pfam03477 62928009268 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 62928009269 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 62928009270 catalytic motif [active] 62928009271 Zn binding site [ion binding]; other site 62928009272 RibD C-terminal domain; Region: RibD_C; cl17279 62928009273 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 62928009274 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 62928009275 ATP binding site [chemical binding]; other site 62928009276 substrate interface [chemical binding]; other site 62928009277 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 62928009278 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 62928009279 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 62928009280 protein binding site [polypeptide binding]; other site 62928009281 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 62928009282 Catalytic dyad [active] 62928009283 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 62928009284 Cortexillin I, coiled coil; Region: Cortex-I_coil; pfam09304 62928009285 Peptidase family M23; Region: Peptidase_M23; pfam01551 62928009286 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 62928009287 catalytic core [active] 62928009288 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 62928009289 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 62928009290 dimerization interface [polypeptide binding]; other site 62928009291 putative DNA binding site [nucleotide binding]; other site 62928009292 putative Zn2+ binding site [ion binding]; other site 62928009293 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 62928009294 active site residue [active] 62928009295 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 62928009296 GSH binding site [chemical binding]; other site 62928009297 catalytic residues [active] 62928009298 preprotein translocase subunit SecB; Validated; Region: PRK05751 62928009299 SecA binding site; other site 62928009300 Preprotein binding site; other site 62928009301 Bacterial SH3 domain; Region: SH3_4; pfam06347 62928009302 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 62928009303 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 62928009304 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 62928009305 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 62928009306 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 62928009307 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 62928009308 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928009309 active site 62928009310 biotin synthase; Region: bioB; TIGR00433 62928009311 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 62928009312 FeS/SAM binding site; other site 62928009313 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 62928009314 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 62928009315 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 62928009316 S-adenosylmethionine binding site [chemical binding]; other site 62928009317 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 62928009318 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 62928009319 motif II; other site 62928009320 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928009321 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 62928009322 Coenzyme A binding pocket [chemical binding]; other site 62928009323 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 62928009324 dimer interface [polypeptide binding]; other site 62928009325 active site 62928009326 aspartate-rich active site metal binding site; other site 62928009327 allosteric magnesium binding site [ion binding]; other site 62928009328 Schiff base residues; other site 62928009329 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 62928009330 G1 box; other site 62928009331 GTP/Mg2+ binding site [chemical binding]; other site 62928009332 Switch I region; other site 62928009333 G2 box; other site 62928009334 G3 box; other site 62928009335 Switch II region; other site 62928009336 G4 box; other site 62928009337 G5 box; other site 62928009338 Cytochrome c553 [Energy production and conversion]; Region: COG2863 62928009339 Cytochrome c; Region: Cytochrom_C; cl11414 62928009340 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 62928009341 dinuclear metal binding motif [ion binding]; other site 62928009342 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 62928009343 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 62928009344 dimer interface [polypeptide binding]; other site 62928009345 putative functional site; other site 62928009346 putative MPT binding site; other site 62928009347 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 62928009348 tetramer (dimer of dimers) interface [polypeptide binding]; other site 62928009349 active site 62928009350 dimer interface [polypeptide binding]; other site 62928009351 transcriptional regulator PhoU; Provisional; Region: PRK11115 62928009352 PhoU domain; Region: PhoU; pfam01895 62928009353 PhoU domain; Region: PhoU; pfam01895 62928009354 oxidative damage protection protein; Provisional; Region: PRK05408 62928009355 PAS domain; Region: PAS_9; pfam13426 62928009356 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 62928009357 putative active site [active] 62928009358 heme pocket [chemical binding]; other site 62928009359 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 62928009360 PAS domain; Region: PAS_9; pfam13426 62928009361 putative active site [active] 62928009362 heme pocket [chemical binding]; other site 62928009363 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928009364 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928009365 metal binding site [ion binding]; metal-binding site 62928009366 active site 62928009367 I-site; other site 62928009368 N-acetylglutamate synthase; Validated; Region: PRK05279 62928009369 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 62928009370 putative feedback inhibition sensing region; other site 62928009371 putative nucleotide binding site [chemical binding]; other site 62928009372 putative substrate binding site [chemical binding]; other site 62928009373 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928009374 Coenzyme A binding pocket [chemical binding]; other site 62928009375 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 62928009376 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 62928009377 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 62928009378 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 62928009379 RNA methyltransferase, RsmE family; Region: TIGR00046 62928009380 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 62928009381 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 62928009382 active site 62928009383 phosphoribulokinase; Provisional; Region: PRK15453 62928009384 transketolase; Reviewed; Region: PRK12753 62928009385 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 62928009386 TPP-binding site [chemical binding]; other site 62928009387 dimer interface [polypeptide binding]; other site 62928009388 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 62928009389 PYR/PP interface [polypeptide binding]; other site 62928009390 dimer interface [polypeptide binding]; other site 62928009391 TPP binding site [chemical binding]; other site 62928009392 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 62928009393 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 62928009394 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 62928009395 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 62928009396 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 62928009397 Phosphoglycerate kinase; Region: PGK; pfam00162 62928009398 substrate binding site [chemical binding]; other site 62928009399 hinge regions; other site 62928009400 ADP binding site [chemical binding]; other site 62928009401 catalytic site [active] 62928009402 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 62928009403 pyruvate kinase; Provisional; Region: PRK05826 62928009404 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 62928009405 domain interfaces; other site 62928009406 active site 62928009407 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 62928009408 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 62928009409 intersubunit interface [polypeptide binding]; other site 62928009410 active site 62928009411 zinc binding site [ion binding]; other site 62928009412 Na+ binding site [ion binding]; other site 62928009413 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 62928009414 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 62928009415 Trp docking motif [polypeptide binding]; other site 62928009416 cytochrome domain interface [polypeptide binding]; other site 62928009417 active site 62928009418 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928009419 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 62928009420 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 62928009421 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 62928009422 Walker A motif; other site 62928009423 ATP binding site [chemical binding]; other site 62928009424 Walker B motif; other site 62928009425 arginine finger; other site 62928009426 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928009427 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 62928009428 putative active site pocket [active] 62928009429 dimerization interface [polypeptide binding]; other site 62928009430 putative catalytic residue [active] 62928009431 HAMP domain; Region: HAMP; pfam00672 62928009432 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928009433 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928009434 metal binding site [ion binding]; metal-binding site 62928009435 active site 62928009436 I-site; other site 62928009437 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 62928009438 putative substrate translocation pore; other site 62928009439 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins; Region: GDPD_EcGlpQ_like_1; cd08560 62928009440 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 62928009441 putative active site [active] 62928009442 catalytic site [active] 62928009443 putative metal binding site [ion binding]; other site 62928009444 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 62928009445 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 62928009446 NAD binding site [chemical binding]; other site 62928009447 catalytic residues [active] 62928009448 Uncharacterized low-complexity protein [Function unknown]; Region: COG3767 62928009449 hypothetical protein; Provisional; Region: PRK05409 62928009450 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 62928009451 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 62928009452 DoxX; Region: DoxX; cl17842 62928009453 RNA polymerase sigma factor; Provisional; Region: PRK12532 62928009454 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928009455 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 62928009456 DNA binding residues [nucleotide binding] 62928009457 Putative zinc-finger; Region: zf-HC2; pfam13490 62928009458 putative hydrolase; Provisional; Region: PRK11460 62928009459 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 62928009460 von Willebrand factor type A domain; Region: VWA_2; pfam13519 62928009461 metal ion-dependent adhesion site (MIDAS); other site 62928009462 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 62928009463 Protein of unknown function DUF58; Region: DUF58; pfam01882 62928009464 MoxR-like ATPases [General function prediction only]; Region: COG0714 62928009465 ATPase family associated with various cellular activities (AAA); Region: AAA_3; pfam07726 62928009466 Walker A motif; other site 62928009467 ATP binding site [chemical binding]; other site 62928009468 Walker B motif; other site 62928009469 arginine finger; other site 62928009470 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928009471 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 62928009472 metal ion-dependent adhesion site (MIDAS); other site 62928009473 putative monooxygenase; Provisional; Region: PRK11118 62928009474 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 62928009475 PAS domain; Region: PAS_9; pfam13426 62928009476 putative active site [active] 62928009477 heme pocket [chemical binding]; other site 62928009478 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928009479 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928009480 metal binding site [ion binding]; metal-binding site 62928009481 active site 62928009482 I-site; other site 62928009483 LysR family transcriptional regulator; Provisional; Region: PRK14997 62928009484 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928009485 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 62928009486 putative effector binding pocket; other site 62928009487 dimerization interface [polypeptide binding]; other site 62928009488 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 62928009489 putative active site [active] 62928009490 metal binding site [ion binding]; metal-binding site 62928009491 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 62928009492 YceI-like domain; Region: YceI; smart00867 62928009493 Uncharacterized conserved protein [Function unknown]; Region: COG2353 62928009494 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 62928009495 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 62928009496 ATP binding site [chemical binding]; other site 62928009497 active site 62928009498 substrate binding site [chemical binding]; other site 62928009499 RES domain; Region: RES; smart00953 62928009500 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 62928009501 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 62928009502 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 62928009503 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 62928009504 active site 62928009505 Zn binding site [ion binding]; other site 62928009506 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 62928009507 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 62928009508 catalytic residues [active] 62928009509 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 62928009510 PAS domain S-box; Region: sensory_box; TIGR00229 62928009511 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 62928009512 PAS domain; Region: PAS_9; pfam13426 62928009513 putative active site [active] 62928009514 heme pocket [chemical binding]; other site 62928009515 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928009516 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928009517 metal binding site [ion binding]; metal-binding site 62928009518 active site 62928009519 I-site; other site 62928009520 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 62928009521 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 62928009522 putative catalytic site [active] 62928009523 putative phosphate binding site [ion binding]; other site 62928009524 active site 62928009525 metal binding site A [ion binding]; metal-binding site 62928009526 DNA binding site [nucleotide binding] 62928009527 putative AP binding site [nucleotide binding]; other site 62928009528 putative metal binding site B [ion binding]; other site 62928009529 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928009530 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 62928009531 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 62928009532 ligand binding site [chemical binding]; other site 62928009533 flexible hinge region; other site 62928009534 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 62928009535 putative switch regulator; other site 62928009536 non-specific DNA interactions [nucleotide binding]; other site 62928009537 DNA binding site [nucleotide binding] 62928009538 sequence specific DNA binding site [nucleotide binding]; other site 62928009539 putative cAMP binding site [chemical binding]; other site 62928009540 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 62928009541 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 62928009542 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 62928009543 S-adenosylmethionine binding site [chemical binding]; other site 62928009544 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 62928009545 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 62928009546 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 62928009547 SurA N-terminal domain; Region: SurA_N; pfam09312 62928009548 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 62928009549 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 62928009550 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 62928009551 OstA-like protein; Region: OstA; cl00844 62928009552 Organic solvent tolerance protein; Region: OstA_C; pfam04453 62928009553 Phosphotransferase enzyme family; Region: APH; pfam01636 62928009554 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 62928009555 active site 62928009556 ATP binding site [chemical binding]; other site 62928009557 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 62928009558 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 62928009559 Substrate binding site; other site 62928009560 metal-binding site 62928009561 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 62928009562 proline aminopeptidase P II; Provisional; Region: PRK10879 62928009563 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 62928009564 active site 62928009565 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 62928009566 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928009567 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 62928009568 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 62928009569 FMN binding site [chemical binding]; other site 62928009570 active site 62928009571 catalytic residues [active] 62928009572 substrate binding site [chemical binding]; other site 62928009573 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 62928009574 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 62928009575 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 62928009576 purine monophosphate binding site [chemical binding]; other site 62928009577 dimer interface [polypeptide binding]; other site 62928009578 putative catalytic residues [active] 62928009579 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 62928009580 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 62928009581 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 62928009582 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 62928009583 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 62928009584 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 62928009585 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 62928009586 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 62928009587 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 62928009588 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 62928009589 Sulfate transporter family; Region: Sulfate_transp; pfam00916 62928009590 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 62928009591 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 62928009592 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 62928009593 RimM N-terminal domain; Region: RimM; pfam01782 62928009594 PRC-barrel domain; Region: PRC; pfam05239 62928009595 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 62928009596 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 62928009597 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 62928009598 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 62928009599 Predicted permeases [General function prediction only]; Region: COG0795 62928009600 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 62928009601 multifunctional aminopeptidase A; Provisional; Region: PRK00913 62928009602 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 62928009603 interface (dimer of trimers) [polypeptide binding]; other site 62928009604 Substrate-binding/catalytic site; other site 62928009605 Zn-binding sites [ion binding]; other site 62928009606 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 62928009607 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 62928009608 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 62928009609 HIGH motif; other site 62928009610 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 62928009611 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 62928009612 active site 62928009613 KMSKS motif; other site 62928009614 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 62928009615 tRNA binding surface [nucleotide binding]; other site 62928009616 anticodon binding site; other site 62928009617 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 62928009618 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 62928009619 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 62928009620 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 62928009621 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 62928009622 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928009623 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 62928009624 Walker A/P-loop; other site 62928009625 ATP binding site [chemical binding]; other site 62928009626 Q-loop/lid; other site 62928009627 ABC transporter signature motif; other site 62928009628 Walker B; other site 62928009629 D-loop; other site 62928009630 H-loop/switch region; other site 62928009631 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 62928009632 Walker A/P-loop; other site 62928009633 ATP binding site [chemical binding]; other site 62928009634 Q-loop/lid; other site 62928009635 ABC transporter signature motif; other site 62928009636 Walker B; other site 62928009637 D-loop; other site 62928009638 H-loop/switch region; other site 62928009639 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 62928009640 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 62928009641 HlyD family secretion protein; Region: HlyD; pfam00529 62928009642 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928009643 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928009644 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 62928009645 Type II transport protein GspH; Region: GspH; pfam12019 62928009646 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 62928009647 Prokaryotic N-terminal methylation site; Region: N_methyl_3; pfam13633 62928009648 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 62928009649 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 62928009650 PilX N-terminal; Region: PilX_N; pfam14341 62928009651 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 62928009652 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 62928009653 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 62928009654 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 62928009655 CPxP motif; other site 62928009656 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 62928009657 Peptidase family M48; Region: Peptidase_M48; cl12018 62928009658 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 62928009659 trimer interface [polypeptide binding]; other site 62928009660 dimer interface [polypeptide binding]; other site 62928009661 putative active site [active] 62928009662 Nitrogen fixation protein of unknown function; Region: Nif11; pfam07862 62928009663 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 62928009664 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 62928009665 Walker A/P-loop; other site 62928009666 ATP binding site [chemical binding]; other site 62928009667 Q-loop/lid; other site 62928009668 ABC transporter signature motif; other site 62928009669 Walker B; other site 62928009670 D-loop; other site 62928009671 H-loop/switch region; other site 62928009672 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 62928009673 ThiS family; Region: ThiS; pfam02597 62928009674 charged pocket; other site 62928009675 hydrophobic patch; other site 62928009676 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 62928009677 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928009678 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928009679 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 62928009680 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 62928009681 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 62928009682 4Fe-4S dicluster domain; Region: Fer4_11; pfam13247 62928009683 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 62928009684 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 62928009685 GAF domain; Region: GAF; pfam01590 62928009686 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 62928009687 Walker A motif; other site 62928009688 ATP binding site [chemical binding]; other site 62928009689 Walker B motif; other site 62928009690 arginine finger; other site 62928009691 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928009692 Cytochrome c; Region: Cytochrom_C; pfam00034 62928009693 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 62928009694 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 62928009695 substrate binding pocket [chemical binding]; other site 62928009696 membrane-bound complex binding site; other site 62928009697 hinge residues; other site 62928009698 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 62928009699 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 62928009700 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 62928009701 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 62928009702 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 62928009703 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 62928009704 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 62928009705 Cytochrome c; Region: Cytochrom_C; cl11414 62928009706 Protein of unknown function (DUF779); Region: DUF779; pfam05610 62928009707 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 62928009708 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 62928009709 NAD(P) binding site [chemical binding]; other site 62928009710 catalytic residues [active] 62928009711 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 62928009712 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 62928009713 Walker A motif; other site 62928009714 ATP binding site [chemical binding]; other site 62928009715 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 62928009716 Protein of unknown function (DUF3274); Region: DUF3274; pfam11678 62928009717 Protein of unknown function (DUF2875); Region: DUF2875; pfam11394 62928009718 Predicted metal-binding protein [General function prediction only]; Region: COG3019 62928009719 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 62928009720 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 62928009721 dimerization interface [polypeptide binding]; other site 62928009722 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 62928009723 dimer interface [polypeptide binding]; other site 62928009724 phosphorylation site [posttranslational modification] 62928009725 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 62928009726 ATP binding site [chemical binding]; other site 62928009727 G-X-G motif; other site 62928009728 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 62928009729 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 62928009730 active site 62928009731 phosphorylation site [posttranslational modification] 62928009732 intermolecular recognition site; other site 62928009733 dimerization interface [polypeptide binding]; other site 62928009734 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 62928009735 DNA binding site [nucleotide binding] 62928009736 Outer membrane efflux protein; Region: OEP; pfam02321 62928009737 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 62928009738 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 62928009739 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 62928009740 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 62928009741 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 62928009742 Outer membrane efflux protein; Region: OEP; pfam02321 62928009743 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 62928009744 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928009745 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928009746 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 62928009747 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 62928009748 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 62928009749 YHS domain; Region: YHS; pfam04945 62928009750 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 62928009751 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 62928009752 Soluble P-type ATPase [General function prediction only]; Region: COG4087 62928009753 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 62928009754 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 62928009755 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 62928009756 putative substrate translocation pore; other site 62928009757 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 62928009758 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928009759 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 62928009760 DNA binding residues [nucleotide binding] 62928009761 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 62928009762 Chromate transporter; Region: Chromate_transp; pfam02417 62928009763 Chromate resistance exported protein; Region: Chrome_Resist; pfam09828 62928009764 Pirin-related protein [General function prediction only]; Region: