-- dump date 20140620_063547 -- class Genbank::misc_feature -- table misc_feature_note -- id note 407976000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 407976000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 407976000003 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 407976000004 Walker A motif; other site 407976000005 ATP binding site [chemical binding]; other site 407976000006 Walker B motif; other site 407976000007 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 407976000008 arginine finger; other site 407976000009 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 407976000010 DnaA box-binding interface [nucleotide binding]; other site 407976000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 407976000012 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 407976000013 putative DNA binding surface [nucleotide binding]; other site 407976000014 dimer interface [polypeptide binding]; other site 407976000015 beta-clamp/clamp loader binding surface; other site 407976000016 beta-clamp/translesion DNA polymerase binding surface; other site 407976000017 recombination protein F; Reviewed; Region: recF; PRK00064 407976000018 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976000019 Walker A/P-loop; other site 407976000020 ATP binding site [chemical binding]; other site 407976000021 Q-loop/lid; other site 407976000022 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976000023 ABC transporter signature motif; other site 407976000024 Walker B; other site 407976000025 D-loop; other site 407976000026 H-loop/switch region; other site 407976000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 407976000028 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 407976000029 ATP binding site [chemical binding]; other site 407976000030 Mg2+ binding site [ion binding]; other site 407976000031 G-X-G motif; other site 407976000032 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 407976000033 anchoring element; other site 407976000034 dimer interface [polypeptide binding]; other site 407976000035 ATP binding site [chemical binding]; other site 407976000036 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 407976000037 active site 407976000038 putative metal-binding site [ion binding]; other site 407976000039 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 407976000040 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 407976000041 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976000042 putative C-terminal domain interface [polypeptide binding]; other site 407976000043 putative GSH binding site (G-site) [chemical binding]; other site 407976000044 putative dimer interface [polypeptide binding]; other site 407976000045 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 407976000046 putative N-terminal domain interface [polypeptide binding]; other site 407976000047 putative dimer interface [polypeptide binding]; other site 407976000048 putative substrate binding pocket (H-site) [chemical binding]; other site 407976000049 Cytochrome c; Region: Cytochrom_C; cl11414 407976000050 sulfite oxidase; Provisional; Region: PLN00177 407976000051 Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate...; Region: SO_family_Moco_dimer; cd02110 407976000052 Moco binding site; other site 407976000053 metal coordination site [ion binding]; other site 407976000054 dimerization interface [polypeptide binding]; other site 407976000055 Cytochrome c; Region: Cytochrom_C; cl11414 407976000056 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]; Region: DUR1; COG1984 407976000057 HDOD domain; Region: HDOD; pfam08668 407976000058 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976000059 Zn2+ binding site [ion binding]; other site 407976000060 Mg2+ binding site [ion binding]; other site 407976000061 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 407976000062 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 407976000063 dimer interface [polypeptide binding]; other site 407976000064 motif 1; other site 407976000065 active site 407976000066 motif 2; other site 407976000067 motif 3; other site 407976000068 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 407976000069 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 407976000070 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976000071 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976000072 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 407976000073 Amidohydrolase; Region: Amidohydro_5; pfam13594 407976000074 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; cd01292 407976000075 active site 407976000076 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 407976000077 MOSC domain; Region: MOSC; pfam03473 407976000078 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 407976000079 CPxP motif; other site 407976000080 Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic...; Region: sensor_globin; cd01068 407976000081 heme-binding site [chemical binding]; other site 407976000082 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976000083 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976000084 metal binding site [ion binding]; metal-binding site 407976000085 active site 407976000086 I-site; other site 407976000087 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 407976000088 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 407976000089 dimer interface [polypeptide binding]; other site 407976000090 active site 407976000091 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 407976000092 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 407976000093 substrate binding site [chemical binding]; other site 407976000094 oxyanion hole (OAH) forming residues; other site 407976000095 trimer interface [polypeptide binding]; other site 407976000096 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 407976000097 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 407976000098 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 407976000099 proline dipeptidase; Provisional; Region: PRK13607 407976000100 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 407976000101 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 407976000102 active site 407976000103 hypothetical protein; Provisional; Region: PRK11568 407976000104 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 407976000105 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 407976000106 Cation transport protein; Region: TrkH; cl17365 407976000107 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 407976000108 Flavodoxin domain; Region: Flavodoxin_5; cl17428 407976000109 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 407976000110 dimerization interface [polypeptide binding]; other site 407976000111 putative DNA binding site [nucleotide binding]; other site 407976000112 putative Zn2+ binding site [ion binding]; other site 407976000113 Flavodoxin domain; Region: Flavodoxin_5; cl17428 407976000114 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 407976000115 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 407976000116 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 407976000117 TrkA-N domain; Region: TrkA_N; pfam02254 407976000118 TrkA-C domain; Region: TrkA_C; pfam02080 407976000119 TrkA-N domain; Region: TrkA_N; pfam02254 407976000120 TrkA-C domain; Region: TrkA_C; pfam02080 407976000121 16S rRNA methyltransferase B; Provisional; Region: PRK10901 407976000122 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 407976000123 putative RNA binding site [nucleotide binding]; other site 407976000124 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 407976000125 S-adenosylmethionine binding site [chemical binding]; other site 407976000126 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 407976000127 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 407976000128 putative active site [active] 407976000129 substrate binding site [chemical binding]; other site 407976000130 putative cosubstrate binding site; other site 407976000131 catalytic site [active] 407976000132 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 407976000133 substrate binding site [chemical binding]; other site 407976000134 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 407976000135 active site 407976000136 catalytic residues [active] 407976000137 metal binding site [ion binding]; metal-binding site 407976000138 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976000139 DNA protecting protein DprA; Region: dprA; TIGR00732 407976000140 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 407976000141 Protein of unknown function (DUF494); Region: DUF494; pfam04361 407976000142 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 407976000143 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 