COG1741 62928009765 Pirin; Region: Pirin; pfam02678 62928009766 DoxX; Region: DoxX; pfam07681 62928009767 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928009768 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 62928009769 The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; Region: PBP2_HupR; cd08431 62928009770 putative dimerization interface [polypeptide binding]; other site 62928009771 NAD(P)H:quinone oxidoreductase; Provisional; Region: PRK03767 62928009772 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928009773 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928009774 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 62928009775 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928009776 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 62928009777 active site 62928009778 phosphorylation site [posttranslational modification] 62928009779 intermolecular recognition site; other site 62928009780 dimerization interface [polypeptide binding]; other site 62928009781 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 62928009782 DNA binding residues [nucleotide binding] 62928009783 dimerization interface [polypeptide binding]; other site 62928009784 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 62928009785 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 62928009786 Mg2+ binding site [ion binding]; other site 62928009787 G-X-G motif; other site 62928009788 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 62928009789 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 62928009790 dimer interface [polypeptide binding]; other site 62928009791 Trp docking motif [polypeptide binding]; other site 62928009792 active site 62928009793 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 62928009794 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 62928009795 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 62928009796 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 62928009797 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 62928009798 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 62928009799 dimer interface [polypeptide binding]; other site 62928009800 Trp docking motif [polypeptide binding]; other site 62928009801 active site 62928009802 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 62928009803 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 62928009804 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928009805 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928009806 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 62928009807 N-terminal plug; other site 62928009808 ligand-binding site [chemical binding]; other site 62928009809 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 62928009810 dimerization interface [polypeptide binding]; other site 62928009811 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 62928009812 Histidine kinase; Region: HisKA_3; pfam07730 62928009813 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 62928009814 ATP binding site [chemical binding]; other site 62928009815 Mg2+ binding site [ion binding]; other site 62928009816 G-X-G motif; other site 62928009817 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928009818 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 62928009819 active site 62928009820 phosphorylation site [posttranslational modification] 62928009821 intermolecular recognition site; other site 62928009822 dimerization interface [polypeptide binding]; other site 62928009823 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 62928009824 DNA binding residues [nucleotide binding] 62928009825 dimerization interface [polypeptide binding]; other site 62928009826 Uncharacterized conserved protein [Function unknown]; Region: COG3287 62928009827 FIST N domain; Region: FIST; smart00897 62928009828 FIST C domain; Region: FIST_C; pfam10442 62928009829 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928009830 dimer interface [polypeptide binding]; other site 62928009831 putative CheW interface [polypeptide binding]; other site 62928009832 Domain of unknown function (DUF4258); Region: DUF4258; pfam14076 62928009833 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 62928009834 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 62928009835 Transposase [DNA replication, recombination, and repair]; Region: COG5433 62928009836 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 62928009837 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 62928009838 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 62928009839 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 62928009840 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928009841 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 62928009842 S-adenosylmethionine binding site [chemical binding]; other site 62928009843 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 62928009844 RibD C-terminal domain; Region: RibD_C; cl17279 62928009845 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928009846 Predicted flavoprotein [General function prediction only]; Region: COG0431 62928009847 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 62928009848 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 62928009849 dimer interface [polypeptide binding]; other site 62928009850 active site 62928009851 heme binding site [chemical binding]; other site 62928009852 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 62928009853 Isochorismatase family; Region: Isochorismatase; pfam00857 62928009854 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 62928009855 catalytic triad [active] 62928009856 dimer interface [polypeptide binding]; other site 62928009857 conserved cis-peptide bond; other site 62928009858 Pirin-related protein [General function prediction only]; Region: COG1741 62928009859 Pirin; Region: Pirin; pfam02678 62928009860 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 62928009861 LysR family transcriptional regulator; Provisional; Region: PRK14997 62928009862 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928009863 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 62928009864 putative effector binding pocket; other site 62928009865 putative dimerization interface [polypeptide binding]; other site 62928009866 RibD C-terminal domain; Region: RibD_C; cl17279 62928009867 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 62928009868 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 62928009869 N-terminal plug; other site 62928009870 ligand-binding site [chemical binding]; other site 62928009871 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 62928009872 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 62928009873 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 62928009874 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 62928009875 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 62928009876 N-terminal plug; other site 62928009877 ligand-binding site [chemical binding]; other site 62928009878 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928009879 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 62928009880 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 62928009881 Peptidase M15; Region: Peptidase_M15_3; cl01194 62928009882 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 62928009883 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 62928009884 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 62928009885 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 62928009886 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 62928009887 active site residue [active] 62928009888 N-formylglutamate amidohydrolase; Region: FGase; cl01522 62928009889 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928009890 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928009891 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 62928009892 dimerization interface [polypeptide binding]; other site 62928009893 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 62928009894 hydroxyglutarate oxidase; Provisional; Region: PRK11728 62928009895 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 62928009896 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 62928009897 Ligand binding site [chemical binding]; other site 62928009898 Electron transfer flavoprotein domain; Region: ETF; pfam01012 62928009899 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 62928009900 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 62928009901 Ligand Binding Site [chemical binding]; other site 62928009902 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 62928009903 HutD; Region: HutD; pfam05962 62928009904 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 62928009905 hydroxyglutarate oxidase; Provisional; Region: PRK11728 62928009906 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 62928009907 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 62928009908 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 62928009909 non-specific DNA binding site [nucleotide binding]; other site 62928009910 salt bridge; other site 62928009911 sequence-specific DNA binding site [nucleotide binding]; other site 62928009912 Cupin domain; Region: Cupin_2; pfam07883 62928009913 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 62928009914 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 62928009915 Glutamate synthase domain 1 [Amino acid transport and metabolism]; Region: GltB; COG0067 62928009916 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 62928009917 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 62928009918 active site 62928009919 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 62928009920 domain_subunit interface; other site 62928009921 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 62928009922 Conserved region in glutamate synthase; Region: Glu_synthase; pfam01645 62928009923 active site 62928009924 FMN binding site [chemical binding]; other site 62928009925 substrate binding site [chemical binding]; other site 62928009926 3Fe-4S cluster binding site [ion binding]; other site 62928009927 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 62928009928 Nitrogen regulatory protein P-II; Region: P-II; smart00938 62928009929 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 62928009930 Protein of unknown function (DUF3750); Region: DUF3750; pfam12570 62928009931 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 62928009932 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 62928009933 trimer interface [polypeptide binding]; other site 62928009934 eyelet of channel; other site 62928009935 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928009936 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928009937 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 62928009938 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 62928009939 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 62928009940 NAD(P) binding site [chemical binding]; other site 62928009941 catalytic residues [active] 62928009942 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 62928009943 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 62928009944 Trp docking motif [polypeptide binding]; other site 62928009945 cytochrome domain interface [polypeptide binding]; other site 62928009946 active site 62928009947 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928009948 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928009949 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 62928009950 N-terminal plug; other site 62928009951 ligand-binding site [chemical binding]; other site 62928009952 Domain of unknown function DUF302; Region: DUF302; cl01364 62928009953 Uncharacterized conserved protein [Function unknown]; Region: COG1359 62928009954 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_C39G; cd02423 62928009955 putative active site [active] 62928009956 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 62928009957 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 62928009958 Walker A motif; other site 62928009959 ATP binding site [chemical binding]; other site 62928009960 Walker B motif; other site 62928009961 arginine finger; other site 62928009962 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928009963 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 62928009964 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 62928009965 catalytic loop [active] 62928009966 iron binding site [ion binding]; other site 62928009967 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 62928009968 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 62928009969 [4Fe-4S] binding site [ion binding]; other site 62928009970 molybdopterin cofactor binding site; other site 62928009971 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 62928009972 molybdopterin cofactor binding site; other site 62928009973 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 62928009974 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH...; Region: TRX_Fd_NuoE_W_FDH_beta; cd03082 62928009975 putative dimer interface [polypeptide binding]; other site 62928009976 [2Fe-2S] cluster binding site [ion binding]; other site 62928009977 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 62928009978 SLBB domain; Region: SLBB; pfam10531 62928009979 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 62928009980 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 62928009981 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 62928009982 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928009983 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 62928009984 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 62928009985 Rubredoxin; Region: Rubredoxin; pfam00301 62928009986 iron binding site [ion binding]; other site 62928009987 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 62928009988 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 62928009989 NAD(P) binding site [chemical binding]; other site 62928009990 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 62928009991 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928009992 substrate binding site [chemical binding]; other site 62928009993 oxyanion hole (OAH) forming residues; other site 62928009994 trimer interface [polypeptide binding]; other site 62928009995 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 62928009996 active site 62928009997 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 62928009998 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928009999 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928010000 Walker A/P-loop; other site 62928010001 ATP binding site [chemical binding]; other site 62928010002 Q-loop/lid; other site 62928010003 ABC transporter signature motif; other site 62928010004 Walker B; other site 62928010005 D-loop; other site 62928010006 H-loop/switch region; other site 62928010007 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928010008 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928010009 Walker A/P-loop; other site 62928010010 ATP binding site [chemical binding]; other site 62928010011 Q-loop/lid; other site 62928010012 ABC transporter signature motif; other site 62928010013 Walker B; other site 62928010014 D-loop; other site 62928010015 H-loop/switch region; other site 62928010016 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928010017 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928010018 TM-ABC transporter signature motif; other site 62928010019 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928010020 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928010021 TM-ABC transporter signature motif; other site 62928010022 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928010023 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 62928010024 putative ligand binding site [chemical binding]; other site 62928010025 Hemerythrin-like domain; Region: Hr-like; cd12108 62928010026 Fe binding site [ion binding]; other site 62928010027 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 62928010028 Benzoate CoA ligase (BCL) and 4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase); Region: BCL_4HBCL; cd05959 62928010029 dimer interface [polypeptide binding]; other site 62928010030 acyl-activating enzyme (AAE) consensus motif; other site 62928010031 putative active site [active] 62928010032 putative AMP binding site [chemical binding]; other site 62928010033 putative CoA binding site [chemical binding]; other site 62928010034 chemical substrate binding site [chemical binding]; other site 62928010035 aldehyde dehydrogenase; Provisional; Region: PRK11903 62928010036 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 62928010037 NAD(P) binding site [chemical binding]; other site 62928010038 catalytic residues [active] 62928010039 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 62928010040 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 62928010041 non-specific DNA binding site [nucleotide binding]; other site 62928010042 salt bridge; other site 62928010043 sequence-specific DNA binding site [nucleotide binding]; other site 62928010044 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 62928010045 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 62928010046 G1 box; other site 62928010047 GTP/Mg2+ binding site [chemical binding]; other site 62928010048 ADP binding site [chemical binding]; other site 62928010049 magnesium binding site [ion binding]; other site 62928010050 putative shikimate binding site; other site 62928010051 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 62928010052 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928010053 substrate binding site [chemical binding]; other site 62928010054 oxyanion hole (OAH) forming residues; other site 62928010055 trimer interface [polypeptide binding]; other site 62928010056 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928010057 substrate binding site [chemical binding]; other site 62928010058 oxyanion hole (OAH) forming residues; other site 62928010059 trimer interface [polypeptide binding]; other site 62928010060 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 62928010061 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 62928010062 4Fe-4S binding domain; Region: Fer4; pfam00037 62928010063 4Fe-4S binding domain; Region: Fer4; pfam00037 62928010064 These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer...; Region: CYPOR_like_FNR; cd06208 62928010065 dimerization interface [polypeptide binding]; other site 62928010066 FAD binding pocket [chemical binding]; other site 62928010067 FAD binding motif [chemical binding]; other site 62928010068 catalytic residues [active] 62928010069 NAD binding pocket [chemical binding]; other site 62928010070 phosphate binding motif [ion binding]; other site 62928010071 beta-alpha-beta structure motif; other site 62928010072 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 62928010073 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 62928010074 dimer interface [polypeptide binding]; other site 62928010075 active site 62928010076 Hemerythrin-like domain; Region: Hr-like; cd12108 62928010077 Fe binding site [ion binding]; other site 62928010078 PAS fold; Region: PAS_4; pfam08448 62928010079 GAF domain; Region: GAF_2; pfam13185 62928010080 GAF domain; Region: GAF; pfam01590 62928010081 PAS domain S-box; Region: sensory_box; TIGR00229 62928010082 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 62928010083 putative active site [active] 62928010084 heme pocket [chemical binding]; other site 62928010085 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928010086 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928010087 metal binding site [ion binding]; metal-binding site 62928010088 active site 62928010089 I-site; other site 62928010090 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 62928010091 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 62928010092 EamA-like transporter family; Region: EamA; pfam00892 62928010093 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 62928010094 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 62928010095 putative DNA binding site [nucleotide binding]; other site 62928010096 putative Zn2+ binding site [ion binding]; other site 62928010097 AsnC family; Region: AsnC_trans_reg; pfam01037 62928010098 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 62928010099 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 62928010100 active site 62928010101 catalytic residues [active] 62928010102 metal binding site [ion binding]; metal-binding site 62928010103 AMP-binding domain protein; Validated; Region: PRK08315 62928010104 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928010105 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 62928010106 acyl-activating enzyme (AAE) consensus motif; other site 62928010107 putative AMP binding site [chemical binding]; other site 62928010108 putative active site [active] 62928010109 putative CoA binding site [chemical binding]; other site 62928010110 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 62928010111 putative active site [active] 62928010112 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 62928010113 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 62928010114 ATP-grasp domain; Region: ATP-grasp_4; cl17255 62928010115 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 62928010116 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 62928010117 carboxyltransferase (CT) interaction site; other site 62928010118 biotinylation site [posttranslational modification]; other site 62928010119 enoyl-CoA hydratase; Provisional; Region: PRK05995 62928010120 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928010121 substrate binding site [chemical binding]; other site 62928010122 oxyanion hole (OAH) forming residues; other site 62928010123 trimer interface [polypeptide binding]; other site 62928010124 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 62928010125 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 62928010126 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 62928010127 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928010128 active site 62928010129 ATP binding site [chemical binding]; other site 62928010130 substrate binding site [chemical binding]; other site 62928010131 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 62928010132 Predicted transcriptional regulator [Transcription]; Region: COG2378 62928010133 HTH domain; Region: HTH_11; pfam08279 62928010134 WYL domain; Region: WYL; pfam13280 62928010135 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 62928010136 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928010137 isovaleryl-CoA dehydrogenase; Region: PLN02519 62928010138 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 62928010139 substrate binding site [chemical binding]; other site 62928010140 FAD binding site [chemical binding]; other site 62928010141 catalytic base [active] 62928010142 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 62928010143 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 62928010144 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928010145 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 62928010146 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 62928010147 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 62928010148 ligand binding site [chemical binding]; other site 62928010149 flexible hinge region; other site 62928010150 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 62928010151 non-specific DNA interactions [nucleotide binding]; other site 62928010152 DNA binding site [nucleotide binding] 62928010153 sequence specific DNA binding site [nucleotide binding]; other site 62928010154 putative cAMP binding site [chemical binding]; other site 62928010155 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 62928010156 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 62928010157 Fe binding site [ion binding]; other site 62928010158 Cytochrome c; Region: Cytochrom_C; pfam00034 62928010159 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 62928010160 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 62928010161 D-pathway; other site 62928010162 Low-spin heme binding site [chemical binding]; other site 62928010163 Putative water exit pathway; other site 62928010164 Binuclear center (active site) [active] 62928010165 K-pathway; other site 62928010166 Putative proton exit pathway; other site 62928010167 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 62928010168 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 62928010169 TrkA-N domain; Region: TrkA_N; pfam02254 62928010170 TrkA-C domain; Region: TrkA_C; pfam02080 62928010171 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 62928010172 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 62928010173 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 62928010174 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 62928010175 active site 62928010176 phosphorylation site [posttranslational modification] 62928010177 intermolecular recognition site; other site 62928010178 dimerization interface [polypeptide binding]; other site 62928010179 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 62928010180 DNA binding site [nucleotide binding] 62928010181 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 62928010182 GAF domain; Region: GAF; cl17456 62928010183 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 62928010184 dimer interface [polypeptide binding]; other site 62928010185 phosphorylation site [posttranslational modification] 62928010186 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 62928010187 ATP binding site [chemical binding]; other site 62928010188 Mg2+ binding site [ion binding]; other site 62928010189 G-X-G motif; other site 62928010190 MoxR-like ATPases [General function prediction only]; Region: COG0714 62928010191 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 62928010192 Walker A motif; other site 62928010193 ATP binding site [chemical binding]; other site 62928010194 Walker B motif; other site 62928010195 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 62928010196 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 62928010197 4Fe-4S binding domain; Region: Fer4_5; pfam12801 62928010198 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 62928010199 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 62928010200 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 62928010201 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 62928010202 ligand binding site [chemical binding]; other site 62928010203 flexible hinge region; other site 62928010204 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 62928010205 putative switch regulator; other site 62928010206 non-specific DNA interactions [nucleotide binding]; other site 62928010207 DNA binding site [nucleotide binding] 62928010208 sequence specific DNA binding site [nucleotide binding]; other site 62928010209 putative cAMP binding site [chemical binding]; other site 62928010210 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 62928010211 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 62928010212 ligand binding site [chemical binding]; other site 62928010213 NAD binding site [chemical binding]; other site 62928010214 tetramer interface [polypeptide binding]; other site 62928010215 catalytic site [active] 62928010216 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 62928010217 L-serine binding site [chemical binding]; other site 62928010218 ACT domain interface; other site 62928010219 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 62928010220 4Fe-4S binding domain; Region: Fer4_5; pfam12801 62928010221 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 62928010222 Transcriptional regulator; Region: Rrf2; cl17282 62928010223 Rrf2 family protein; Region: rrf2_super; TIGR00738 62928010224 HPP family; Region: HPP; pfam04982 62928010225 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 62928010226 FOG: CBS domain [General function prediction only]; Region: COG0517 62928010227 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 62928010228 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 62928010229 Protein of unknown function (DUF3565); Region: DUF3565; pfam12088 62928010230 NosL; Region: NosL; cl01769 62928010231 NosL; Region: NosL; pfam05573 62928010232 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 62928010233 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 62928010234 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 62928010235 Walker A/P-loop; other site 62928010236 ATP binding site [chemical binding]; other site 62928010237 Q-loop/lid; other site 62928010238 ABC transporter signature motif; other site 62928010239 Walker B; other site 62928010240 D-loop; other site 62928010241 H-loop/switch region; other site 62928010242 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 62928010243 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 62928010244 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 62928010245 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 62928010246 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 62928010247 4Fe-4S binding domain; Region: Fer4_5; pfam12801 62928010248 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 62928010249 nitrous-oxide reductase; Validated; Region: PRK02888 62928010250 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 62928010251 aspartate kinase; Reviewed; Region: PRK06635 62928010252 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 62928010253 putative nucleotide binding site [chemical binding]; other site 62928010254 putative catalytic residues [active] 62928010255 putative Mg ion binding site [ion binding]; other site 62928010256 putative aspartate binding site [chemical binding]; other site 62928010257 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 62928010258 putative allosteric regulatory site; other site 62928010259 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 62928010260 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 62928010261 non-specific DNA binding site [nucleotide binding]; other site 62928010262 salt bridge; other site 62928010263 sequence-specific DNA binding site [nucleotide binding]; other site 62928010264 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 62928010265 FeS/SAM binding site; other site 62928010266 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 62928010267 active site 62928010268 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 62928010269 Fatty acid desaturase; Region: FA_desaturase; pfam00487 62928010270 Di-iron ligands [ion binding]; other site 62928010271 Transposase; Region: DDE_Tnp_ISL3; pfam01610 62928010272 Mechanosensitive ion channel; Region: MS_channel; pfam00924 62928010273 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 62928010274 PLD-like domain; Region: PLDc_2; pfam13091 62928010275 putative active site [active] 62928010276 catalytic site [active] 62928010277 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 62928010278 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 62928010279 S-adenosylmethionine binding site [chemical binding]; other site 62928010280 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 62928010281 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 62928010282 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 62928010283 active site 62928010284 substrate binding site [chemical binding]; other site 62928010285 cosubstrate binding site; other site 62928010286 catalytic site [active] 62928010287 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 62928010288 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 62928010289 ATP binding site [chemical binding]; other site 62928010290 Mg2+ binding site [ion binding]; other site 62928010291 G-X-G motif; other site 62928010292 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 62928010293 ATP binding site [chemical binding]; other site 62928010294 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 62928010295 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 62928010296 nickel responsive regulator; Provisional; Region: PRK02967 62928010297 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 62928010298 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 62928010299 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 62928010300 DNA binding site [nucleotide binding] 62928010301 active site 62928010302 DNA polymerase LigD, ligase domain; Region: NHEJ_ligase_lig; TIGR02779 62928010303 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 62928010304 DNA binding site [nucleotide binding] 62928010305 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 62928010306 IPP transferase; Region: IPPT; pfam01715 62928010307 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 62928010308 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 62928010309 HlyD family secretion protein; Region: HlyD_2; pfam12700 62928010310 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928010311 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928010312 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 62928010313 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 62928010314 dimerization interface [polypeptide binding]; other site 62928010315 putative ATP binding site [chemical binding]; other site 62928010316 Domain of unknown function DUF20; Region: UPF0118; pfam01594 62928010317 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 62928010318 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 62928010319 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 62928010320 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 62928010321 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 62928010322 poly(A) polymerase; Region: pcnB; TIGR01942 62928010323 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 62928010324 active site 62928010325 NTP binding site [chemical binding]; other site 62928010326 metal binding triad [ion binding]; metal-binding site 62928010327 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 62928010328 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 62928010329 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 62928010330 catalytic center binding site [active] 62928010331 ATP binding site [chemical binding]; other site 62928010332 Protein of unknown function, DUF486; Region: DUF486; pfam04342 62928010333 thymidylate kinase; Region: DTMP_kinase; TIGR00041 62928010334 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 62928010335 Substrate-binding site [chemical binding]; other site 62928010336 Substrate specificity [chemical binding]; other site 62928010337 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 62928010338 active site 62928010339 oligomerization interface [polypeptide binding]; other site 62928010340 metal binding site [ion binding]; metal-binding site 62928010341 pantoate--beta-alanine ligase; Region: panC; TIGR00018 62928010342 Pantoate-beta-alanine ligase; Region: PanC; cd00560 62928010343 active site 62928010344 ATP-binding site [chemical binding]; other site 62928010345 pantoate-binding site; other site 62928010346 HXXH motif; other site 62928010347 FOG: CBS domain [General function prediction only]; Region: COG0517 62928010348 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 62928010349 aminopeptidase N; Provisional; Region: pepN; PRK14015 62928010350 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 62928010351 Zn binding site [ion binding]; other site 62928010352 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 62928010353 Ligand Binding Site [chemical binding]; other site 62928010354 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 62928010355 Ligand Binding Site [chemical binding]; other site 62928010356 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 62928010357 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 62928010358 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 62928010359 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 62928010360 Soluble P-type ATPase [General function prediction only]; Region: COG4087 62928010361 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 62928010362 RDD family; Region: RDD; pfam06271 62928010363 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 62928010364 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 62928010365 RNA polymerase factor sigma-70; Validated; Region: PRK09047 62928010366 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 62928010367 DNA binding residues [nucleotide binding] 62928010368 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 62928010369 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 62928010370 PYR/PP interface [polypeptide binding]; other site 62928010371 dimer interface [polypeptide binding]; other site 62928010372 TPP binding site [chemical binding]; other site 62928010373 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 62928010374 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 62928010375 TPP-binding site [chemical binding]; other site 62928010376 dimer interface [polypeptide binding]; other site 62928010377 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 62928010378 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 62928010379 putative valine binding site [chemical binding]; other site 62928010380 dimer interface [polypeptide binding]; other site 62928010381 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 62928010382 ketol-acid reductoisomerase; Provisional; Region: PRK05479 62928010383 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 62928010384 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 62928010385 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 62928010386 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 62928010387 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928010388 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 62928010389 active site 62928010390 phosphorylation site [posttranslational modification] 62928010391 intermolecular recognition site; other site 62928010392 dimerization interface [polypeptide binding]; other site 62928010393 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 62928010394 DNA binding site [nucleotide binding] 62928010395 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928010396 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 62928010397 dimer interface [polypeptide binding]; other site 62928010398 phosphorylation site [posttranslational modification] 62928010399 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 62928010400 ATP binding site [chemical binding]; other site 62928010401 Mg2+ binding site [ion binding]; other site 62928010402 G-X-G motif; other site 62928010403 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 62928010404 S-adenosylmethionine binding site [chemical binding]; other site 62928010405 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 62928010406 2-isopropylmalate synthase; Validated; Region: PRK00915 62928010407 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 62928010408 active site 62928010409 catalytic residues [active] 62928010410 metal binding site [ion binding]; metal-binding site 62928010411 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 62928010412 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 62928010413 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 62928010414 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928010415 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 62928010416 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 62928010417 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 62928010418 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 62928010419 GTPase CgtA; Reviewed; Region: obgE; PRK12299 62928010420 GTP1/OBG; Region: GTP1_OBG; pfam01018 62928010421 Obg GTPase; Region: Obg; cd01898 62928010422 G1 box; other site 62928010423 GTP/Mg2+ binding site [chemical binding]; other site 62928010424 Switch I region; other site 62928010425 G2 box; other site 62928010426 G3 box; other site 62928010427 Switch II region; other site 62928010428 G4 box; other site 62928010429 G5 box; other site 62928010430 gamma-glutamyl kinase; Provisional; Region: PRK05429 62928010431 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 62928010432 nucleotide binding site [chemical binding]; other site 62928010433 homotetrameric interface [polypeptide binding]; other site 62928010434 putative phosphate binding site [ion binding]; other site 62928010435 putative allosteric binding site; other site 62928010436 PUA domain; Region: PUA; pfam01472 62928010437 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 62928010438 Ligand Binding Site [chemical binding]; other site 62928010439 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 62928010440 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 62928010441 acyl-activating enzyme (AAE) consensus motif; other site 62928010442 putative AMP binding site [chemical binding]; other site 62928010443 putative active site [active] 62928010444 putative CoA binding site [chemical binding]; other site 62928010445 Pseudomonas fluorescens MupV-like, extended (e) SDRs; Region: MupV_like_SDR_e; cd05263 62928010446 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 62928010447 putative NAD(P) binding site [chemical binding]; other site 62928010448 active site 62928010449 putative substrate binding site [chemical binding]; other site 62928010450 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928010451 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 62928010452 S-adenosylmethionine binding site [chemical binding]; other site 62928010453 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 62928010454 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928010455 FtsX-like permease family; Region: FtsX; pfam02687 62928010456 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 62928010457 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 62928010458 FtsX-like permease family; Region: FtsX; pfam02687 62928010459 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 62928010460 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 62928010461 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928010462 acyl-activating enzyme (AAE) consensus motif; other site 62928010463 AMP binding site [chemical binding]; other site 62928010464 active site 62928010465 CoA binding site [chemical binding]; other site 62928010466 Response regulator receiver domain; Region: Response_reg; pfam00072 62928010467 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 62928010468 active site 62928010469 phosphorylation site [posttranslational modification] 62928010470 intermolecular recognition site; other site 62928010471 dimerization interface [polypeptide binding]; other site 62928010472 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928010473 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928010474 metal binding site [ion binding]; metal-binding site 62928010475 active site 62928010476 I-site; other site 62928010477 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 62928010478 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 62928010479 NADP binding site [chemical binding]; other site 62928010480 dimer interface [polypeptide binding]; other site 62928010481 HDOD domain; Region: HDOD; pfam08668 62928010482 LemA family; Region: LemA; pfam04011 62928010483 E3 Ubiquitin ligase; Region: GIDE; pfam12483 62928010484 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 62928010485 ABC transporter ATPase component; Reviewed; Region: PRK11147 62928010486 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928010487 Walker A/P-loop; other site 62928010488 ATP binding site [chemical binding]; other site 62928010489 Q-loop/lid; other site 62928010490 ABC transporter signature motif; other site 62928010491 Walker B; other site 62928010492 D-loop; other site 62928010493 H-loop/switch region; other site 62928010494 ABC transporter; Region: ABC_tran_2; pfam12848 62928010495 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 62928010496 Site-specific recombinase; Region: SpecificRecomb; pfam10136 62928010497 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928010498 Sel1-like repeats; Region: SEL1; smart00671 62928010499 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 62928010500 Sel1-like repeats; Region: SEL1; smart00671 62928010501 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 62928010502 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928010503 catalytic residue [active] 62928010504 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 62928010505 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 62928010506 NAD binding site [chemical binding]; other site 62928010507 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 62928010508 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 62928010509 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 62928010510 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 62928010511 binding surface 62928010512 TPR motif; other site 62928010513 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 62928010514 TPR motif; other site 62928010515 binding surface 62928010516 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 62928010517 binding surface 62928010518 TPR motif; other site 62928010519 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 62928010520 TPR motif; other site 62928010521 binding surface 62928010522 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 62928010523 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 62928010524 active site 62928010525 phosphorylation site [posttranslational modification] 62928010526 intermolecular recognition site; other site 62928010527 dimerization interface [polypeptide binding]; other site 62928010528 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 62928010529 Walker A motif; other site 62928010530 ATP binding site [chemical binding]; other site 62928010531 Walker B motif; other site 62928010532 arginine finger; other site 62928010533 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928010534 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 62928010535 GAF domain; Region: GAF_3; pfam13492 62928010536 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 62928010537 dimer interface [polypeptide binding]; other site 62928010538 phosphorylation site [posttranslational modification] 62928010539 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 62928010540 ATP binding site [chemical binding]; other site 62928010541 Mg2+ binding site [ion binding]; other site 62928010542 G-X-G motif; other site 62928010543 sugar transferase, PEP-CTERM system associated; Region: EpsB_2; TIGR03013 62928010544 Bacterial sugar transferase; Region: Bac_transf; pfam02397 62928010545 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 62928010546 dimer interaction site [polypeptide binding]; other site 62928010547 substrate-binding tunnel; other site 62928010548 active site 62928010549 catalytic site [active] 62928010550 substrate binding site [chemical binding]; other site 62928010551 thymidylate synthase; Reviewed; Region: thyA; PRK01827 62928010552 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 62928010553 dimerization interface [polypeptide binding]; other site 62928010554 active site 62928010555 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 62928010556 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 62928010557 folate binding site [chemical binding]; other site 62928010558 NADP+ binding site [chemical binding]; other site 62928010559 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 62928010560 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 62928010561 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 62928010562 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 62928010563 catalytic residue [active] 62928010564 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 62928010565 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 62928010566 trimer interface [polypeptide binding]; other site 62928010567 active site 62928010568 antiporter inner membrane protein; Provisional; Region: PRK11670 62928010569 Domain of unknown function DUF59; Region: DUF59; pfam01883 62928010570 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 62928010571 Walker A motif; other site 62928010572 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 62928010573 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928010574 ligand binding site [chemical binding]; other site 62928010575 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 62928010576 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 62928010577 active site 62928010578 HIGH motif; other site 62928010579 KMSKS motif; other site 62928010580 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 62928010581 tRNA binding surface [nucleotide binding]; other site 62928010582 anticodon binding site; other site 62928010583 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 62928010584 dimer interface [polypeptide binding]; other site 62928010585 putative tRNA-binding site [nucleotide binding]; other site 62928010586 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 62928010587 putative transporter; Provisional; Region: PRK11660 62928010588 Sulfate transporter family; Region: Sulfate_transp; pfam00916 62928010589 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 62928010590 Acylphosphatase; Region: Acylphosphatase; pfam00708 62928010591 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 62928010592 Sulfatase; Region: Sulfatase; pfam00884 62928010593 Uncharacterized conserved protein [Function unknown]; Region: COG3391 62928010594 Strictosidine synthase; Region: Str_synth; pfam03088 62928010595 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 62928010596 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 62928010597 putative active site [active] 62928010598 putative PHP Thumb interface [polypeptide binding]; other site 62928010599 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 62928010600 generic binding surface I; other site 62928010601 generic binding surface II; other site 62928010602 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 62928010603 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 62928010604 NADP binding site [chemical binding]; other site 62928010605 dimer interface [polypeptide binding]; other site 62928010606 Phospholipase A1; Region: PLA1; pfam02253 62928010607 substrate binding site [chemical binding]; other site 62928010608 dimerization interface [polypeptide binding]; other site 62928010609 active site 62928010610 calcium binding site [ion binding]; other site 62928010611 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 62928010612 Malic enzyme, N-terminal domain; Region: malic; pfam00390 62928010613 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 62928010614 putative NAD(P) binding site [chemical binding]; other site 62928010615 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 62928010616 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 62928010617 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 62928010618 P-loop; other site 62928010619 Magnesium ion binding site [ion binding]; other site 62928010620 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 62928010621 Magnesium ion binding site [ion binding]; other site 62928010622 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 62928010623 Part of AAA domain; Region: AAA_19; pfam13245 62928010624 Family description; Region: UvrD_C_2; pfam13538 62928010625 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 62928010626 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 62928010627 HIGH motif; other site 62928010628 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 62928010629 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 62928010630 active site 62928010631 KMSKS motif; other site 62928010632 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 62928010633 tRNA binding surface [nucleotide binding]; other site 62928010634 Lipopolysaccharide-assembly; Region: LptE; pfam04390 62928010635 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 62928010636 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 62928010637 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 62928010638 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 62928010639 putative catalytic cysteine [active] 62928010640 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 62928010641 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 62928010642 active site 62928010643 Int/Topo IB signature motif; other site 62928010644 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 62928010645 putative deacylase active site [active] 62928010646 H-NS histone family; Region: Histone_HNS; pfam00816 62928010647 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 62928010648 Dihydroneopterin aldolase; Region: FolB; smart00905 62928010649 active site 62928010650 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 62928010651 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 62928010652 tRNA threonylcarbamoyl adenosine modification protein YgjD; Region: T6A_YgjD; TIGR03723 62928010653 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 62928010654 DNA primase; Validated; Region: dnaG; PRK05667 62928010655 CHC2 zinc finger; Region: zf-CHC2; pfam01807 62928010656 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 62928010657 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 62928010658 active site 62928010659 metal binding site [ion binding]; metal-binding site 62928010660 interdomain interaction site; other site 62928010661 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 62928010662 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 62928010663 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 62928010664 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 62928010665 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 62928010666 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 62928010667 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928010668 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 62928010669 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 62928010670 DNA binding residues [nucleotide binding] 62928010671 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 62928010672 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928010673 dimer interface [polypeptide binding]; other site 62928010674 active site 62928010675 glutathione binding site [chemical binding]; other site 62928010676 Protein of unknown function DUF45; Region: DUF45; pfam01863 62928010677 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 62928010678 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 62928010679 putative MPT binding site; other site 62928010680 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 62928010681 signal recognition particle protein; Provisional; Region: PRK10867 62928010682 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 62928010683 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 62928010684 GTP binding site [chemical binding]; other site 62928010685 Signal peptide binding domain; Region: SRP_SPB; pfam02978 62928010686 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 62928010687 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 62928010688 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 62928010689 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 62928010690 Walker A motif; other site 62928010691 ATP binding site [chemical binding]; other site 62928010692 Walker B motif; other site 62928010693 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 62928010694 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 62928010695 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 62928010696 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 62928010697 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 62928010698 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 62928010699 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 62928010700 Uncharacterized conserved protein [Function unknown]; Region: COG2928 62928010701 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 62928010702 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 62928010703 dimer interface [polypeptide binding]; other site 62928010704 anticodon binding site; other site 62928010705 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 62928010706 homodimer interface [polypeptide binding]; other site 62928010707 motif 1; other site 62928010708 active site 62928010709 motif 2; other site 62928010710 GAD domain; Region: GAD; pfam02938 62928010711 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 62928010712 motif 3; other site 62928010713 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 62928010714 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 62928010715 active site 62928010716 phosphorylation site [posttranslational modification] 62928010717 intermolecular recognition site; other site 62928010718 dimerization interface [polypeptide binding]; other site 62928010719 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 62928010720 active site 62928010721 barstar interaction site; other site 62928010722 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 62928010723 putative RNAase interaction site [polypeptide binding]; other site 62928010724 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 62928010725 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 62928010726 putative dimer interface [polypeptide binding]; other site 62928010727 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 62928010728 feedback inhibition sensing region; other site 62928010729 homohexameric interface [polypeptide binding]; other site 62928010730 carbamate kinase; Reviewed; Region: PRK12686 62928010731 nucleotide binding site [chemical binding]; other site 62928010732 N-acetyl-L-glutamate binding site [chemical binding]; other site 62928010733 Right handed beta helix region; Region: Beta_helix; pfam13229 62928010734 acyl-CoA ligase (AMP-forming), exosortase A-associated; Region: ligase_PEP_1; TIGR03098 62928010735 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928010736 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_6; cd05922 62928010737 acyl-activating enzyme (AAE) consensus motif; other site 62928010738 acyl-activating enzyme (AAE) consensus motif; other site 62928010739 putative AMP binding site [chemical binding]; other site 62928010740 putative active site [active] 62928010741 putative CoA binding site [chemical binding]; other site 62928010742 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 62928010743 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 62928010744 Ligand Binding Site [chemical binding]; other site 62928010745 Molecular Tunnel; other site 62928010746 pyridoxal-dependent decarboxylase, exosortase A