407976000144 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 407976000145 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 407976000146 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 407976000147 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 407976000148 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 407976000149 apolar tunnel; other site 407976000150 heme binding site [chemical binding]; other site 407976000151 dimerization interface [polypeptide binding]; other site 407976000152 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 407976000153 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 407976000154 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 407976000155 shikimate binding site; other site 407976000156 NAD(P) binding site [chemical binding]; other site 407976000157 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 407976000158 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 407976000159 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 407976000160 trimer interface [polypeptide binding]; other site 407976000161 putative metal binding site [ion binding]; other site 407976000162 Flagellin N-methylase; Region: FliB; cl00497 407976000163 Transcriptional regulator; Region: Rrf2; cl17282 407976000164 Rrf2 family protein; Region: rrf2_super; TIGR00738 407976000165 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 407976000166 putative active site [active] 407976000167 putative catalytic site [active] 407976000168 NodB motif; other site 407976000169 Zn binding site [ion binding]; other site 407976000170 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 407976000171 C-terminal peptidase (prc); Region: prc; TIGR00225 407976000172 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 407976000173 protein binding site [polypeptide binding]; other site 407976000174 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 407976000175 Catalytic dyad [active] 407976000176 AmiB activator; Provisional; Region: PRK11637 407976000177 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976000178 phosphoglyceromutase; Provisional; Region: PRK05434 407976000179 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 407976000180 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 407976000181 active site residue [active] 407976000182 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 407976000183 SecA binding site; other site 407976000184 Preprotein binding site; other site 407976000185 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 407976000186 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 407976000187 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 407976000188 HI0933-like protein; Region: HI0933_like; pfam03486 407976000189 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976000190 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 407976000191 Divergent AAA domain; Region: AAA_4; pfam04326 407976000192 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 407976000193 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 407976000194 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 407976000195 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 407976000196 TrkA-N domain; Region: TrkA_N; pfam02254 407976000197 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976000198 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 407976000199 active site 407976000200 phosphorylation site [posttranslational modification] 407976000201 intermolecular recognition site; other site 407976000202 dimerization interface [polypeptide binding]; other site 407976000203 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 407976000204 DNA binding site [nucleotide binding] 407976000205 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 407976000206 dimer interface [polypeptide binding]; other site 407976000207 phosphorylation site [posttranslational modification] 407976000208 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 407976000209 ATP binding site [chemical binding]; other site 407976000210 Mg2+ binding site [ion binding]; other site 407976000211 G-X-G motif; other site 407976000212 Pirin-related protein [General function prediction only]; Region: COG1741 407976000213 Pirin; Region: Pirin; pfam02678 407976000214 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 407976000215 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 407976000216 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 407976000217 GAF domain; Region: GAF_3; pfam13492 407976000218 Histidine kinase; Region: His_kinase; pfam06580 407976000219 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 407976000220 ATP binding site [chemical binding]; other site 407976000221 Mg2+ binding site [ion binding]; other site 407976000222 G-X-G motif; other site 407976000223 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 407976000224 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 407976000225 active site 407976000226 phosphorylation site [posttranslational modification] 407976000227 intermolecular recognition site; other site 407976000228 dimerization interface [polypeptide binding]; other site 407976000229 LytTr DNA-binding domain; Region: LytTR; pfam04397 407976000230 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 407976000231 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976000232 NlpC/P60 family; Region: NLPC_P60; pfam00877 407976000233 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 407976000234 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 407976000235 putative substrate translocation pore; other site 407976000236 Transcriptional regulators [Transcription]; Region: PurR; COG1609 407976000237 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976000238 DNA binding site [nucleotide binding] 407976000239 domain linker motif; other site 407976000240 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_3; cd06279 407976000241 putative dimerization interface [polypeptide binding]; other site 407976000242 putative ligand binding site [chemical binding]; other site 407976000243 sucrose phosphorylase; Provisional; Region: PRK13840 407976000244 Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase); Region: AmyAc_Sucrose_phosphorylase; cd11355 407976000245 active site 407976000246 homodimer interface [polypeptide binding]; other site 407976000247 catalytic site [active] 407976000248 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 407976000249 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 407976000250 putative substrate translocation pore; other site 407976000251 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976000252 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 407976000253 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 407976000254 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 407976000255 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 407976000256 putative substrate binding site [chemical binding]; other site 407976000257 putative ATP binding site [chemical binding]; other site 407976000258 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 407976000259 MPT binding site; other site 407976000260 trimer interface [polypeptide binding]; other site 407976000261 Phage shock protein B; Region: PspB; cl05946 407976000262 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 407976000263 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 407976000264 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 407976000265 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976000266 Walker A/P-loop; other site 407976000267 ATP binding site [chemical binding]; other site 407976000268 Q-loop/lid; other site 407976000269 ABC transporter signature motif; other site 407976000270 Walker B; other site 407976000271 D-loop; other site 407976000272 H-loop/switch region; other site 407976000273 TAP-like protein; Region: Abhydrolase_4; pfam08386 407976000274 Predicted transcriptional regulators [Transcription]; Region: COG1725 407976000275 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976000276 DNA-binding site [nucleotide binding]; DNA binding site 407976000277 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 407976000278 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 407976000279 Walker A/P-loop; other site 407976000280 ATP binding site [chemical binding]; other site 407976000281 Q-loop/lid; other site 407976000282 ABC transporter signature motif; other site 407976000283 Walker B; other site 407976000284 D-loop; other site 407976000285 H-loop/switch region; other site 407976000286 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 407976000287 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 407976000288 acyl-activating enzyme (AAE) consensus motif; other site 407976000289 putative AMP binding site [chemical binding]; other site 407976000290 putative active site [active] 407976000291 putative CoA binding site [chemical binding]; other site 407976000292 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976000293 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976000294 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976000295 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 407976000296 active site 407976000297 HPP family; Region: HPP; pfam04982 407976000298 Predicted acetyltransferase [General function prediction only]; Region: COG2388 407976000299 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 407976000300 active site 407976000301 Uncharacterized conserved protein [Function unknown]; Region: COG3791 407976000302 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 407976000303 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 407976000304 DNA binding residues [nucleotide binding] 407976000305 putative dimer interface [polypeptide binding]; other site 407976000306 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 407976000307 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 407976000308 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 407976000309 Membrane domain of glycerophosphoryl diester phosphodiesterase; Region: GPDPase_memb; pfam10110 407976000310 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 407976000311 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_memb_like; cd08579 407976000312 putative active site [active] 407976000313 catalytic site [active] 407976000314 putative metal binding site [ion binding]; other site 407976000315 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 407976000316 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 407976000317 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 407976000318 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 407976000319 Transcriptional regulators [Transcription]; Region: MarR; COG1846 407976000320 MarR family; Region: MarR_2; pfam12802 407976000321 MarR family; Region: MarR_2; cl17246 407976000322 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 407976000323 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 407976000324 FAD binding pocket [chemical binding]; other site 407976000325 FAD binding motif [chemical binding]; other site 407976000326 phosphate binding motif [ion binding]; other site 407976000327 NAD binding pocket [chemical binding]; other site 407976000328 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976000329 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976000330 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976000331 imidazolonepropionase; Validated; Region: PRK09356 407976000332 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 407976000333 active site 407976000334 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976000335 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976000336 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976000337 urocanate hydratase; Provisional; Region: PRK05414 407976000338 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 407976000339 active sites [active] 407976000340 tetramer interface [polypeptide binding]; other site 407976000341 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 407976000342 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 407976000343 [4Fe-4S] binding site [ion binding]; other site 407976000344 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 407976000345 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 407976000346 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 407976000347 molybdopterin cofactor binding site; other site 407976000348 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 407976000349 4Fe-4S binding domain; Region: Fer4; pfam00037 407976000350 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 407976000351 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 407976000352 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 407976000353 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 407976000354 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 407976000355 selenocysteine synthase; Provisional; Region: PRK04311 407976000356 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 407976000357 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 407976000358 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 407976000359 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 407976000360 G1 box; other site 407976000361 putative GEF interaction site [polypeptide binding]; other site 407976000362 GTP/Mg2+ binding site [chemical binding]; other site 407976000363 Switch I region; other site 407976000364 G2 box; other site 407976000365 G3 box; other site 407976000366 Switch II region; other site 407976000367 G4 box; other site 407976000368 G5 box; other site 407976000369 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 407976000370 Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu...; Region: Translation_factor_III; cl02786 407976000371 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 407976000372 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 407976000373 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 407976000374 putative inner membrane protein; Provisional; Region: PRK11099 407976000375 YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system...; Region: YedF; cd03422 407976000376 CPxP motif; other site 407976000377 Peptidase family M48; Region: Peptidase_M48; cl12018 407976000378 Pilin (bacterial filament); Region: Pilin; pfam00114 407976000379 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 407976000380 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 407976000381 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976000382 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_16; cd07263 407976000383 Protein of unknown function, DUF481; Region: DUF481; cl01213 407976000384 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 407976000385 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 407976000386 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 407976000387 Mechanosensitive ion channel; Region: MS_channel; pfam00924 407976000388 LysE type translocator; Region: LysE; cl00565 407976000389 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 407976000390 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 407976000391 putative acyl-acceptor binding pocket; other site 407976000392 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 407976000393 SnoaL-like domain; Region: SnoaL_3; pfam13474 407976000394 NRDE protein; Region: NRDE; cl01315 407976000395 putative antibiotic transporter; Provisional; Region: PRK10739 407976000396 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4412 407976000397 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 407976000398 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 407976000399 Chorismate lyase; Region: Chor_lyase; cl01230 407976000400 flagellar basal body-associated protein FliL-like protein; Validated; Region: PRK05697 407976000401 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 407976000402 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 407976000403 S-adenosylmethionine binding site [chemical binding]; other site 407976000404 Putative hemolysin [General function prediction only]; Region: Hlx; COG3042 407976000405 Domain of unknown function (DUF333); Region: DUF333; pfam03891 407976000406 Inhibitor of apoptosis-promoting Bax1; Region: Bax1-I; pfam01027 407976000407 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 407976000408 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 407976000409 ATP binding site [chemical binding]; other site 407976000410 substrate interface [chemical binding]; other site 407976000411 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 407976000412 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 407976000413 dimer interface [polypeptide binding]; other site 407976000414 putative functional site; other site 407976000415 putative MPT binding site; other site 407976000416 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 407976000417 Ferritin-like domain; Region: Ferritin; pfam00210 407976000418 ferroxidase diiron center [ion binding]; other site 407976000419 Nitrate and nitrite sensing; Region: NIT; pfam08376 407976000420 Nitrate and nitrite sensing; Region: NIT; pfam08376 407976000421 HAMP domain; Region: HAMP; pfam00672 407976000422 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 407976000423 PAS domain; Region: PAS_9; pfam13426 407976000424 putative active site [active] 407976000425 heme pocket [chemical binding]; other site 407976000426 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976000427 