system-associated; Region: dCO2ase_PEP1; TIGR03099 62928010747 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase; Region: PLPDE_III_Btrk_like; cd06839 62928010748 dimer interface [polypeptide binding]; other site 62928010749 active site 62928010750 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 62928010751 catalytic residues [active] 62928010752 substrate binding site [chemical binding]; other site 62928010753 TPR repeat; Region: TPR_11; pfam13414 62928010754 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 62928010755 TPR motif; other site 62928010756 exosortase A system-associated hydrolase 1; Region: hydr1_PEP; TIGR03100 62928010757 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 62928010758 exosortase A system-associated hydrolase 2; Region: hydr2_PEP; TIGR03101 62928010759 acyl carrier protein; Provisional; Region: PRK07639 62928010760 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 62928010761 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 62928010762 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 62928010763 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 62928010764 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 62928010765 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 62928010766 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 62928010767 active site 62928010768 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 62928010769 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 62928010770 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 62928010771 active site 62928010772 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 62928010773 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 62928010774 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 62928010775 active site 62928010776 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928010777 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 62928010778 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 62928010779 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 62928010780 Disaggregatase related repeat; Region: Disaggr_repeat; pfam06848 62928010781 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 62928010782 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 62928010783 active site 62928010784 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 62928010785 O-Antigen ligase; Region: Wzy_C; cl04850 62928010786 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 62928010787 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 62928010788 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928010789 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 62928010790 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 62928010791 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 62928010792 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 62928010793 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 62928010794 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 62928010795 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 62928010796 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 62928010797 active site 62928010798 dimer interface [polypeptide binding]; other site 62928010799 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 62928010800 Ligand Binding Site [chemical binding]; other site 62928010801 Molecular Tunnel; other site 62928010802 PEP-CTERM/exosortase A-associated glycosyltransferase, Daro_2409 family; Region: stp3; TIGR04063 62928010803 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 62928010804 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 62928010805 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 62928010806 active site 62928010807 dimer interface [polypeptide binding]; other site 62928010808 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 62928010809 Ligand Binding Site [chemical binding]; other site 62928010810 Molecular Tunnel; other site 62928010811 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 62928010812 This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis; Region: GT1_WbnK_like; cd03807 62928010813 putative ADP-binding pocket [chemical binding]; other site 62928010814 exosortase A; Region: exosortase_1; TIGR03109 62928010815 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 62928010816 Protein of unknown function (DUF3485); Region: DUF3485; pfam11984 62928010817 FemAB-related protein, PEP-CTERM system-associated; Region: pepcterm_femAB; TIGR03019 62928010818 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); Region: CE4_PuuE_HpPgdA_like_2; cd10941 62928010819 polysaccharide deacetylase family protein, PEP-CTERM locus subfamily; Region: pepcterm_polyde; TIGR03006 62928010820 putative active site [active] 62928010821 putative catalytic site [active] 62928010822 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 62928010823 active site 62928010824 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 62928010825 homodimer interface [polypeptide binding]; other site 62928010826 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 62928010827 AAA domain; Region: AAA_14; pfam13173 62928010828 uncharacterized protein, PEP-CTERM system associated; Region: pepcterm_hypo_1; TIGR03016 62928010829 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 62928010830 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 62928010831 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 62928010832 Chain length determinant protein; Region: Wzz; pfam02706 62928010833 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 62928010834 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 62928010835 SLBB domain; Region: SLBB; pfam10531 62928010836 hypothetical protein; Provisional; Region: PRK14852 62928010837 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 62928010838 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 62928010839 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 62928010840 Walker A/P-loop; other site 62928010841 ATP binding site [chemical binding]; other site 62928010842 Q-loop/lid; other site 62928010843 ABC transporter signature motif; other site 62928010844 Walker B; other site 62928010845 D-loop; other site 62928010846 H-loop/switch region; other site 62928010847 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928010848 Beta-Casp domain; Region: Beta-Casp; smart01027 62928010849 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 62928010850 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 62928010851 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 62928010852 trimer interface [polypeptide binding]; other site 62928010853 eyelet of channel; other site 62928010854 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 62928010855 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 62928010856 trimer interface [polypeptide binding]; other site 62928010857 eyelet of channel; other site 62928010858 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 62928010859 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 62928010860 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 62928010861 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 62928010862 DNA binding residues [nucleotide binding] 62928010863 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 62928010864 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 62928010865 Cu(I) binding site [ion binding]; other site 62928010866 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 62928010867 UbiA prenyltransferase family; Region: UbiA; pfam01040 62928010868 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 62928010869 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 62928010870 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 62928010871 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 62928010872 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 62928010873 Subunit III/VIIa interface [polypeptide binding]; other site 62928010874 Phospholipid binding site [chemical binding]; other site 62928010875 Subunit I/III interface [polypeptide binding]; other site 62928010876 Subunit III/VIb interface [polypeptide binding]; other site 62928010877 Subunit III/VIa interface; other site 62928010878 Subunit III/Vb interface [polypeptide binding]; other site 62928010879 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 62928010880 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 62928010881 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 62928010882 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 62928010883 Subunit I/III interface [polypeptide binding]; other site 62928010884 D-pathway; other site 62928010885 Subunit I/VIIc interface [polypeptide binding]; other site 62928010886 Subunit I/IV interface [polypeptide binding]; other site 62928010887 Subunit I/II interface [polypeptide binding]; other site 62928010888 Low-spin heme (heme a) binding site [chemical binding]; other site 62928010889 Subunit I/VIIa interface [polypeptide binding]; other site 62928010890 Subunit I/VIa interface [polypeptide binding]; other site 62928010891 Dimer interface; other site 62928010892 Putative water exit pathway; other site 62928010893 Binuclear center (heme a3/CuB) [ion binding]; other site 62928010894 K-pathway; other site 62928010895 Subunit I/Vb interface [polypeptide binding]; other site 62928010896 Putative proton exit pathway; other site 62928010897 Subunit I/VIb interface; other site 62928010898 Subunit I/VIc interface [polypeptide binding]; other site 62928010899 Electron transfer pathway; other site 62928010900 Subunit I/VIIIb interface [polypeptide binding]; other site 62928010901 Subunit I/VIIb interface [polypeptide binding]; other site 62928010902 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 62928010903 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 62928010904 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 62928010905 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 62928010906 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928010907 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 62928010908 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 62928010909 active site 62928010910 nucleotide binding site [chemical binding]; other site 62928010911 HIGH motif; other site 62928010912 KMSKS motif; other site 62928010913 Na/Pi-cotransporter; Region: NaPi_cotrn_rel; TIGR00704 62928010914 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 62928010915 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 62928010916 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 62928010917 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 62928010918 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 62928010919 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928010920 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 62928010921 DNA binding residues [nucleotide binding] 62928010922 B12 binding domain; Region: B12-binding_2; pfam02607 62928010923 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 62928010924 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 62928010925 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928010926 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 62928010927 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 62928010928 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 62928010929 S-adenosylmethionine binding site [chemical binding]; other site 62928010930 MFS/sugar transport protein; Region: MFS_2; pfam13347 62928010931 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 62928010932 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928010933 NAD(P) binding site [chemical binding]; other site 62928010934 active site 62928010935 SnoaL-like domain; Region: SnoaL_2; pfam12680 62928010936 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 62928010937 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 62928010938 NADP binding site [chemical binding]; other site 62928010939 dimer interface [polypeptide binding]; other site 62928010940 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 62928010941 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 62928010942 ATP binding site [chemical binding]; other site 62928010943 putative Mg++ binding site [ion binding]; other site 62928010944 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 62928010945 nucleotide binding region [chemical binding]; other site 62928010946 ATP-binding site [chemical binding]; other site 62928010947 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 62928010948 HRDC domain; Region: HRDC; pfam00570 62928010949 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 62928010950 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 62928010951 methionine sulfoxide reductase A; Provisional; Region: PRK14054 62928010952 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 62928010953 Family of unknown function (DUF490); Region: DUF490; pfam04357 62928010954 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 62928010955 active site 62928010956 ribulose/triose binding site [chemical binding]; other site 62928010957 phosphate binding site [ion binding]; other site 62928010958 substrate (anthranilate) binding pocket [chemical binding]; other site 62928010959 product (indole) binding pocket [chemical binding]; other site 62928010960 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 62928010961 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 62928010962 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 62928010963 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 62928010964 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 62928010965 glutamine binding [chemical binding]; other site 62928010966 catalytic triad [active] 62928010967 anthranilate synthase component I; Provisional; Region: PRK13565 62928010968 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 62928010969 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 62928010970 phosphoglycolate phosphatase; Provisional; Region: PRK13222 62928010971 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 62928010972 motif II; other site 62928010973 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 62928010974 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 62928010975 substrate binding site [chemical binding]; other site 62928010976 hexamer interface [polypeptide binding]; other site 62928010977 metal binding site [ion binding]; metal-binding site 62928010978 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 62928010979 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 62928010980 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 62928010981 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 62928010982 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 62928010983 Walker A motif; other site 62928010984 ATP binding site [chemical binding]; other site 62928010985 Walker B motif; other site 62928010986 cAMP phosphodiesterases class-II; Region: PDEase_II; cl17776 62928010987 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 62928010988 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 62928010989 phosphopeptide binding site; other site 62928010990 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 62928010991 active site 62928010992 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 62928010993 CoA binding domain; Region: CoA_binding; smart00881 62928010994 CoA-ligase; Region: Ligase_CoA; pfam00549 62928010995 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 62928010996 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 62928010997 CoA-ligase; Region: Ligase_CoA; pfam00549 62928010998 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 62928010999 Uncharacterized conserved protein [Function unknown]; Region: COG0327 62928011000 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 62928011001 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 62928011002 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928011003 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 62928011004 protein binding site [polypeptide binding]; other site 62928011005 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 62928011006 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 62928011007 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 62928011008 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 62928011009 metal binding site [ion binding]; metal-binding site 62928011010 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 62928011011 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 62928011012 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 62928011013 substrate binding site [chemical binding]; other site 62928011014 glutamase interaction surface [polypeptide binding]; other site 62928011015 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 62928011016 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 62928011017 catalytic residues [active] 62928011018 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 62928011019 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 62928011020 putative active site [active] 62928011021 oxyanion strand; other site 62928011022 catalytic triad [active] 62928011023 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 62928011024 putative active site pocket [active] 62928011025 4-fold oligomerization interface [polypeptide binding]; other site 62928011026 metal binding residues [ion binding]; metal-binding site 62928011027 3-fold/trimer interface [polypeptide binding]; other site 62928011028 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 62928011029 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 62928011030 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928011031 homodimer interface [polypeptide binding]; other site 62928011032 catalytic residue [active] 62928011033 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 62928011034 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928011035 catalytic residue [active] 62928011036 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 62928011037 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 62928011038 amidase catalytic site [active] 62928011039 Zn binding residues [ion binding]; other site 62928011040 substrate binding site [chemical binding]; other site 62928011041 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 62928011042 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 62928011043 Walker A/P-loop; other site 62928011044 ATP binding site [chemical binding]; other site 62928011045 Q-loop/lid; other site 62928011046 ABC transporter signature motif; other site 62928011047 Walker B; other site 62928011048 D-loop; other site 62928011049 H-loop/switch region; other site 62928011050 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 62928011051 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928011052 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 62928011053 active site 62928011054 phosphorylation site [posttranslational modification] 62928011055 intermolecular recognition site; other site 62928011056 dimerization interface [polypeptide binding]; other site 62928011057 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 62928011058 Walker A motif; other site 62928011059 ATP binding site [chemical binding]; other site 62928011060 Walker B motif; other site 62928011061 arginine finger; other site 62928011062 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928011063 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928011064 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 62928011065 dimer interface [polypeptide binding]; other site 62928011066 phosphorylation site [posttranslational modification] 62928011067 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 62928011068 ATP binding site [chemical binding]; other site 62928011069 Mg2+ binding site [ion binding]; other site 62928011070 G-X-G motif; other site 62928011071 methionine aminotransferase; Validated; Region: PRK09082 62928011072 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 62928011073 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928011074 homodimer interface [polypeptide binding]; other site 62928011075 catalytic residue [active] 62928011076 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 62928011077 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 62928011078 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 62928011079 intersubunit interface [polypeptide binding]; other site 62928011080 active site 62928011081 Zn2+ binding site [ion binding]; other site 62928011082 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 62928011083 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 62928011084 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 62928011085 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 62928011086 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 62928011087 glycosyl transferase family protein; Provisional; Region: PRK08136 62928011088 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 62928011089 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl17275 62928011090 molybdenum transport protein ModD; Provisional; Region: PRK06096 62928011091 active site 62928011092 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 62928011093 NifZ domain; Region: NifZ; pfam04319 62928011094 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 62928011095 dimer interface [polypeptide binding]; other site 62928011096 [2Fe-2S] cluster binding site [ion binding]; other site 62928011097 Pirin-related protein [General function prediction only]; Region: COG1741 62928011098 Pirin; Region: Pirin; pfam02678 62928011099 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 62928011100 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 62928011101 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928011102 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928011103 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928011104 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 62928011105 putative effector binding pocket; other site 62928011106 dimerization interface [polypeptide binding]; other site 62928011107 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 62928011108 PilZ domain; Region: PilZ; cl01260 62928011109 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 62928011110 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 62928011111 Protein export membrane protein; Region: SecD_SecF; cl14618 62928011112 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 62928011113 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 62928011114 HlyD family secretion protein; Region: HlyD_3; pfam13437 62928011115 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 62928011116 putative active site [active] 62928011117 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 62928011118 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 62928011119 putative ATP binding site [chemical binding]; other site 62928011120 putative substrate interface [chemical binding]; other site 62928011121 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928011122 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 62928011123 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 62928011124 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928011125 homodimer interface [polypeptide binding]; other site 62928011126 catalytic residue [active] 62928011127 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928011128 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 62928011129 active site 62928011130 phosphorylation site [posttranslational modification] 62928011131 intermolecular recognition site; other site 62928011132 dimerization interface [polypeptide binding]; other site 62928011133 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928011134 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 62928011135 active site 62928011136 phosphorylation site [posttranslational modification] 62928011137 intermolecular recognition site; other site 62928011138 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 62928011139 PAS fold; Region: PAS_3; pfam08447 62928011140 putative active site [active] 62928011141 heme pocket [chemical binding]; other site 62928011142 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 62928011143 PAS domain; Region: PAS_9; pfam13426 62928011144 putative active site [active] 62928011145 heme pocket [chemical binding]; other site 62928011146 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928011147 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928011148 metal binding site [ion binding]; metal-binding site 62928011149 active site 62928011150 I-site; other site 62928011151 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 62928011152 Response regulator receiver domain; Region: Response_reg; pfam00072 62928011153 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 62928011154 active site 62928011155 phosphorylation site [posttranslational modification] 62928011156 intermolecular recognition site; other site 62928011157 dimerization interface [polypeptide binding]; other site 62928011158 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 62928011159 PAS fold; Region: PAS_3; pfam08447 62928011160 putative active site [active] 62928011161 heme pocket [chemical binding]; other site 62928011162 PAS domain S-box; Region: sensory_box; TIGR00229 62928011163 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 62928011164 putative active site [active] 62928011165 heme pocket [chemical binding]; other site 62928011166 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 62928011167 PAS fold; Region: PAS_3; pfam08447 62928011168 putative active site [active] 62928011169 heme pocket [chemical binding]; other site 62928011170 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 62928011171 dimer interface [polypeptide binding]; other site 62928011172 phosphorylation site [posttranslational modification] 62928011173 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 62928011174 ATP binding site [chemical binding]; other site 62928011175 Mg2+ binding site [ion binding]; other site 62928011176 G-X-G motif; other site 62928011177 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 62928011178 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 62928011179 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 62928011180 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 62928011181 dimer interface [polypeptide binding]; other site 62928011182 ssDNA binding site [nucleotide binding]; other site 62928011183 tetramer (dimer of dimers) interface [polypeptide binding]; other site 62928011184 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 62928011185 Major Facilitator Superfamily; Region: MFS_1; pfam07690 62928011186 putative substrate translocation pore; other site 62928011187 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 62928011188 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 62928011189 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 62928011190 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 62928011191 UDP-glucose 4-epimerase; Region: PLN02240 62928011192 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 62928011193 NAD binding site [chemical binding]; other site 62928011194 homodimer interface [polypeptide binding]; other site 62928011195 active site 62928011196 substrate binding site [chemical binding]; other site 62928011197 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 62928011198 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 62928011199 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 62928011200 alphaNTD homodimer interface [polypeptide binding]; other site 62928011201 alphaNTD - beta interaction site [polypeptide binding]; other site 62928011202 alphaNTD - beta' interaction site [polypeptide binding]; other site 62928011203 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 62928011204 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 62928011205 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 62928011206 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 62928011207 RNA binding surface [nucleotide binding]; other site 62928011208 30S ribosomal protein S11; Validated; Region: PRK05309 62928011209 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 62928011210 30S ribosomal protein S13; Region: bact_S13; TIGR03631 62928011211 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 62928011212 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 62928011213 rRNA binding site [nucleotide binding]; other site 62928011214 predicted 30S ribosome binding site; other site 62928011215 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 62928011216 SecY translocase; Region: SecY; pfam00344 62928011217 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 62928011218 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 62928011219 23S rRNA binding site [nucleotide binding]; other site 62928011220 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 62928011221 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 62928011222 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 62928011223 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 62928011224 5S rRNA interface [nucleotide binding]; other site 62928011225 23S rRNA interface [nucleotide binding]; other site 62928011226 L5 interface [polypeptide binding]; other site 62928011227 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 62928011228 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 62928011229 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 62928011230 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 62928011231 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 62928011232 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 62928011233 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 62928011234 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 62928011235 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 62928011236 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 62928011237 RNA binding site [nucleotide binding]; other site 62928011238 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 62928011239 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 62928011240 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 62928011241 23S rRNA interface [nucleotide binding]; other site 62928011242 putative translocon interaction site; other site 62928011243 signal recognition particle (SRP54) interaction site; other site 62928011244 L23 interface [polypeptide binding]; other site 62928011245 trigger factor interaction site; other site 62928011246 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 62928011247 23S rRNA interface [nucleotide binding]; other site 62928011248 5S rRNA interface [nucleotide binding]; other site 62928011249 putative antibiotic binding site [chemical binding]; other site 62928011250 L25 interface [polypeptide binding]; other site 62928011251 L27 interface [polypeptide binding]; other site 62928011252 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 62928011253 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 62928011254 G-X-X-G motif; other site 62928011255 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 62928011256 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 62928011257 putative translocon binding site; other site 62928011258 protein-rRNA interface [nucleotide binding]; other site 62928011259 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 62928011260 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 62928011261 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 62928011262 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 62928011263 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 62928011264 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 62928011265 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 62928011266 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 62928011267 elongation factor Tu; Reviewed; Region: PRK00049 62928011268 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 62928011269 G1 box; other site 62928011270 GEF interaction site [polypeptide binding]; other site 62928011271 GTP/Mg2+ binding site [chemical binding]; other site 62928011272 Switch I region; other site 62928011273 G2 box; other site 62928011274 G3 box; other site 62928011275 Switch II region; other site 62928011276 G4 box; other site 62928011277 G5 box; other site 62928011278 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 62928011279 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 62928011280 Antibiotic Binding Site [chemical binding]; other site 62928011281 elongation factor G; Reviewed; Region: PRK00007 62928011282 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 62928011283 G1 box; other site 62928011284 putative GEF interaction site [polypeptide binding]; other site 62928011285 GTP/Mg2+ binding site [chemical binding]; other site 62928011286 Switch I region; other site 62928011287 G2 box; other site 62928011288 G3 box; other site 62928011289 Switch II region; other site 62928011290 G4 box; other site 62928011291 G5 box; other site 62928011292 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 62928011293 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 62928011294 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 62928011295 30S ribosomal protein S7; Validated; Region: PRK05302 62928011296 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 62928011297 S17 interaction site [polypeptide binding]; other site 62928011298 S8 interaction site; other site 62928011299 16S rRNA interaction site [nucleotide binding]; other site 62928011300 streptomycin interaction site [chemical binding]; other site 62928011301 23S rRNA interaction site [nucleotide binding]; other site 62928011302 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 62928011303 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 62928011304 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 62928011305 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 62928011306 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 62928011307 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 62928011308 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 62928011309 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 62928011310 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 62928011311 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 62928011312 DNA binding site [nucleotide binding] 62928011313 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 62928011314 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 62928011315 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 62928011316 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 62928011317 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 62928011318 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 62928011319 RPB3 interaction site [polypeptide binding]; other site 62928011320 RPB1 interaction site [polypeptide binding]; other site 62928011321 RPB11 interaction site [polypeptide binding]; other site 62928011322 RPB10 interaction site [polypeptide binding]; other site 62928011323 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 62928011324 core dimer interface [polypeptide binding]; other site 62928011325 peripheral dimer interface [polypeptide binding]; other site 62928011326 L10 interface [polypeptide binding]; other site 62928011327 L11 interface [polypeptide binding]; other site 62928011328 putative EF-Tu interaction site [polypeptide binding]; other site 62928011329 putative EF-G interaction site [polypeptide binding]; other site 62928011330 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 62928011331 23S rRNA interface [nucleotide binding]; other site 62928011332 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 62928011333 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 62928011334 mRNA/rRNA interface [nucleotide binding]; other site 62928011335 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 62928011336 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 62928011337 23S rRNA interface [nucleotide binding]; other site 62928011338 L7/L12 interface [polypeptide binding]; other site 62928011339 putative thiostrepton binding site; other site 62928011340 L25 interface [polypeptide binding]; other site 62928011341 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 62928011342 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 62928011343 putative homodimer interface [polypeptide binding]; other site 62928011344 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 62928011345 heterodimer interface [polypeptide binding]; other site 62928011346 homodimer interface [polypeptide binding]; other site 62928011347 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 62928011348 elongation factor Tu; Reviewed; Region: PRK00049 62928011349 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 62928011350 G1 box; other site 62928011351 GEF interaction site [polypeptide binding]; other site 62928011352 GTP/Mg2+ binding site [chemical binding]; other site 62928011353 Switch I region; other site 62928011354 G2 box; other site 62928011355 G3 box; other site 62928011356 Switch II region; other site 62928011357 G4 box; other site 62928011358 G5 box; other site 62928011359 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 62928011360 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 62928011361 Antibiotic Binding Site [chemical binding]; other site 62928011362 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 62928011363 FAD binding domain; Region: FAD_binding_4; pfam01565 62928011364 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 62928011365 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 62928011366 dimer interface [polypeptide binding]; other site 62928011367 PYR/PP interface [polypeptide binding]; other site 62928011368 TPP binding site [chemical binding]; other site 62928011369 substrate binding site [chemical binding]; other site 62928011370 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 62928011371 TPP-binding site; other site 62928011372 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 62928011373 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 62928011374 S-adenosylmethionine binding site [chemical binding]; other site 62928011375 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 62928011376 P-loop; other site 62928011377 Magnesium ion binding site [ion binding]; other site 62928011378 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 62928011379 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 62928011380 active site 62928011381 phosphorylation site [posttranslational modification] 62928011382 intermolecular recognition site; other site 62928011383 dimerization interface [polypeptide binding]; other site 62928011384 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 62928011385 DNA binding residues [nucleotide binding] 62928011386 dimerization interface [polypeptide binding]; other site 62928011387 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 62928011388 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 62928011389 dimerization interface [polypeptide binding]; other site 62928011390 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928011391 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 62928011392 dimer interface [polypeptide binding]; other site 62928011393 phosphorylation site [posttranslational modification] 62928011394 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 62928011395 ATP binding site [chemical binding]; other site 62928011396 Mg2+ binding site [ion binding]; other site 62928011397 G-X-G motif; other site 62928011398 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928011399 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 62928011400 phosphorylation site [posttranslational modification] 62928011401 intermolecular recognition site; other site 62928011402 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 62928011403 CoA-transferase family III; Region: CoA_transf_3; pfam02515 62928011404 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 62928011405 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928011406 acyl-activating enzyme (AAE) consensus motif; other site 62928011407 AMP binding site [chemical binding]; other site 62928011408 active site 62928011409 CoA binding site [chemical binding]; other site 62928011410 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928011411 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928011412 Walker A/P-loop; other site 62928011413 ATP binding site [chemical binding]; other site 62928011414 Q-loop/lid; other site 62928011415 ABC transporter signature motif; other site 62928011416 Walker B; other site 62928011417 D-loop; other site 62928011418 H-loop/switch region; other site 62928011419 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 62928011420 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928011421 putative ligand binding site [chemical binding]; other site 62928011422 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928011423 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928011424 TM-ABC transporter signature motif; other site 62928011425 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928011426 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928011427 TM-ABC transporter signature motif; other site 62928011428 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928011429 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928011430 Walker A/P-loop; other site 62928011431 ATP binding site [chemical binding]; other site 62928011432 Q-loop/lid; other site 62928011433 ABC transporter signature motif; other site 62928011434 Walker B; other site 62928011435 D-loop; other site 62928011436 H-loop/switch region; other site 62928011437 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 62928011438 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 62928011439 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 62928011440 acyl-activating enzyme (AAE) consensus motif; other site 62928011441 putative AMP binding site [chemical binding]; other site 62928011442 putative active site [active] 62928011443 putative CoA binding site [chemical binding]; other site 62928011444 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 62928011445 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 62928011446 inhibitor-cofactor binding pocket; inhibition site 62928011447 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928011448 catalytic residue [active] 62928011449 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 62928011450 thiamine phosphate binding site [chemical binding]; other site 62928011451 active site 62928011452 pyrophosphate binding site [ion binding]; other site 62928011453 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 62928011454 dimer interface [polypeptide binding]; other site 62928011455 substrate binding site [chemical binding]; other site 62928011456 ATP binding site [chemical binding]; other site 62928011457 Rubredoxin [Energy production and conversion]; Region: COG1773 62928011458 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 62928011459 iron binding site [ion binding]; other site 62928011460 Response regulator receiver domain; Region: Response_reg; pfam00072 62928011461 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 62928011462 active site 62928011463 phosphorylation site [posttranslational modification] 62928011464 intermolecular recognition site; other site 62928011465 dimerization interface [polypeptide binding]; other site 62928011466 Response regulator receiver domain; Region: Response_reg; pfam00072 62928011467 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 62928011468 active site 62928011469 phosphorylation site [posttranslational modification] 62928011470 intermolecular recognition site; other site 62928011471 dimerization interface [polypeptide binding]; other site 62928011472 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 62928011473 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 62928011474 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928011475 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928011476 dimer interface [polypeptide binding]; other site 62928011477 putative CheW interface [polypeptide binding]; other site 62928011478 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 62928011479 putative binding surface; other site 62928011480 active site 62928011481 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 62928011482 putative binding surface; other site 62928011483 active site 62928011484 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 62928011485 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 62928011486 ATP binding site [chemical binding]; other site 62928011487 Mg2+ binding site [ion binding]; other site 62928011488 G-X-G motif; other site 62928011489 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 62928011490 Response regulator receiver domain; Region: Response_reg; pfam00072 62928011491 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 62928011492 active site 62928011493 phosphorylation site [posttranslational modification] 62928011494 intermolecular recognition site; other site 62928011495 dimerization interface [polypeptide binding]; other site 62928011496 DNA photolyase; Region: DNA_photolyase; pfam00875 62928011497 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 62928011498 hypothetical protein; Validated; Region: PRK00228 62928011499 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 62928011500 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928011501 active site 62928011502 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 62928011503 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 62928011504 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 62928011505 dihydroorotase; Provisional; Region: PRK07627 62928011506 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 62928011507 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 62928011508 active site 62928011509 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 62928011510 YGGT family; Region: YGGT; pfam02325 62928011511 YGGT family; Region: YGGT; pfam02325 62928011512 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 62928011513 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 62928011514 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 62928011515 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 62928011516 catalytic residue [active] 62928011517 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 62928011518 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 62928011519 Walker A motif; other site 62928011520 ATP binding site [chemical binding]; other site 62928011521 Walker B motif; other site 62928011522 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 62928011523 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 62928011524 Walker A motif; other site 62928011525 ATP binding site [chemical binding]; other site 62928011526 Walker B motif; other site 62928011527 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 62928011528 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 62928011529 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 62928011530 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 62928011531 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4253 62928011532 Protein of unknown function (DUF3274); Region: DUF3274; pfam11678 62928011533 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 62928011534 dimerization interface [polypeptide binding]; other site 62928011535 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928011536 dimer interface [polypeptide binding]; other site 62928011537 putative CheW interface [polypeptide binding]; other site 62928011538 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 62928011539 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 62928011540 PAS domain; Region: PAS_9; pfam13426 62928011541 putative active site [active] 62928011542 heme pocket [chemical binding]; other site 62928011543 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 62928011544 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 62928011545 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 62928011546 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 62928011547 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 62928011548 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 62928011549 4Fe-4S binding domain; Region: Fer4; cl02805 62928011550 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 62928011551 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 62928011552 [4Fe-4S] binding site [ion binding]; other site 62928011553 molybdopterin cofactor binding site; other site 62928011554 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 62928011555 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 62928011556 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 62928011557 molybdopterin cofactor binding site; other site 62928011558 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 62928011559 4Fe-4S binding domain; Region: Fer4; pfam00037 62928011560 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 62928011561 4Fe-4S binding domain; Region: Fer4; pfam00037 62928011562 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 62928011563 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 62928011564 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 62928011565 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 62928011566 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 62928011567 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 62928011568 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 62928011569 GTP binding site; other site 62928011570 Helix-turn-helix domain; Region: HTH_17; pfam12728 62928011571 PBP superfamily domain; Region: PBP_like; pfam12727 62928011572 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 62928011573 Walker A motif; other site 62928011574 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 62928011575 dimer interface [polypeptide binding]; other site 62928011576 phosphorylation site [posttranslational modification] 62928011577 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 62928011578 ATP binding site [chemical binding]; other site 62928011579 Mg2+ binding site [ion binding]; other site 62928011580 G-X-G motif; other site 62928011581 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928011582 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 62928011583 active site 62928011584 phosphorylation site [posttranslational modification] 62928011585 intermolecular recognition site; other site 62928011586 dimerization interface [polypeptide binding]; other site 62928011587 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 62928011588 Walker A motif; other site 62928011589 ATP binding site [chemical binding]; other site 62928011590 Walker B motif; other site 62928011591 arginine finger; other site 62928011592 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928011593 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 62928011594 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928011595 NAD(P) binding site [chemical binding]; other site 62928011596 active site 62928011597 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 62928011598 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 62928011599 catalytic loop [active] 62928011600 iron binding site [ion binding]; other site 62928011601 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 62928011602 FAD binding pocket [chemical binding]; other site 62928011603 FAD binding motif [chemical binding]; other site 62928011604 phosphate binding motif [ion binding]; other site 62928011605 beta-alpha-beta structure motif; other site 62928011606 NAD binding pocket [chemical binding]; other site 62928011607 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 62928011608 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928011609 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 62928011610 ATP binding site [chemical binding]; other site 62928011611 Mg2+ binding site [ion binding]; other site 62928011612 G-X-G motif; other site 62928011613 Response regulator receiver domain; Region: Response_reg; pfam00072 62928011614 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 62928011615 active site 62928011616 phosphorylation site [posttranslational modification] 62928011617 intermolecular recognition site; other site 62928011618 dimerization interface [polypeptide binding]; other site 62928011619 PAS domain S-box; Region: sensory_box; TIGR00229 62928011620 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 62928011621 putative active site [active] 62928011622 heme pocket [chemical binding]; other site 62928011623 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928011624 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928011625 metal binding site [ion binding]; metal-binding site 62928011626 active site 62928011627 I-site; other site 62928011628 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 62928011629 Cytochrome c; Region: Cytochrom_C; cl11414 62928011630 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 62928011631 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 62928011632 UreF; Region: UreF; pfam01730 62928011633 Urease accessory protein UreE [Posttranslational modification, protein turnover, chaperones]; Region: UreE; COG2371 62928011634 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 62928011635 dimer interface [polypeptide binding]; other site 62928011636 catalytic residues [active] 62928011637 urease subunit alpha; Reviewed; Region: ureC; PRK13207 62928011638 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 62928011639 subunit interactions [polypeptide binding]; other site 62928011640 active site 62928011641 flap region; other site 62928011642 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 62928011643 gamma-beta subunit interface [polypeptide binding]; other site 62928011644 alpha-beta subunit interface [polypeptide binding]; other site 62928011645 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 62928011646 alpha-gamma subunit interface [polypeptide binding]; other site 62928011647 beta-gamma subunit interface [polypeptide binding]; other site 62928011648 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 62928011649 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 62928011650 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 62928011651 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 62928011652 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 62928011653 Sulfatase; Region: Sulfatase; pfam00884 62928011654 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 62928011655 NMT1/THI5 like; Region: NMT1; pfam09084 62928011656 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 62928011657 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 62928011658 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 62928011659 Walker A/P-loop; other site 62928011660 ATP binding site [chemical binding]; other site 62928011661 Q-loop/lid; other site 62928011662 ABC transporter signature motif; other site 62928011663 Walker B; other site 62928011664 D-loop; other site 62928011665 H-loop/switch region; other site 62928011666 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 62928011667 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 62928011668 dimer interface [polypeptide binding]; other site 62928011669 conserved gate region; other site 62928011670 putative PBP binding loops; other site 62928011671 ABC-ATPase subunit interface; other site 62928011672 Predicted transcriptional regulators [Transcription]; Region: COG1733 62928011673 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 62928011674 dimerization interface [polypeptide binding]; other site 62928011675 putative DNA binding site [nucleotide binding]; other site 62928011676 putative Zn2+ binding site [ion binding]; other site 62928011677 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 62928011678 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 62928011679 cobyric acid synthase; Provisional; Region: PRK00784 62928011680 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 62928011681 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 62928011682 catalytic triad [active] 62928011683 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 62928011684 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 62928011685 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 62928011686 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928011687 homodimer interface [polypeptide binding]; other site 62928011688 catalytic residue [active] 62928011689 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 62928011690 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 62928011691 cobalamin binding residues [chemical binding]; other site 62928011692 putative BtuC binding residues; other site 62928011693 dimer interface [polypeptide binding]; other site 62928011694 Peptidase family M48; Region: Peptidase_M48; cl12018 62928011695 helicase 45; Provisional; Region: PTZ00424 62928011696 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 62928011697 ATP binding site [chemical binding]; other site 62928011698 Mg++ binding site [ion binding]; other site 62928011699 motif III; other site 62928011700 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 62928011701 nucleotide binding region [chemical binding]; other site 62928011702 ATP-binding site [chemical binding]; other site 62928011703 2-isopropylmalate synthase; Validated; Region: PRK03739 62928011704 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 62928011705 active site 62928011706 catalytic residues [active] 62928011707 metal binding site [ion binding]; metal-binding site 62928011708 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 62928011709 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 62928011710 putative FMN binding site [chemical binding]; other site 62928011711 Methyltransferase domain; Region: Methyltransf_18; pfam12847 62928011712 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 62928011713 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928011714 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928011715 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928011716 metal binding site [ion binding]; metal-binding site 62928011717 active site 62928011718 I-site; other site 62928011719 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 62928011720 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 62928011721 ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism]; Region: CbiM; cl00397 62928011722 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 62928011723 active site 62928011724 SAM binding site [chemical binding]; other site 62928011725 homodimer interface [polypeptide binding]; other site 62928011726 