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976000428 metal binding site [ion binding]; metal-binding site 407976000429 active site 407976000430 I-site; other site 407976000431 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 407976000432 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 407976000433 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 407976000434 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 407976000435 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 407976000436 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976000437 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 407976000438 GIY-YIG motif/motif A; other site 407976000439 putative active site [active] 407976000440 putative metal binding site [ion binding]; other site 407976000441 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 407976000442 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 407976000443 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 407976000444 S-adenosylmethionine binding site [chemical binding]; other site 407976000445 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 407976000446 putative active site [active] 407976000447 Zn binding site [ion binding]; other site 407976000448 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 407976000449 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976000450 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 407976000451 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 407976000452 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 407976000453 active site 407976000454 substrate-binding site [chemical binding]; other site 407976000455 metal-binding site [ion binding] 407976000456 ATP binding site [chemical binding]; other site 407976000457 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 407976000458 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 407976000459 dimerization interface [polypeptide binding]; other site 407976000460 domain crossover interface; other site 407976000461 redox-dependent activation switch; other site 407976000462 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 407976000463 RNA binding surface [nucleotide binding]; other site 407976000464 putative type II secretion protein GspC; Provisional; Region: PRK09681 407976000465 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 407976000466 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 407976000467 type II secretion system protein D; Region: type_II_gspD; TIGR02517 407976000468 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 407976000469 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 407976000470 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 407976000471 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 407976000472 type II secretion system protein E; Region: type_II_gspE; TIGR02533 407976000473 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 407976000474 Walker A motif; other site 407976000475 ATP binding site [chemical binding]; other site 407976000476 Walker B motif; other site 407976000477 type II secretion system protein F; Region: GspF; TIGR02120 407976000478 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 407976000479 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 407976000480 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 407976000481 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 407976000482 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 407976000483 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 407976000484 Type II transport protein GspH; Region: GspH; pfam12019 407976000485 Prokaryotic N-terminal methylation motif; Region: N_methyl; pfam07963 407976000486 type II secretion system protein I; Region: gspI; TIGR01707 407976000487 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 407976000488 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 407976000489 type II secretion system protein J; Region: gspJ; TIGR01711 407976000490 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 407976000491 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 407976000492 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 407976000493 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 407976000494 GspL periplasmic domain; Region: GspL_C; pfam12693 407976000495 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 407976000496 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 407976000497 fimbrial assembly chaperone StbE; Provisional; Region: PRK15246 407976000498 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 407976000499 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 407976000500 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 407976000501 PapC N-terminal domain; Region: PapC_N; pfam13954 407976000502 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 407976000503 PapC C-terminal domain; Region: PapC_C; pfam13953 407976000504 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976000505 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976000506 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976000507 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976000508 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976000509 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976000510 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional; Region: PRK09959 407976000511 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 407976000512 substrate binding pocket [chemical binding]; other site 407976000513 membrane-bound complex binding site; other site 407976000514 hinge residues; other site 407976000515 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 407976000516 substrate binding pocket [chemical binding]; other site 407976000517 membrane-bound complex binding site; other site 407976000518 hinge residues; other site 407976000519 PAS domain; Region: PAS; smart00091 407976000520 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 407976000521 dimer interface [polypeptide binding]; other site 407976000522 phosphorylation site [posttranslational modification] 407976000523 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 407976000524 ATP binding site [chemical binding]; other site 407976000525 Mg2+ binding site [ion binding]; other site 407976000526 G-X-G motif; other site 407976000527 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 407976000528 active site 407976000529 phosphorylation site [posttranslational modification] 407976000530 intermolecular recognition site; other site 407976000531 dimerization interface [polypeptide binding]; other site 407976000532 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 407976000533 putative binding surface; other site 407976000534 active site 407976000535 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976000536 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 407976000537 active site 407976000538 phosphorylation site [posttranslational modification] 407976000539 intermolecular recognition site; other site 407976000540 dimerization interface [polypeptide binding]; other site 407976000541 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 407976000542 DNA binding residues [nucleotide binding] 407976000543 dimerization interface [polypeptide binding]; other site 407976000544 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976000545 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 407976000546 active site 407976000547 phosphorylation site [posttranslational modification] 407976000548 intermolecular recognition site; other site 407976000549 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 407976000550 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 407976000551 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 407976000552 acyl-activating enzyme (AAE) consensus motif; other site 407976000553 putative AMP binding site [chemical binding]; other site 407976000554 putative active site [active] 407976000555 putative CoA binding site [chemical binding]; other site 407976000556 O-succinylbenzoate synthase; Provisional; Region: PRK05105 407976000557 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 407976000558 active site 407976000559 Lipase. 