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 62928011727 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 62928011728 putative active site [active] 62928011729 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 62928011730 putative active site [active] 62928011731 Precorrin-8X methylmutase; Region: CbiC; pfam02570 62928011732 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 62928011733 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 62928011734 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 62928011735 active site 62928011736 putative homodimer interface [polypeptide binding]; other site 62928011737 SAM binding site [chemical binding]; other site 62928011738 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 62928011739 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 62928011740 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 62928011741 active site 62928011742 SAM binding site [chemical binding]; other site 62928011743 homodimer interface [polypeptide binding]; other site 62928011744 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 62928011745 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 62928011746 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 62928011747 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 62928011748 active site 62928011749 SAM binding site [chemical binding]; other site 62928011750 homodimer interface [polypeptide binding]; other site 62928011751 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 62928011752 dimer interface [polypeptide binding]; other site 62928011753 [2Fe-2S] cluster binding site [ion binding]; other site 62928011754 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 62928011755 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 62928011756 DNA-binding site [nucleotide binding]; DNA binding site 62928011757 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 62928011758 pyridoxal 5'-phosphate binding site [chemical binding]; other site 62928011759 homodimer interface [polypeptide binding]; other site 62928011760 catalytic residue [active] 62928011761 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928011762 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 62928011763 S-adenosylmethionine binding site [chemical binding]; other site 62928011764 putative S-transferase; Provisional; Region: PRK11752 62928011765 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 62928011766 C-terminal domain interface [polypeptide binding]; other site 62928011767 GSH binding site (G-site) [chemical binding]; other site 62928011768 dimer interface [polypeptide binding]; other site 62928011769 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 62928011770 N-terminal domain interface [polypeptide binding]; other site 62928011771 dimer interface [polypeptide binding]; other site 62928011772 substrate binding pocket (H-site) [chemical binding]; other site 62928011773 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 62928011774 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 62928011775 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 62928011776 leucine export protein LeuE; Provisional; Region: PRK10958 62928011777 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 62928011778 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 62928011779 active site 62928011780 Zn binding site [ion binding]; other site 62928011781 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 62928011782 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 62928011783 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 62928011784 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 62928011785 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 62928011786 catalytic triad [active] 62928011787 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 62928011788 active site 62928011789 SAM binding site [chemical binding]; other site 62928011790 homodimer interface [polypeptide binding]; other site 62928011791 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 62928011792 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 62928011793 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 62928011794 homodimer interface [polypeptide binding]; other site 62928011795 Walker A motif; other site 62928011796 ATP binding site [chemical binding]; other site 62928011797 hydroxycobalamin binding site [chemical binding]; other site 62928011798 Walker B motif; other site 62928011799 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 62928011800 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 62928011801 Walker A/P-loop; other site 62928011802 ATP binding site [chemical binding]; other site 62928011803 Q-loop/lid; other site 62928011804 ABC transporter signature motif; other site 62928011805 Walker B; other site 62928011806 D-loop; other site 62928011807 H-loop/switch region; other site 62928011808 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 62928011809 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 62928011810 ABC-ATPase subunit interface; other site 62928011811 dimer interface [polypeptide binding]; other site 62928011812 putative PBP binding regions; other site 62928011813 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 62928011814 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 62928011815 N-terminal plug; other site 62928011816 ligand-binding site [chemical binding]; other site 62928011817 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 62928011818 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 62928011819 N-terminal plug; other site 62928011820 ligand-binding site [chemical binding]; other site 62928011821 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 62928011822 homotrimer interface [polypeptide binding]; other site 62928011823 Walker A motif; other site 62928011824 GTP binding site [chemical binding]; other site 62928011825 Walker B motif; other site 62928011826 Peptidase family M48; Region: Peptidase_M48; cl12018 62928011827 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 62928011828 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 62928011829 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 62928011830 putative dimer interface [polypeptide binding]; other site 62928011831 active site pocket [active] 62928011832 putative cataytic base [active] 62928011833 cobalamin synthase; Reviewed; Region: cobS; PRK00235 62928011834 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 62928011835 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 62928011836 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 62928011837 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 62928011838 NADP binding site [chemical binding]; other site 62928011839 homopentamer interface [polypeptide binding]; other site 62928011840 substrate binding site [chemical binding]; other site 62928011841 active site 62928011842 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 62928011843 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 62928011844 putative active site [active] 62928011845 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 62928011846 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 62928011847 putative active site [active] 62928011848 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928011849 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 62928011850 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 62928011851 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 62928011852 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 62928011853 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 62928011854 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928011855 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 62928011856 Walker A/P-loop; other site 62928011857 ATP binding site [chemical binding]; other site 62928011858 Q-loop/lid; other site 62928011859 ABC transporter signature motif; other site 62928011860 Walker B; other site 62928011861 D-loop; other site 62928011862 H-loop/switch region; other site 62928011863 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 62928011864 active site 62928011865 ATP binding site [chemical binding]; other site 62928011866 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 62928011867 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 62928011868 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 62928011869 putative ADP-binding pocket [chemical binding]; other site 62928011870 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 62928011871 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 62928011872 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 62928011873 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 62928011874 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 62928011875 NAD(P) binding site [chemical binding]; other site 62928011876 homodimer interface [polypeptide binding]; other site 62928011877 substrate binding site [chemical binding]; other site 62928011878 active site 62928011879 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 62928011880 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 62928011881 Mg++ binding site [ion binding]; other site 62928011882 putative catalytic motif [active] 62928011883 putative substrate binding site [chemical binding]; other site 62928011884 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 62928011885 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 62928011886 putative NAD(P) binding site [chemical binding]; other site 62928011887 active site 62928011888 putative substrate binding site [chemical binding]; other site 62928011889 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928011890 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_4; cd03795 62928011891 putative ADP-binding pocket [chemical binding]; other site 62928011892 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 62928011893 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 62928011894 metal-binding site 62928011895 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 62928011896 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 62928011897 NADP binding site [chemical binding]; other site 62928011898 active site 62928011899 putative substrate binding site [chemical binding]; other site 62928011900 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 62928011901 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 62928011902 NADP-binding site; other site 62928011903 homotetramer interface [polypeptide binding]; other site 62928011904 substrate binding site [chemical binding]; other site 62928011905 homodimer interface [polypeptide binding]; other site 62928011906 active site 62928011907 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 62928011908 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 62928011909 Ligand binding site; other site 62928011910 Putative Catalytic site; other site 62928011911 DXD motif; other site 62928011912 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 62928011913 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 62928011914 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 62928011915 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928011916 NAD(P) binding site [chemical binding]; other site 62928011917 active site 62928011918 FAD dependent oxidoreductase; Region: DAO; pfam01266 62928011919 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 62928011920 Methyltransferase domain; Region: Methyltransf_23; pfam13489 62928011921 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 62928011922 S-adenosylmethionine binding site [chemical binding]; other site 62928011923 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928011924 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 62928011925 S-adenosylmethionine binding site [chemical binding]; other site 62928011926 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 62928011927 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 62928011928 Walker A/P-loop; other site 62928011929 ATP binding site [chemical binding]; other site 62928011930 Q-loop/lid; other site 62928011931 ABC transporter signature motif; other site 62928011932 Walker B; other site 62928011933 D-loop; other site 62928011934 H-loop/switch region; other site 62928011935 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 62928011936 putative carbohydrate binding site [chemical binding]; other site 62928011937 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 62928011938 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 62928011939 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 62928011940 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 62928011941 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 62928011942 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 62928011943 NADP binding site [chemical binding]; other site 62928011944 active site 62928011945 putative substrate binding site [chemical binding]; other site 62928011946 DNA polymerase I; Provisional; Region: PRK05755 62928011947 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 62928011948 active site 62928011949 metal binding site 1 [ion binding]; metal-binding site 62928011950 putative 5' ssDNA interaction site; other site 62928011951 metal binding site 3; metal-binding site 62928011952 metal binding site 2 [ion binding]; metal-binding site 62928011953 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 62928011954 putative DNA binding site [nucleotide binding]; other site 62928011955 putative metal binding site [ion binding]; other site 62928011956 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 62928011957 active site 62928011958 catalytic site [active] 62928011959 substrate binding site [chemical binding]; other site 62928011960 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 62928011961 active site 62928011962 DNA binding site [nucleotide binding] 62928011963 catalytic site [active] 62928011964 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 62928011965 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 62928011966 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 62928011967 putative active site [active] 62928011968 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 62928011969 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 62928011970 putative active site [active] 62928011971 putative substrate binding site [chemical binding]; other site 62928011972 ATP binding site [chemical binding]; other site 62928011973 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 62928011974 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 62928011975 active site 62928011976 (T/H)XGH motif; other site 62928011977 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 62928011978 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 62928011979 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 62928011980 active site 62928011981 catalytic residues [active] 62928011982 metal binding site [ion binding]; metal-binding site 62928011983 Maf-like protein; Region: Maf; pfam02545 62928011984 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 62928011985 active site 62928011986 dimer interface [polypeptide binding]; other site 62928011987 ribonuclease G; Provisional; Region: PRK11712 62928011988 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 62928011989 homodimer interface [polypeptide binding]; other site 62928011990 oligonucleotide binding site [chemical binding]; other site 62928011991 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 62928011992 UbiA prenyltransferase family; Region: UbiA; pfam01040 62928011993 osmolarity response regulator; Provisional; Region: ompR; PRK09468 62928011994 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 62928011995 active site 62928011996 phosphorylation site [posttranslational modification] 62928011997 intermolecular recognition site; other site 62928011998 dimerization interface [polypeptide binding]; other site 62928011999 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 62928012000 DNA binding site [nucleotide binding] 62928012001 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 62928012002 dimerization interface [polypeptide binding]; other site 62928012003 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 62928012004 dimer interface [polypeptide binding]; other site 62928012005 phosphorylation site [posttranslational modification] 62928012006 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 62928012007 ATP binding site [chemical binding]; other site 62928012008 Mg2+ binding site [ion binding]; other site 62928012009 G-X-G motif; other site 62928012010 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 62928012011 EF-hand domain pair; Region: EF_hand_5; pfam13499 62928012012 Ca2+ binding site [ion binding]; other site 62928012013 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 62928012014 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928012015 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 62928012016 dimerization interface [polypeptide binding]; other site 62928012017 substrate binding pocket [chemical binding]; other site 62928012018 cyclase homology domain; Region: CHD; cd07302 62928012019 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 62928012020 nucleotidyl binding site; other site 62928012021 metal binding site [ion binding]; metal-binding site 62928012022 dimer interface [polypeptide binding]; other site 62928012023 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 62928012024 phosphopeptide binding site; other site 62928012025 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 62928012026 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928012027 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928012028 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 62928012029 putative effector binding pocket; other site 62928012030 putative dimerization interface [polypeptide binding]; other site 62928012031 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 62928012032 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 62928012033 substrate binding site [chemical binding]; other site 62928012034 catalytic Zn binding site [ion binding]; other site 62928012035 NAD binding site [chemical binding]; other site 62928012036 structural Zn binding site [ion binding]; other site 62928012037 dimer interface [polypeptide binding]; other site 62928012038 S-formylglutathione hydrolase; Region: PLN02442 62928012039 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 62928012040 TIR domain; Region: TIR_2; pfam13676 62928012041 putative chaperone; Provisional; Region: PRK11678 62928012042 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 62928012043 nucleotide binding site [chemical binding]; other site 62928012044 putative NEF/HSP70 interaction site [polypeptide binding]; other site 62928012045 SBD interface [polypeptide binding]; other site 62928012046 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 62928012047 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 62928012048 N-acetyl-D-glucosamine binding site [chemical binding]; other site 62928012049 catalytic residue [active] 62928012050 Transcriptional regulator [Transcription]; Region: LysR; COG0583 62928012051 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928012052 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA; cd08478 62928012053 putative effector binding pocket; other site 62928012054 dimerization interface [polypeptide binding]; other site 62928012055 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 62928012056 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 62928012057 putative substrate translocation pore; other site 62928012058 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 62928012059 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 62928012060 active site 62928012061 catalytic tetrad [active] 62928012062 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 62928012063 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 62928012064 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012065 Walker A/P-loop; other site 62928012066 ATP binding site [chemical binding]; other site 62928012067 Q-loop/lid; other site 62928012068 ABC transporter signature motif; other site 62928012069 Walker B; other site 62928012070 D-loop; other site 62928012071 H-loop/switch region; other site 62928012072 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 62928012073 3HB-oligomer hydrolase (3HBOH); Region: 3HBOH; pfam10605 62928012074 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928012075 Coenzyme A binding pocket [chemical binding]; other site 62928012076 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 62928012077 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 62928012078 glutaminase active site [active] 62928012079 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 62928012080 dimer interface [polypeptide binding]; other site 62928012081 active site 62928012082 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 62928012083 dimer interface [polypeptide binding]; other site 62928012084 active site 62928012085 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 62928012086 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 62928012087 Substrate binding site; other site 62928012088 Mg++ binding site; other site 62928012089 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 62928012090 active site 62928012091 substrate binding site [chemical binding]; other site 62928012092 CoA binding site [chemical binding]; other site 62928012093 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 62928012094 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 62928012095 dimer interaction site [polypeptide binding]; other site 62928012096 substrate-binding tunnel; other site 62928012097 active site 62928012098 catalytic site [active] 62928012099 substrate binding site [chemical binding]; other site 62928012100 phosphate acetyltransferase; Provisional; Region: PRK11890 62928012101 Acetokinase family; Region: Acetate_kinase; cl17229 62928012102 propionate/acetate kinase; Provisional; Region: PRK12379 62928012103 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 62928012104 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 62928012105 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 62928012106 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 62928012107 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 62928012108 active site 62928012109 dimer interface [polypeptide binding]; other site 62928012110 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 62928012111 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 62928012112 active site 62928012113 FMN binding site [chemical binding]; other site 62928012114 substrate binding site [chemical binding]; other site 62928012115 3Fe-4S cluster binding site [ion binding]; other site 62928012116 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 62928012117 domain interface; other site 62928012118 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 62928012119 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928012120 Zn2+ binding site [ion binding]; other site 62928012121 Mg2+ binding site [ion binding]; other site 62928012122 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 62928012123 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 62928012124 active site 62928012125 dimer interface [polypeptide binding]; other site 62928012126 metal binding site [ion binding]; metal-binding site 62928012127 shikimate kinase; Reviewed; Region: aroK; PRK00131 62928012128 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 62928012129 ADP binding site [chemical binding]; other site 62928012130 magnesium binding site [ion binding]; other site 62928012131 putative shikimate binding site; other site 62928012132 AMIN domain; Region: AMIN; pfam11741 62928012133 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 62928012134 Secretin and TonB N terminus short domain; Region: STN; smart00965 62928012135 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 62928012136 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 62928012137 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 62928012138 Pilus assembly protein, PilP; Region: PilP; pfam04351 62928012139 Pilus assembly protein, PilO; Region: PilO; pfam04350 62928012140 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 62928012141 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 62928012142 Cell division protein FtsA; Region: FtsA; cl17206 62928012143 Competence protein A; Region: Competence_A; pfam11104 62928012144 Cell division protein FtsA; Region: FtsA; pfam14450 62928012145 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 62928012146 Transglycosylase; Region: Transgly; pfam00912 62928012147 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 62928012148 putative iron binding site [ion binding]; other site 62928012149 iron donor protein CyaY; Region: FeS_CyaY; TIGR03421 62928012150 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 62928012151 diaminopimelate decarboxylase; Region: lysA; TIGR01048 62928012152 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 62928012153 active site 62928012154 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 62928012155 substrate binding site [chemical binding]; other site 62928012156 catalytic residues [active] 62928012157 dimer interface [polypeptide binding]; other site 62928012158 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 62928012159 Predicted membrane protein [Function unknown]; Region: COG3671 62928012160 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 62928012161 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 62928012162 active site 62928012163 dimer interface [polypeptide binding]; other site 62928012164 NAD-dependent deacetylase; Provisional; Region: PRK00481 62928012165 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 62928012166 NAD+ binding site [chemical binding]; other site 62928012167 substrate binding site [chemical binding]; other site 62928012168 Zn binding site [ion binding]; other site 62928012169 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 62928012170 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 62928012171 putative [4Fe-4S] binding site [ion binding]; other site 62928012172 putative molybdopterin cofactor binding site [chemical binding]; other site 62928012173 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 62928012174 putative molybdopterin cofactor binding site; other site 62928012175 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928012176 active site 62928012177 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 62928012178 putative active site [active] 62928012179 putative catalytic site [active] 62928012180 putative DNA binding site [nucleotide binding]; other site 62928012181 putative phosphate binding site [ion binding]; other site 62928012182 metal binding site A [ion binding]; metal-binding site 62928012183 putative AP binding site [nucleotide binding]; other site 62928012184 putative metal binding site B [ion binding]; other site 62928012185 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928012186 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 62928012187 active site 62928012188 phosphorylation site [posttranslational modification] 62928012189 intermolecular recognition site; other site 62928012190 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 62928012191 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928012192 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928012193 metal binding site [ion binding]; metal-binding site 62928012194 active site 62928012195 I-site; other site 62928012196 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 62928012197 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928012198 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 62928012199 dimer interface [polypeptide binding]; other site 62928012200 phosphorylation site [posttranslational modification] 62928012201 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 62928012202 ATP binding site [chemical binding]; other site 62928012203 Mg2+ binding site [ion binding]; other site 62928012204 G-X-G motif; other site 62928012205 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 62928012206 Predicted membrane protein [Function unknown]; Region: COG5393 62928012207 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928012208 active site 62928012209 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 62928012210 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 62928012211 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 62928012212 active site 62928012213 phosphorylation site [posttranslational modification] 62928012214 intermolecular recognition site; other site 62928012215 dimerization interface [polypeptide binding]; other site 62928012216 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 62928012217 DNA binding site [nucleotide binding] 62928012218 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 62928012219 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 62928012220 ATP binding site [chemical binding]; other site 62928012221 Mg2+ binding site [ion binding]; other site 62928012222 G-X-G motif; other site 62928012223 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 62928012224 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 62928012225 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 62928012226 protein binding site [polypeptide