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 process of...; Region: Lipase; cl14883 407976000560 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 407976000561 nucleophilic elbow; other site 407976000562 catalytic triad; other site 407976000563 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 407976000564 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 407976000565 dimer interface [polypeptide binding]; other site 407976000566 tetramer interface [polypeptide binding]; other site 407976000567 PYR/PP interface [polypeptide binding]; other site 407976000568 TPP binding site [chemical binding]; other site 407976000569 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 407976000570 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 407976000571 TPP-binding site; other site 407976000572 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976000573 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976000574 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 407976000575 dimerization interface [polypeptide binding]; other site 407976000576 radical SAM peptide maturase, FibroRumin system; Region: rSAM_FibroRumin; TIGR04136 407976000577 cytochrome c nitrite reductase, pentaheme subunit; Region: cyt_nit_nrfB; TIGR03146 407976000578 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 407976000579 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 407976000580 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 407976000581 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 407976000582 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 407976000583 dimerization interface [polypeptide binding]; other site 407976000584 putative Zn2+ binding site [ion binding]; other site 407976000585 putative DNA binding site [nucleotide binding]; other site 407976000586 AsnC family; Region: AsnC_trans_reg; pfam01037 407976000587 Spore germination protein; Region: Spore_permease; cl17796 407976000588 putative transporter; Provisional; Region: PRK11021 407976000589 HDOD domain; Region: HDOD; pfam08668 407976000590 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 407976000591 putative metal binding site [ion binding]; other site 407976000592 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 407976000593 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 407976000594 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 407976000595 Sel1-like repeats; Region: SEL1; smart00671 407976000596 Cache domain; Region: Cache_1; pfam02743 407976000597 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 407976000598 dimerization interface [polypeptide binding]; other site 407976000599 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976000600 dimer interface [polypeptide binding]; other site 407976000601 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 407976000602 putative CheW interface [polypeptide binding]; other site 407976000603 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 407976000604 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976000605 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 407976000606 substrate binding pocket [chemical binding]; other site 407976000607 dimerization interface [polypeptide binding]; other site 407976000608 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 407976000609 multidrug efflux system protein MdtL; Provisional; Region: PRK10473 407976000610 putative substrate translocation pore; other site 407976000611 DTW domain; Region: DTW; cl01221 407976000612 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 407976000613 PAS domain; Region: PAS_9; pfam13426 407976000614 putative active site [active] 407976000615 heme pocket [chemical binding]; other site 407976000616 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976000617 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976000618 metal binding site [ion binding]; metal-binding site 407976000619 active site 407976000620 I-site; other site 407976000621 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 407976000622 Methyltransferase domain; Region: Methyltransf_23; pfam13489 407976000623 Methyltransferase domain; Region: Methyltransf_11; pfam08241 407976000624 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 407976000625 NIPSNAP; Region: NIPSNAP; pfam07978 407976000626 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 407976000627 dimerization interface [polypeptide binding]; other site 407976000628 putative DNA binding site [nucleotide binding]; other site 407976000629 putative Zn2+ binding site [ion binding]; other site 407976000630 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 407976000631 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 407976000632 metal binding site [ion binding]; metal-binding site 407976000633 putative dimer interface [polypeptide binding]; other site 407976000634 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976000635 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976000636 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976000637 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976000638 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976000639 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976000640 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976000641 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976000642 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976000643 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 407976000644 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 407976000645 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 407976000646 substrate binding pocket [chemical binding]; other site 407976000647 membrane-bound complex binding site; other site 407976000648 hinge residues; other site 407976000649 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 407976000650 EamA-like transporter family; Region: EamA; pfam00892 407976000651 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 407976000652 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976000653 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 407976000654 substrate binding pocket [chemical binding]; other site 407976000655 dimerization interface [polypeptide binding]; other site 407976000656 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 407976000657 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 407976000658 active site 407976000659 nucleophile elbow; other site 407976000660 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976000661 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976000662 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 407976000663 putative effector binding pocket; other site 407976000664 dimerization interface [polypeptide binding]; other site 407976000665 enterobactin receptor protein; Provisional; Region: PRK13483 407976000666 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 407976000667 N-terminal plug; other site 407976000668 ligand-binding site [chemical binding]; other site 407976000669 Sec63 Brl domain; Region: Sec63; pfam02889 407976000670 coproporphyrinogen III oxidase; Provisional; Region: PRK08629 407976000671 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 407976000672 FeS/SAM binding site; other site 407976000673 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 407976000674 Sodium Bile acid symporter family; Region: SBF; pfam01758 407976000675 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 407976000676 Sel1-like repeats; Region: SEL1; smart00671 407976000677 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 407976000678 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976000679 HAMP domain; Region: HAMP; pfam00672 407976000680 dimerization interface [polypeptide binding]; other site 407976000681 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976000682 dimer interface [polypeptide binding]; other site 407976000683 putative CheW interface [polypeptide binding]; other site 407976000684 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 407976000685 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 407976000686 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 407976000687 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 407976000688 [4Fe-4S] binding site [ion binding]; other site 407976000689 molybdopterin cofactor binding site; other site 407976000690 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 407976000691 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 407976000692 molybdopterin cofactor binding site; other site 407976000693 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 407976000694 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 407976000695 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 407976000696 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 407976000697 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 407976000698 [4Fe-4S] binding site [ion binding]; other site 407976000699 molybdopterin cofactor binding site; other site 407976000700 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 407976000701 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 407976000702 molybdopterin cofactor binding site; other site 407976000703 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 407976000704 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 407976000705 Ferredoxin [Energy production and conversion]; Region: COG1146 407976000706 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 407976000707 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 407976000708 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 407976000709 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 407976000710 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 407976000711 Helix-turn-helix domain; Region: HTH_17; pfam12728 407976000712 PBP superfamily domain; Region: PBP_like; pfam12727 407976000713 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 407976000714 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976000715 Coenzyme A binding pocket [chemical binding]; other site 407976000716 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976000717 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 407976000718 dimer interface [polypeptide binding]; other site 407976000719 phosphorylation site [posttranslational modification] 407976000720 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 407976000721 ATP binding site [chemical binding]; other site 407976000722 Mg2+ binding site [ion binding]; other site 407976000723 G-X-G motif; other site 407976000724 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976000725 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 407976000726 active site 407976000727 phosphorylation site [posttranslational modification] 407976000728 intermolecular recognition site; other site 407976000729 dimerization interface [polypeptide binding]; other site 407976000730 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 407976000731 DNA binding site [nucleotide binding] 407976000732 Predicted membrane protein [Function unknown]; Region: COG3212 407976000733 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 407976000734 Dihaem cytochrome c; Region: DHC; pfam09626 407976000735 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 407976000736 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 407976000737 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 407976000738 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 407976000739 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 407976000740 NAD(P) binding site [chemical binding]; other site 407976000741 catalytic residues [active] 407976000742 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 407976000743 GAF domain; Region: GAF; pfam01590 407976000744 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 407976000745 Walker A motif; other site 407976000746 ATP binding site [chemical binding]; other site 407976000747 Walker B motif; other site 407976000748 arginine finger; other site 407976000749 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976000750 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 407976000751 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 407976000752 NADP binding site [chemical binding]; other site 407976000753 dimer interface [polypeptide binding]; other site 407976000754 two-component sensor protein; Provisional; Region: cpxA; PRK09470 407976000755 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 407976000756 dimerization interface [polypeptide binding]; other site 407976000757 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 407976000758 dimer interface [polypeptide binding]; other site 407976000759 phosphorylation site [posttranslational modification] 407976000760 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 407976000761 ATP binding site [chemical binding]; other site 407976000762 Mg2+ binding site [ion binding]; other site 407976000763 G-X-G motif; other site 407976000764 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 407976000765 active site 407976000766 phosphorylation site [posttranslational modification] 407976000767 intermolecular recognition site; other site 407976000768 dimerization interface [polypeptide binding]; other site 407976000769 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 407976000770 DNA binding site [nucleotide binding] 407976000771 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 407976000772 dimer interface [polypeptide binding]; other site 407976000773 Cation efflux family; Region: Cation_efflux; cl00316 407976000774 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 407976000775 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 407976000776 nitrogen regulation protein NR(I); Provisional; Region: glnG; PRK10923 407976000777 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 407976000778 active site 407976000779 phosphorylation site [posttranslational modification] 407976000780 intermolecular recognition site; other site 407976000781 dimerization interface [polypeptide binding]; other site 407976000782 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 407976000783 Walker A motif; other site 407976000784 ATP binding site [chemical binding]; other site 407976000785 Walker B motif; other site 407976000786 arginine finger; other site 407976000787 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976000788 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 407976000789 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 407976000790 dimer interface [polypeptide binding]; other site 407976000791 phosphorylation site [posttranslational modification] 407976000792 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 407976000793 ATP binding site [chemical binding]; other site 407976000794 Mg2+ binding site [ion binding]; other site 407976000795 G-X-G motif; other site 407976000796 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 407976000797 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976000798 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 407976000799 putative C-terminal domain interface [polypeptide binding]; other site 407976000800 putative GSH binding site (G-site) [chemical binding]; other site 407976000801 putative dimer interface [polypeptide binding]; other site 407976000802 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 407976000803 N-terminal domain interface [polypeptide binding]; other site 407976000804 dimer interface [polypeptide binding]; other site 407976000805 substrate binding pocket (H-site) [chemical binding]; other site 407976000806 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 407976000807 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 407976000808 potential catalytic triad [active] 407976000809 conserved cys residue [active] 407976000810 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 407976000811 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 407976000812 dimer interface [polypeptide binding]; other site 407976000813 active site 407976000814 metal binding site [ion binding]; metal-binding site 407976000815 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976000816 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976000817 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 407976000818 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976000819 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976000820 dimer interface [polypeptide binding]; other site 407976000821 putative CheW interface [polypeptide binding]; other site 407976000822 5-histidylcysteine sulfoxide synthase; Region: ovoA_Nterm; TIGR04344 407976000823 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 407976000824 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 407976000825 S-adenosylmethionine binding site [chemical binding]; other site 407976000826 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 407976000827 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 407976000828 substrate binding site [chemical binding]; other site 407976000829 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 407976000830 ATP binding site [chemical binding]; other site 407976000831 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976000832 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976000833 metal binding site [ion binding]; metal-binding site 407976000834 active site 407976000835 I-site; other site 407976000836 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 407976000837 MOSC domain; Region: MOSC; pfam03473 407976000838 3-alpha domain; Region: 3-alpha; pfam03475 407976000839 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 407976000840 Cache domain; Region: Cache_1; pfam02743 407976000841 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 407976000842 dimerization interface [polypeptide binding]; other site 407976000843 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976000844 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976000845 dimer interface [polypeptide binding]; other site 407976000846 putative CheW interface [polypeptide binding]; other site 407976000847 