binding]; other site 62928012227 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 62928012228 protein binding site [polypeptide binding]; other site 62928012229 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 62928012230 maleylacetoacetate isomerase; Region: maiA; TIGR01262 62928012231 C-terminal domain interface [polypeptide binding]; other site 62928012232 GSH binding site (G-site) [chemical binding]; other site 62928012233 putative dimer interface [polypeptide binding]; other site 62928012234 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 62928012235 dimer interface [polypeptide binding]; other site 62928012236 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 62928012237 N-terminal domain interface [polypeptide binding]; other site 62928012238 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 62928012239 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 62928012240 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 62928012241 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 62928012242 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928012243 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 62928012244 Zn binding site [ion binding]; other site 62928012245 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 62928012246 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 62928012247 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928012248 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928012249 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 62928012250 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 62928012251 Transcriptional regulator [Transcription]; Region: IclR; COG1414 62928012252 Bacterial transcriptional regulator; Region: IclR; pfam01614 62928012253 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 62928012254 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 62928012255 substrate binding pocket [chemical binding]; other site 62928012256 membrane-bound complex binding site; other site 62928012257 hinge residues; other site 62928012258 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 62928012259 PAS domain; Region: PAS_9; pfam13426 62928012260 putative active site [active] 62928012261 heme pocket [chemical binding]; other site 62928012262 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 62928012263 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 62928012264 putative active site [active] 62928012265 heme pocket [chemical binding]; other site 62928012266 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 62928012267 dimer interface [polypeptide binding]; other site 62928012268 phosphorylation site [posttranslational modification] 62928012269 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 62928012270 ATP binding site [chemical binding]; other site 62928012271 Mg2+ binding site [ion binding]; other site 62928012272 G-X-G motif; other site 62928012273 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928012274 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 62928012275 active site 62928012276 phosphorylation site [posttranslational modification] 62928012277 intermolecular recognition site; other site 62928012278 dimerization interface [polypeptide binding]; other site 62928012279 Response regulator receiver domain; Region: Response_reg; pfam00072 62928012280 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 62928012281 active site 62928012282 phosphorylation site [posttranslational modification] 62928012283 intermolecular recognition site; other site 62928012284 dimerization interface [polypeptide binding]; other site 62928012285 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 62928012286 putative binding surface; other site 62928012287 active site 62928012288 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 62928012289 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 62928012290 active site 62928012291 phosphorylation site [posttranslational modification] 62928012292 intermolecular recognition site; other site 62928012293 dimerization interface [polypeptide binding]; other site 62928012294 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928012295 Zn2+ binding site [ion binding]; other site 62928012296 Mg2+ binding site [ion binding]; other site 62928012297 Cytochrome c; Region: Cytochrom_C; cl11414 62928012298 Cytochrome c; Region: Cytochrom_C; cl11414 62928012299 Protein of unknown function (DUF861); Region: Cupin_3; cl17594 62928012300 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 62928012301 FAD binding domain; Region: FAD_binding_4; pfam01565 62928012302 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 62928012303 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 62928012304 Predicted membrane protein [Function unknown]; Region: COG4125 62928012305 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 62928012306 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928012307 dimer interface [polypeptide binding]; other site 62928012308 putative CheW interface [polypeptide binding]; other site 62928012309 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 62928012310 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 62928012311 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 62928012312 active site 62928012313 HIGH motif; other site 62928012314 dimer interface [polypeptide binding]; other site 62928012315 KMSKS motif; other site 62928012316 Domon-like domain of UDP-N-acetylenolpyruvoylglucosamine reductase; Region: DOMON_murB_like; cd09627 62928012317 putative heme binding site [chemical binding]; other site 62928012318 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 62928012319 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 62928012320 catalytic residues [active] 62928012321 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 62928012322 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 62928012323 S-adenosylmethionine binding site [chemical binding]; other site 62928012324 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 62928012325 Ceramidase; Region: Ceramidase; pfam05875 62928012326 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 62928012327 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 62928012328 conserved cys residue [active] 62928012329 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928012330 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928012331 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 62928012332 S-adenosylmethionine binding site [chemical binding]; other site 62928012333 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 62928012334 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 62928012335 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928012336 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 62928012337 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 62928012338 Coenzyme A binding pocket [chemical binding]; other site 62928012339 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 62928012340 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928012341 Coenzyme A binding pocket [chemical binding]; other site 62928012342 Methyltransferase domain; Region: Methyltransf_31; pfam13847 62928012343 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 62928012344 S-adenosylmethionine binding site [chemical binding]; other site 62928012345 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 62928012346 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 62928012347 nudix motif; other site 62928012348 Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm; Region: BLMA_like; cd08349 62928012349 dimer interface [polypeptide binding]; other site 62928012350 ligand binding site [chemical binding]; other site 62928012351 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 62928012352 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 62928012353 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 62928012354 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928012355 dimer interface [polypeptide binding]; other site 62928012356 putative metal binding site [ion binding]; other site 62928012357 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928012358 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 62928012359 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3779 62928012360 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 62928012361 Transposase; Region: DEDD_Tnp_IS110; pfam01548 62928012362 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 62928012363 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 62928012364 Domain of unknown function (DUF4365); Region: DUF4365; pfam14280 62928012365 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 62928012366 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 62928012367 DNA binding site [nucleotide binding] 62928012368 active site 62928012369 Int/Topo IB signature motif; other site 62928012370 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 62928012371 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 62928012372 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 62928012373 substrate binding pocket [chemical binding]; other site 62928012374 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 62928012375 B12 binding site [chemical binding]; other site 62928012376 cobalt ligand [ion binding]; other site 62928012377 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 62928012378 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 62928012379 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 62928012380 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928012381 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 62928012382 dimerization interface [polypeptide binding]; other site 62928012383 ligand binding site [chemical binding]; other site 62928012384 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 62928012385 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 62928012386 dimerization interface [polypeptide binding]; other site 62928012387 ligand binding site [chemical binding]; other site 62928012388 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 62928012389 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928012390 TM-ABC transporter signature motif; other site 62928012391 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928012392 TM-ABC transporter signature motif; other site 62928012393 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 62928012394 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 62928012395 Walker A/P-loop; other site 62928012396 ATP binding site [chemical binding]; other site 62928012397 Q-loop/lid; other site 62928012398 ABC transporter signature motif; other site 62928012399 Walker B; other site 62928012400 D-loop; other site 62928012401 H-loop/switch region; other site 62928012402 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 62928012403 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 62928012404 Walker A/P-loop; other site 62928012405 ATP binding site [chemical binding]; other site 62928012406 Q-loop/lid; other site 62928012407 ABC transporter signature motif; other site 62928012408 Walker B; other site 62928012409 D-loop; other site 62928012410 H-loop/switch region; other site 62928012411 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 62928012412 putative substrate translocation pore; other site 62928012413 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 62928012414 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 62928012415 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 62928012416 Walker A motif; other site 62928012417 ATP binding site [chemical binding]; other site 62928012418 Walker B motif; other site 62928012419 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 62928012420 Membrane fusogenic activity; Region: BMFP; pfam04380 62928012421 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 62928012422 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 62928012423 Nitrogen regulatory protein P-II; Region: P-II; smart00938 62928012424 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 62928012425 OmpW family; Region: OmpW; cl17427 62928012426 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 62928012427 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 62928012428 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 62928012429 putative active site [active] 62928012430 putative substrate binding site [chemical binding]; other site 62928012431 putative cosubstrate binding site; other site 62928012432 catalytic site [active] 62928012433 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 62928012434 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 62928012435 motif II; other site 62928012436 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 62928012437 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 62928012438 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928012439 Zn2+ binding site [ion binding]; other site 62928012440 Mg2+ binding site [ion binding]; other site 62928012441 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 62928012442 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 62928012443 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012444 Walker A/P-loop; other site 62928012445 ATP binding site [chemical binding]; other site 62928012446 Q-loop/lid; other site 62928012447 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 62928012448 ABC transporter signature motif; other site 62928012449 Walker B; other site 62928012450 D-loop; other site 62928012451 ABC transporter; Region: ABC_tran_2; pfam12848 62928012452 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 62928012453 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 62928012454 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 62928012455 putative catalytic residue [active] 62928012456 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 62928012457 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 62928012458 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928012459 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 62928012460 dimerization interface [polypeptide binding]; other site 62928012461 substrate binding pocket [chemical binding]; other site 62928012462 Isochorismatase family; Region: Isochorismatase; pfam00857 62928012463 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 62928012464 catalytic triad [active] 62928012465 conserved cis-peptide bond; other site 62928012466 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 62928012467 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 62928012468 conserved cys residue [active] 62928012469 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928012470 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 62928012471 EamA-like transporter family; Region: EamA; pfam00892 62928012472 EamA-like transporter family; Region: EamA; pfam00892 62928012473 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 62928012474 Proline dehydrogenase; Region: Pro_dh; pfam01619 62928012475 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 62928012476 Glutamate binding site [chemical binding]; other site 62928012477 NAD binding site [chemical binding]; other site 62928012478 catalytic residues [active] 62928012479 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 62928012480 ApbE family; Region: ApbE; pfam02424 62928012481 glutathione synthetase; Provisional; Region: PRK05246 62928012482 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 62928012483 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 62928012484 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 62928012485 Glutamate-cysteine ligase; Region: GshA; pfam08886 62928012486 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 62928012487 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 62928012488 S-adenosylmethionine binding site [chemical binding]; other site 62928012489 Hemerythrin; Region: Hemerythrin; cd12107 62928012490 Fe binding site [ion binding]; other site 62928012491 Hemerythrin; Region: Hemerythrin; cd12107 62928012492 Fe binding site [ion binding]; other site 62928012493 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 62928012494 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 62928012495 Patatin-like phospholipase; Region: Pat17_PNPLA8_PNPLA9_like4; cd07217 62928012496 active site 62928012497 nucleophile elbow; other site 62928012498 Domain of unknown function (DUF4071); Region: DUF4071; pfam13281 62928012499 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 62928012500 hypothetical protein; Validated; Region: PRK07198 62928012501 GTP cyclohydrolase N terminal; Region: GTP_CH_N; pfam12471 62928012502 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 62928012503 dimerization interface [polypeptide binding]; other site 62928012504 active site 62928012505 Protein of unknown function (DUF1688); Region: DUF1688; pfam07958 62928012506 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 62928012507 active site 62928012508 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 62928012509 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 62928012510 tetramer interface [polypeptide binding]; other site 62928012511 heme binding pocket [chemical binding]; other site 62928012512 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 62928012513 domain interactions; other site 62928012514 cytosine deaminase; Validated; Region: PRK07572 62928012515 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 62928012516 active site 62928012517 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 62928012518 BON domain; Region: BON; pfam04972 62928012519 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 62928012520 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 62928012521 active site 62928012522 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 62928012523 TPR repeat; Region: TPR_11; pfam13414 62928012524 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 62928012525 ligand binding site [chemical binding]; other site 62928012526 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928012527 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928012528 active site 62928012529 ATP binding site [chemical binding]; other site 62928012530 substrate binding site [chemical binding]; other site 62928012531 activation loop (A-loop); other site 62928012532 putative protease; Provisional; Region: PRK15452 62928012533 Peptidase family U32; Region: Peptidase_U32; pfam01136 62928012534 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 62928012535 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 62928012536 heme-binding site [chemical binding]; other site 62928012537 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928012538 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928012539 metal binding site [ion binding]; metal-binding site 62928012540 active site 62928012541 I-site; other site 62928012542 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 62928012543 Coenzyme A binding pocket [chemical binding]; other site 62928012544 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 62928012545 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012546 Walker A/P-loop; other site 62928012547 ATP binding site [chemical binding]; other site 62928012548 Q-loop/lid; other site 62928012549 ABC transporter signature motif; other site 62928012550 Walker B; other site 62928012551 D-loop; other site 62928012552 H-loop/switch region; other site 62928012553 ABC transporter; Region: ABC_tran_2; pfam12848 62928012554 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 62928012555 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 62928012556 active pocket/dimerization site; other site 62928012557 active site 62928012558 phosphorylation site [posttranslational modification] 62928012559 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 62928012560 dimerization domain swap beta strand [polypeptide binding]; other site 62928012561 regulatory protein interface [polypeptide binding]; other site 62928012562 active site 62928012563 regulatory phosphorylation site [posttranslational modification]; other site 62928012564 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 62928012565 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 62928012566 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 62928012567 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 62928012568 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 62928012569 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 62928012570 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 62928012571 hydrogenase 1 large subunit; Provisional; Region: PRK10170 62928012572 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 62928012573 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 62928012574 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 62928012575 sequence-specific DNA binding site [nucleotide binding]; other site 62928012576 salt bridge; other site 62928012577 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 62928012578 catalytic residues [active] 62928012579 dimer interface [polypeptide binding]; other site 62928012580 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 62928012581 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 62928012582 Walker A motif; other site 62928012583 ATP binding site [chemical binding]; other site 62928012584 Walker B motif; other site 62928012585 arginine finger; other site 62928012586 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 62928012587 putative substrate-binding site; other site 62928012588 nickel binding site [ion binding]; other site 62928012589 HupF/HypC family; Region: HupF_HypC; pfam01455 62928012590 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the...; Region: HyaE; cd02965 62928012591 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 62928012592 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 62928012593 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 62928012594 Rubredoxin; Region: Rubredoxin; pfam00301 62928012595 iron binding site [ion binding]; other site 62928012596 [NiFe] hydrogenase assembly chaperone, HybE family; Region: hydrog_HybE; TIGR03993 62928012597 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 62928012598 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 62928012599 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 62928012600 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 62928012601 Acylphosphatase; Region: Acylphosphatase; pfam00708 62928012602 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 62928012603 HypF finger; Region: zf-HYPF; pfam07503 62928012604 HypF finger; Region: zf-HYPF; pfam07503 62928012605 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 62928012606 HupF/HypC family; Region: HupF_HypC; pfam01455 62928012607 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 62928012608 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 62928012609 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 62928012610 dimerization interface [polypeptide binding]; other site 62928012611 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 62928012612 ATP binding site [chemical binding]; other site 62928012613 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928012614 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 62928012615 active site 62928012616 phosphorylation site [posttranslational modification] 62928012617 intermolecular recognition site; other site 62928012618 dimerization interface [polypeptide binding]; other site 62928012619 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 62928012620 Walker A motif; other site 62928012621 ATP binding site [chemical binding]; other site 62928012622 Walker B motif; other site 62928012623 arginine finger; other site 62928012624 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928012625 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 62928012626 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 62928012627 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 62928012628 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928012629 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928012630 metal binding site [ion binding]; metal-binding site 62928012631 active site 62928012632 I-site; other site 62928012633 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 62928012634 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 62928012635 putative active site [active] 62928012636 heme pocket [chemical binding]; other site 62928012637 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 62928012638 dimer interface [polypeptide binding]; other site 62928012639 phosphorylation site [posttranslational modification] 62928012640 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 62928012641 ATP binding site [chemical binding]; other site 62928012642 G-X-G motif; other site 62928012643 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 62928012644 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 62928012645 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 62928012646 minor groove reading motif; other site 62928012647 helix-hairpin-helix signature motif; other site 62928012648 substrate binding pocket [chemical binding]; other site 62928012649 active site 62928012650 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 62928012651 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 62928012652 DNA binding and oxoG recognition site [nucleotide binding] 62928012653 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 62928012654 aromatic acid decarboxylase; Validated; Region: PRK05920 62928012655 Flavoprotein; Region: Flavoprotein; pfam02441 62928012656 Phasin protein; Region: Phasin_2; pfam09361 62928012657 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 62928012658 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 62928012659 conserved cys residue [active] 62928012660 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928012661 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 62928012662 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 62928012663 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 62928012664 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_8; cd06343 62928012665 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 62928012666 putative ligand binding site [chemical binding]; other site 62928012667 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 62928012668 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 62928012669 TM-ABC transporter signature motif; other site 62928012670 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 62928012671 TM-ABC transporter signature motif; other site 62928012672 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 62928012673 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 62928012674 FMN binding site [chemical binding]; other site 62928012675 substrate binding site [chemical binding]; other site 62928012676 putative catalytic residue [active] 62928012677 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 62928012678 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 62928012679 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 62928012680 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates; Region: Bacterial_IMPase_like_1; cd01641 62928012681 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 62928012682 active site 62928012683 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 62928012684 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 62928012685 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012686 Walker A/P-loop; other site 62928012687 ATP binding site [chemical binding]; other site 62928012688 Q-loop/lid; other site 62928012689 ABC transporter signature motif; other site 62928012690 Walker B; other site 62928012691 D-loop; other site 62928012692 H-loop/switch region; other site 62928012693 TOBE domain; Region: TOBE_2; pfam08402 62928012694 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 62928012695 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 62928012696 ABC-ATPase subunit interface; other site 62928012697 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 62928012698 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; cl17531 62928012699 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 62928012700 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 62928012701 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 62928012702 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 62928012703 PBP superfamily domain; Region: PBP_like_2; pfam12849 62928012704 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 62928012705 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 62928012706 PBP superfamily domain; Region: PBP_like; pfam12727 62928012707 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 62928012708 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 62928012709 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 62928012710 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 62928012711 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928012712 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 62928012713 N-terminal plug; other site 62928012714 ligand-binding site [chemical binding]; other site 62928012715 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 62928012716 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012717 Walker A/P-loop; other site 62928012718 ATP binding site [chemical binding]; other site 62928012719 Q-loop/lid; other