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 407976000848 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 407976000849 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 407976000850 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 407976000851 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 407976000852 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 407976000853 FeS/SAM binding site; other site 407976000854 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 407976000855 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 407976000856 trimer interface [polypeptide binding]; other site 407976000857 dimer interface [polypeptide binding]; other site 407976000858 putative active site [active] 407976000859 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 407976000860 MoaE interaction surface [polypeptide binding]; other site 407976000861 MoeB interaction surface [polypeptide binding]; other site 407976000862 thiocarboxylated glycine; other site 407976000863 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 407976000864 MoaE homodimer interface [polypeptide binding]; other site 407976000865 MoaD interaction [polypeptide binding]; other site 407976000866 active site residues [active] 407976000867 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 407976000868 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 407976000869 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 407976000870 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 407976000871 dimer interface [polypeptide binding]; other site 407976000872 conserved gate region; other site 407976000873 putative PBP binding loops; other site 407976000874 ABC-ATPase subunit interface; other site 407976000875 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976000876 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 407976000877 Walker A/P-loop; other site 407976000878 ATP binding site [chemical binding]; other site 407976000879 Q-loop/lid; other site 407976000880 ABC transporter signature motif; other site 407976000881 Walker B; other site 407976000882 D-loop; other site 407976000883 H-loop/switch region; other site 407976000884 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976000885 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 407976000886 substrate binding pocket [chemical binding]; other site 407976000887 membrane-bound complex binding site; other site 407976000888 hinge residues; other site 407976000889 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 407976000890 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976000891 substrate binding pocket [chemical binding]; other site 407976000892 membrane-bound complex binding site; other site 407976000893 hinge residues; other site 407976000894 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 407976000895 dimer interface [polypeptide binding]; other site 407976000896 phosphorylation site [posttranslational modification] 407976000897 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 407976000898 ATP binding site [chemical binding]; other site 407976000899 Mg2+ binding site [ion binding]; other site 407976000900 G-X-G motif; other site 407976000901 Response regulator receiver domain; Region: Response_reg; pfam00072 407976000902 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 407976000903 active site 407976000904 phosphorylation site [posttranslational modification] 407976000905 intermolecular recognition site; other site 407976000906 dimerization interface [polypeptide binding]; other site 407976000907 Hpt domain; Region: Hpt; pfam01627 407976000908 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976000909 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 407976000910 active site 407976000911 phosphorylation site [posttranslational modification] 407976000912 intermolecular recognition site; other site 407976000913 dimerization interface [polypeptide binding]; other site 407976000914 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 407976000915 DNA binding residues [nucleotide binding] 407976000916 dimerization interface [polypeptide binding]; other site 407976000917 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976000918 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976000919 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976000920 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976000921 CS1 type fimbrial major subunit; Region: Fimbrial_CS1; cl04524 407976000922 putative fimbrial protein TcfA; Provisional; Region: PRK15308 407976000923 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 407976000924 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976000925 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 407976000926 active site 407976000927 phosphorylation site [posttranslational modification] 407976000928 intermolecular recognition site; other site 407976000929 dimerization interface [polypeptide binding]; other site 407976000930 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 407976000931 DNA binding site [nucleotide binding] 407976000932 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976000933 HAMP domain; Region: HAMP; pfam00672 407976000934 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 407976000935 dimer interface [polypeptide binding]; other site 407976000936 phosphorylation site [posttranslational modification] 407976000937 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 407976000938 ATP binding site [chemical binding]; other site 407976000939 Mg2+ binding site [ion binding]; other site 407976000940 G-X-G motif; other site 407976000941 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976000942 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976000943 active site 407976000944 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976000945 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976000946 metal binding site [ion binding]; metal-binding site 407976000947 active site 407976000948 I-site; other site 407976000949 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 407976000950 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976000951 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 407976000952 N-terminal plug; other site 407976000953 ligand-binding site [chemical binding]; other site 407976000954 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 407976000955 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976000956 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 407976000957 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK12489 407976000958 Domain of unknown function (DUF1864); Region: DUF1864; pfam08933 407976000959 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 407976000960 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 407976000961 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976000962 catalytic residue [active] 407976000963 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976000964 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 407976000965 glutamine synthetase; Provisional; Region: glnA; PRK09469 407976000966 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 407976000967 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 407976000968 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 407976000969 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 407976000970 G1 box; other site 407976000971 putative GEF interaction site [polypeptide binding]; other site 407976000972 GTP/Mg2+ binding site [chemical binding]; other site 407976000973 Switch I region; other site 407976000974 G2 box; other site 407976000975 G3 box; other site 407976000976 Switch II region; other site 407976000977 G4 box; other site 407976000978 G5 box; other site 407976000979 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 407976000980 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 407976000981 SnoaL-like domain; Region: SnoaL_3; pfam13474 407976000982 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976000983 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976000984 metal binding site [ion binding]; metal-binding site 407976000985 active site 407976000986 I-site; other site 407976000987 4Fe-4S binding domain; Region: Fer4_5; pfam12801 407976000988 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 407976000989 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 407976000990 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 407976000991 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 407976000992 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 407976000993 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 407976000994 homodimer interface [polypeptide binding]; other site 407976000995 substrate-cofactor binding pocket; other site 