site 62928012720 ABC transporter signature motif; other site 62928012721 Walker B; other site 62928012722 D-loop; other site 62928012723 H-loop/switch region; other site 62928012724 TOBE domain; Region: TOBE; pfam03459 62928012725 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 62928012726 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 62928012727 dimer interface [polypeptide binding]; other site 62928012728 conserved gate region; other site 62928012729 putative PBP binding loops; other site 62928012730 ABC-ATPase subunit interface; other site 62928012731 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 62928012732 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 62928012733 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 62928012734 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 62928012735 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 62928012736 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 62928012737 molybdenum-pterin binding domain; Region: Mop; TIGR00638 62928012738 molybdenum-pterin binding domain; Region: Mop; TIGR00638 62928012739 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012740 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 62928012741 Walker A/P-loop; other site 62928012742 ATP binding site [chemical binding]; other site 62928012743 Q-loop/lid; other site 62928012744 ABC transporter signature motif; other site 62928012745 Walker B; other site 62928012746 D-loop; other site 62928012747 H-loop/switch region; other site 62928012748 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 62928012749 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 62928012750 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 62928012751 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 62928012752 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 62928012753 dimer interface [polypeptide binding]; other site 62928012754 conserved gate region; other site 62928012755 putative PBP binding loops; other site 62928012756 ABC-ATPase subunit interface; other site 62928012757 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 62928012758 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 62928012759 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 62928012760 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 62928012761 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 62928012762 PAS domain; Region: PAS_9; pfam13426 62928012763 putative active site [active] 62928012764 heme pocket [chemical binding]; other site 62928012765 PAS domain S-box; Region: sensory_box; TIGR00229 62928012766 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 62928012767 putative active site [active] 62928012768 heme pocket [chemical binding]; other site 62928012769 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 62928012770 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 62928012771 metal binding site [ion binding]; metal-binding site 62928012772 active site 62928012773 I-site; other site 62928012774 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 62928012775 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 62928012776 Family description; Region: UvrD_C_2; pfam13538 62928012777 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 62928012778 Family description; Region: UvrD_C_2; pfam13538 62928012779 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 62928012780 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 62928012781 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 62928012782 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 62928012783 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 62928012784 S-adenosylmethionine binding site [chemical binding]; other site 62928012785 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 62928012786 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 62928012787 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 62928012788 dimer interface [polypeptide binding]; other site 62928012789 Alkaline phosphatase homologues; Region: alkPPc; smart00098 62928012790 active site 62928012791 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 62928012792 substrate binding site [chemical binding]; other site 62928012793 oxyanion hole (OAH) forming residues; other site 62928012794 trimer interface [polypeptide binding]; other site 62928012795 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 62928012796 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 62928012797 transcriptional activator TtdR; Provisional; Region: PRK09801 62928012798 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 62928012799 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 62928012800 putative effector binding pocket; other site 62928012801 putative dimerization interface [polypeptide binding]; other site 62928012802 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 62928012803 tartrate dehydrogenase; Region: TTC; TIGR02089 62928012804 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 62928012805 MarC family integral membrane protein; Region: MarC; cl00919 62928012806 Part of AAA domain; Region: AAA_19; pfam13245 62928012807 Family description; Region: UvrD_C_2; pfam13538 62928012808 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 62928012809 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 62928012810 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 62928012811 Trp docking motif [polypeptide binding]; other site 62928012812 active site 62928012813 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; pfam13557 62928012814 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 62928012815 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 62928012816 tetramer interface [polypeptide binding]; other site 62928012817 TPP-binding site [chemical binding]; other site 62928012818 heterodimer interface [polypeptide binding]; other site 62928012819 phosphorylation loop region [posttranslational modification] 62928012820 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 62928012821 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 62928012822 alpha subunit interface [polypeptide binding]; other site 62928012823 TPP binding site [chemical binding]; other site 62928012824 heterodimer interface [polypeptide binding]; other site 62928012825 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 62928012826 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 62928012827 E3 interaction surface; other site 62928012828 lipoyl attachment site [posttranslational modification]; other site 62928012829 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 62928012830 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 62928012831 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 62928012832 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 62928012833 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 62928012834 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 62928012835 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 62928012836 active site 62928012837 metal binding site [ion binding]; metal-binding site 62928012838 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 62928012839 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 62928012840 Walker A motif; other site 62928012841 ATP binding site [chemical binding]; other site 62928012842 Walker B motif; other site 62928012843 arginine finger; other site 62928012844 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 62928012845 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 62928012846 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 62928012847 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 62928012848 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 62928012849 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 62928012850 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 62928012851 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 62928012852 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; pfam09937 62928012853 3-oxoacyl-(acyl carrier protein) synthase; Validated; Region: PRK06147 62928012854 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 62928012855 conserved hypothetical protein; Region: TIGR02270 62928012856 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 62928012857 phosphopeptide binding site; other site 62928012858 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 62928012859 active site 62928012860 Protein kinase domain; Region: Pkinase; pfam00069 62928012861 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928012862 active site 62928012863 ATP binding site [chemical binding]; other site 62928012864 substrate binding site [chemical binding]; other site 62928012865 activation loop (A-loop); other site 62928012866 Domain of unknown function (DUF4384); Region: DUF4384; pfam14326 62928012867 Uncharacterized protein conserved in bacteria (DUF2094); Region: DUF2094; pfam09867 62928012868 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 62928012869 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 62928012870 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 62928012871 hypothetical protein; Provisional; Region: PRK07033 62928012872 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 62928012873 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 62928012874 ligand binding site [chemical binding]; other site 62928012875 type VI secretion protein, VC_A0114 family; Region: VI_chp_4; TIGR03353 62928012876 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 62928012877 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 62928012878 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 62928012879 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 62928012880 Protein of unknown function (DUF770); Region: DUF770; pfam05591 62928012881 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517 62928012882 Protein of unknown function (DUF877); Region: DUF877; pfam05943 62928012883 Protein of unknown function (DUF796); Region: DUF796; pfam05638 62928012884 Protein of unknown function (DUF796); Region: DUF796; pfam05638 62928012885 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 62928012886 ImpE protein; Region: ImpE; pfam07024 62928012887 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 62928012888 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 62928012889 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 62928012890 Protein of unknown function (DUF1305); Region: DUF1305; pfam06996 62928012891 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 62928012892 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 62928012893 Walker A motif; other site 62928012894 ATP binding site [chemical binding]; other site 62928012895 Walker B motif; other site 62928012896 arginine finger; other site 62928012897 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 62928012898 Walker A motif; other site 62928012899 ATP binding site [chemical binding]; other site 62928012900 Walker B motif; other site 62928012901 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 62928012902 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 62928012903 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation," the...; Region: Lipase_3; cd00519 62928012904 active site flap/lid [active] 62928012905 nucleophilic elbow; other site 62928012906 catalytic triad [active] 62928012907 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 62928012908 active site 62928012909 catalytic site [active] 62928012910 TPR repeat; Region: TPR_11; pfam13414 62928012911 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 62928012912 TPR motif; other site 62928012913 TPR repeat; Region: TPR_11; pfam13414 62928012914 binding surface 62928012915 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 62928012916 binding surface 62928012917 TPR repeat; Region: TPR_11; pfam13414 62928012918 TPR motif; other site 62928012919 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 62928012920 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 62928012921 S-adenosylmethionine binding site [chemical binding]; other site 62928012922 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 62928012923 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928012924 active site 62928012925 ATP binding site [chemical binding]; other site 62928012926 substrate binding site [chemical binding]; other site 62928012927 activation loop (A-loop); other site 62928012928 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 62928012929 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 62928012930 dimerization interface [polypeptide binding]; other site 62928012931 FecR protein; Region: FecR; pfam04773 62928012932 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 62928012933 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 62928012934 dimer interface [polypeptide binding]; other site 62928012935 active site 62928012936 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 62928012937 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 62928012938 active site 2 [active] 62928012939 active site 1 [active] 62928012940 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 62928012941 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 62928012942 NAD(P) binding site [chemical binding]; other site 62928012943 active site 62928012944 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 62928012945 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 62928012946 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 62928012947 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 62928012948 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 62928012949 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 62928012950 Ligand binding site; other site 62928012951 Putative Catalytic site; other site 62928012952 DXD motif; other site 62928012953 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 62928012954 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 62928012955 putative acyl-acceptor binding pocket; other site 62928012956 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 62928012957 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_5; cd06153 62928012958 homotrimer interaction site [polypeptide binding]; other site 62928012959 putative active site [active] 62928012960 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 62928012961 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 62928012962 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 62928012963 putative DNA binding site [nucleotide binding]; other site 62928012964 putative Zn2+ binding site [ion binding]; other site 62928012965 AsnC family; Region: AsnC_trans_reg; pfam01037 62928012966 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 62928012967 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 62928012968 alanine racemase; Reviewed; Region: dadX; PRK03646 62928012969 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 62928012970 active site 62928012971 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 62928012972 substrate binding site [chemical binding]; other site 62928012973 catalytic residues [active] 62928012974 dimer interface [polypeptide binding]; other site 62928012975 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 62928012976 binding surface 62928012977 TPR motif; other site 62928012978 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 62928012979 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 62928012980 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 62928012981 catalytic residues [active] 62928012982 central insert; other site 62928012983 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 62928012984 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 62928012985 Heme exporter protein D (CcmD); Region: CcmD; cl11475 62928012986 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 62928012987 CcmB protein; Region: CcmB; cl17444 62928012988 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 62928012989 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 62928012990 Walker A/P-loop; other site 62928012991 ATP binding site [chemical binding]; other site 62928012992 Q-loop/lid; other site 62928012993 ABC transporter signature motif; other site 62928012994 Walker B; other site 62928012995 D-loop; other site 62928012996 H-loop/switch region; other site 62928012997 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 62928012998 PAS domain; Region: PAS_9; pfam13426 62928012999 putative active site [active] 62928013000 heme pocket [chemical binding]; other site 62928013001 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 62928013002 dimer interface [polypeptide binding]; other site 62928013003 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 62928013004 putative CheW interface [polypeptide binding]; other site 62928013005 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 62928013006 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 62928013007 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 62928013008 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 62928013009 4Fe-4S binding domain; Region: Fer4_5; pfam12801 62928013010 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 62928013011 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 62928013012 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 62928013013 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 62928013014 [4Fe-4S] binding site [ion binding]; other site 62928013015 molybdopterin cofactor binding site; other site 62928013016 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 62928013017 molybdopterin cofactor binding site; other site 62928013018 NapD protein; Region: NapD; pfam03927 62928013019 ferredoxin-type protein; Provisional; Region: PRK10194 62928013020 sensory histidine kinase AtoS; Provisional; Region: PRK11360 62928013021 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 62928013022 dimer interface [polypeptide binding]; other site 62928013023 phosphorylation site [posttranslational modification] 62928013024 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 62928013025 ATP binding site [chemical binding]; other site 62928013026 Mg2+ binding site [ion binding]; other site 62928013027 G-X-G motif; other site 62928013028 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 62928013029 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 62928013030 active site 62928013031 phosphorylation site [posttranslational modification] 62928013032 intermolecular recognition site; other site 62928013033 dimerization interface [polypeptide binding]; other site 62928013034 Response regulator receiver domain; Region: Response_reg; pfam00072 62928013035 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 62928013036 active site 62928013037 phosphorylation site [posttranslational modification] 62928013038 intermolecular recognition site; other site 62928013039 dimerization interface [polypeptide binding]; other site 62928013040 Response regulator receiver domain; Region: Response_reg; pfam00072 62928013041 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 62928013042 active site 62928013043 phosphorylation site [posttranslational modification] 62928013044 intermolecular recognition site; other site 62928013045 dimerization interface [polypeptide binding]; other site 62928013046 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 62928013047 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 62928013048 dimerization interface [polypeptide binding]; other site 62928013049 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 62928013050 dimer interface [polypeptide binding]; other site 62928013051 phosphorylation site [posttranslational modification] 62928013052 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 62928013053 ATP binding site [chemical binding]; other site 62928013054 Mg2+ binding site [ion binding]; other site 62928013055 G-X-G motif; other site 62928013056 DNA polymerase III subunit epsilon; Validated; Region: PRK06309 62928013057 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 62928013058 active site 62928013059 catalytic site [active] 62928013060 substrate binding site [chemical binding]; other site 62928013061 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 62928013062 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 62928013063 GIY-YIG motif/motif A; other site 62928013064 active site 62928013065 catalytic site [active] 62928013066 putative DNA binding site [nucleotide binding]; other site 62928013067 metal binding site [ion binding]; metal-binding site 62928013068 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 62928013069 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 62928013070 S-adenosylmethionine binding site [chemical binding]; other site 62928013071 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 62928013072 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 62928013073 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 62928013074 Zn2+ binding site [ion binding]; other site 62928013075 Mg2+ binding site [ion binding]; other site 62928013076 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 62928013077 synthetase active site [active] 62928013078 NTP binding site [chemical binding]; other site 62928013079 metal binding site [ion binding]; metal-binding site 62928013080 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 62928013081 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 62928013082 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 62928013083 Guanylate kinase; Region: Guanylate_kin; pfam00625 62928013084 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 62928013085 catalytic site [active] 62928013086 G-X2-G-X-G-K; other site 62928013087 Isochorismatase family; Region: Isochorismatase; pfam00857 62928013088 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 62928013089 catalytic triad [active] 62928013090 dimer interface [polypeptide binding]; other site 62928013091 conserved cis-peptide bond; other site 62928013092 Y-family of DNA polymerases; Region: PolY; cl12025 62928013093 active site 62928013094 DNA binding site [nucleotide binding] 62928013095 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 62928013096 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 62928013097 putative active site [active] 62928013098 putative PHP Thumb interface [polypeptide binding]; other site 62928013099 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 62928013100 generic binding surface II; other site 62928013101 generic binding surface I; other site 62928013102 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 62928013103 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 62928013104 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 62928013105 DNA binding residues [nucleotide binding] 62928013106 putative dimer interface [polypeptide binding]; other site 62928013107 hypothetical protein; Provisional; Region: PRK11820 62928013108 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 62928013109 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 62928013110 Protein kinase domain; Region: Pkinase; pfam00069 62928013111 Catalytic domain of Protein Kinases; Region: PKc; cd00180 62928013112 active site 62928013113 ATP binding site [chemical binding]; other site 62928013114 substrate binding site [chemical binding]; other site 62928013115 activation loop (A-loop); other site 62928013116 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 62928013117 active site 62928013118 ribonuclease PH; Reviewed; Region: rph; PRK00173 62928013119 Ribonuclease PH; Region: RNase_PH_bact; cd11362 62928013120 hexamer interface [polypeptide binding]; other site 62928013121 active site 62928013122 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 62928013123 active site 62928013124 dimerization interface [polypeptide binding]; other site 62928013125 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 62928013126 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 62928013127 FeS/SAM binding site; other site 62928013128 HemN C-terminal domain; Region: HemN_C; pfam06969 62928013129 protease 4; Provisional; Region: PRK10949 62928013130 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 62928013131 tandem repeat interface [polypeptide binding]; other site 62928013132 oligomer interface [polypeptide binding]; other site 62928013133 active site residues [active] 62928013134 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 62928013135 tandem repeat interface [polypeptide binding]; other site 62928013136 oligomer interface [polypeptide binding]; other site 62928013137 active site residues [active] 62928013138 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 62928013139 S-adenosylmethionine binding site [chemical binding]; other site 62928013140 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 62928013141 ThiS interaction site; other site 62928013142 putative active site [active] 62928013143 tetramer interface [polypeptide binding]; other site 62928013144 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 62928013145 thiS-thiF/thiG interaction site; other site 62928013146 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 62928013147 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 62928013148 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 62928013149 S-adenosylmethionine binding site [chemical binding]; other site 62928013150 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 62928013151 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 62928013152 muropeptide transporter; Reviewed; Region: ampG; PRK11902 62928013153 muropeptide transporter; Validated; Region: ampG; cl17669 62928013154 muropeptide transporter; Validated; Region: ampG; cl17669 62928013155 SMUG: single-strand-selective monofunctional uracil-DNA glycosylase; Region: UDG_F3_SMUG; cd10029 62928013156 active site 62928013157 substrate specificity residue; other site 62928013158 DNA binding site [nucleotide binding] 62928013159 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 62928013160 active site clefts [active] 62928013161 zinc binding site [ion binding]; other site 62928013162 dimer interface [polypeptide binding]; other site 62928013163 primosome assembly protein PriA; Validated; Region: PRK05580 62928013164 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 62928013165 ATP binding site [chemical binding]; other site 62928013166 putative Mg++ binding site [ion binding]; other site 62928013167 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 62928013168 substrate binding site [chemical binding]; other site 62928013169 active site 62928013170 Cation transport protein; Region: TrkH; cl17365 62928013171 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 62928013172 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 62928013173 TrkA-N domain; Region: TrkA_N; pfam02254 62928013174 TrkA-C domain; Region: TrkA_C; pfam02080 62928013175 TrkA-N domain; Region: TrkA_N; pfam02254 62928013176 TrkA-C domain; Region: TrkA_C; pfam02080 62928013177 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 62928013178 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 62928013179 active site 62928013180 phosphorylation site [posttranslational modification] 62928013181 intermolecular recognition site; other site 62928013182 dimerization interface [polypeptide binding]; other site 62928013183 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 62928013184 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 62928013185 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 62928013186 dimerization interface [polypeptide binding]; other site 62928013187 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 62928013188 dimer interface [polypeptide binding]; other site 62928013189 phosphorylation site [posttranslational modification] 62928013190 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 62928013191 ATP binding site [chemical binding]; other site 62928013192 Mg2+ binding site [ion binding]; other site 62928013193 G-X-G motif; other site 62928013194 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 62928013195 16S rRNA methyltransferase B; Provisional; Region: PRK10901 62928013196 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 62928013197 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 62928013198 S-adenosylmethionine binding site [chemical binding]; other site 62928013199 spermidine synthase; Provisional; Region: PRK00811 62928013200 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 62928013201 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 62928013202 hypothetical protein; Provisional; Region: PRK10621 62928013203 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 62928013204 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 62928013205 trmE is a tRNA modification GTPase; Region: trmE; cd04164 62928013206 G1 box; other site 62928013207 GTP/Mg2+ binding site [chemical binding]; other site 62928013208 Switch I region; other site 62928013209 G2 box; other site 62928013210 Switch II region; other site 62928013211 G3 box; other site 62928013212 G4 box; other site 62928013213 G5 box; other site 62928013214 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 62928013215 membrane protein insertase; Provisional; Region: PRK01318 62928013216 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 62928013217 Haemolytic domain; Region: Haemolytic; pfam01809 62928013218 Ribonuclease P; Region: Ribonuclease_P; cl00457 62928013219 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399