407976000996 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976000997 catalytic residue [active] 407976000998 Protein of unknown function (DUF2959); Region: DUF2959; pfam11172 407976000999 hypothetical protein; Reviewed; Region: PRK01637 407976001000 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 407976001001 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 407976001002 putative active site [active] 407976001003 dimerization interface [polypeptide binding]; other site 407976001004 putative tRNAtyr binding site [nucleotide binding]; other site 407976001005 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 407976001006 CoenzymeA binding site [chemical binding]; other site 407976001007 subunit interaction site [polypeptide binding]; other site 407976001008 PHB binding site; other site 407976001009 azoreductase; Reviewed; Region: PRK00170 407976001010 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 407976001011 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 407976001012 active site residue [active] 407976001013 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976001014 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 407976001015 non-specific DNA binding site [nucleotide binding]; other site 407976001016 salt bridge; other site 407976001017 sequence-specific DNA binding site [nucleotide binding]; other site 407976001018 Cupin domain; Region: Cupin_2; pfam07883 407976001019 Benzoate membrane transport protein; Region: BenE; pfam03594 407976001020 benzoate transporter; Region: benE; TIGR00843 407976001021 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976001022 Coenzyme A binding pocket [chemical binding]; other site 407976001023 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 407976001024 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 407976001025 dimer interface [polypeptide binding]; other site 407976001026 active site 407976001027 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 407976001028 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976001029 NAD(P) binding site [chemical binding]; other site 407976001030 active site 407976001031 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 407976001032 putative active site 1 [active] 407976001033 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 407976001034 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 407976001035 dimer interface [polypeptide binding]; other site 407976001036 active site 407976001037 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 407976001038 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 407976001039 Predicted exporter [General function prediction only]; Region: COG4258 407976001040 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 407976001041 active site 407976001042 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 407976001043 active sites [active] 407976001044 tetramer interface [polypeptide binding]; other site 407976001045 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 407976001046 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 407976001047 Ligand binding site; other site 407976001048 Putative Catalytic site; other site 407976001049 DXD motif; other site 407976001050 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 407976001051 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 407976001052 putative acyl-acceptor binding pocket; other site 407976001053 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 407976001054 active site 2 [active] 407976001055 dimer interface [polypeptide binding]; other site 407976001056 active site 1 [active] 407976001057 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 407976001058 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 407976001059 acyl-activating enzyme (AAE) consensus motif; other site 407976001060 AMP binding site [chemical binding]; other site 407976001061 active site 407976001062 CoA binding site [chemical binding]; other site 407976001063 Predicted membrane protein [Function unknown]; Region: COG4648 407976001064 acyl carrier protein; Provisional; Region: PRK05350 407976001065 Phosphopantetheine attachment site; Region: PP-binding; cl09936 407976001066 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 407976001067 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 407976001068 putative acyl-acceptor binding pocket; other site 407976001069 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 407976001070 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 407976001071 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 407976001072 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 407976001073 generic binding surface II; other site 407976001074 ssDNA binding site; other site 407976001075 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 407976001076 ATP binding site [chemical binding]; other site 407976001077 putative Mg++ binding site [ion binding]; other site 407976001078 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 407976001079 nucleotide binding region [chemical binding]; other site 407976001080 ATP-binding site [chemical binding]; other site 407976001081 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976001082 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 407976001083 active site 407976001084 phosphorylation site [posttranslational modification] 407976001085 intermolecular recognition site; other site 407976001086 dimerization interface [polypeptide binding]; other site 407976001087 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 407976001088 DNA binding residues [nucleotide binding] 407976001089 dimerization interface [polypeptide binding]; other site 407976001090 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 407976001091 Histidine kinase; Region: HisKA_3; pfam07730 407976001092 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 407976001093 ATP binding site [chemical binding]; other site 407976001094 Mg2+ binding site [ion binding]; other site 407976001095 G-X-G motif; other site 407976001096 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 407976001097 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 407976001098 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 407976001099 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 407976001100 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 407976001101 acyl-activating enzyme (AAE) consensus motif; other site 407976001102 putative AMP binding site [chemical binding]; other site 407976001103 putative active site [active] 407976001104 putative CoA binding site [chemical binding]; other site 407976001105 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 407976001106 homotrimer interaction site [polypeptide binding]; other site 407976001107 putative active site [active] 407976001108 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 407976001109 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976001110 Zn2+ binding site [ion binding]; other site 407976001111 Mg2+ binding site [ion binding]; other site 407976001112 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 407976001113 synthetase active site [active] 407976001114 NTP binding site [chemical binding]; other site 407976001115 metal binding site [ion binding]; metal-binding site 407976001116 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 407976001117 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 407976001118 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 407976001119 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 407976001120 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 407976001121 catalytic site [active] 407976001122 G-X2-G-X-G-K; other site 407976001123 ribonuclease E; Reviewed; Region: rne; PRK10811 407976001124 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 407976001125 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 407976001126 active site 407976001127 Phosphotransferase enzyme family; Region: APH; pfam01636 407976001128 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 407976001129 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 407976001130 putative substrate translocation pore; other site 407976001131 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976001132 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 407976001133 Fic family protein [Function unknown]; Region: COG3177 407976001134 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 407976001135 Fic/DOC family; Region: Fic; pfam02661 407976001136 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b1; cd09203 407976001137 PLD-like domain; Region: PLDc_2; pfam13091 407976001138 putative homodimer interface [polypeptide binding]; other site 407976001139 putative active site [active] 407976001140 catalytic site [active] 407976001141 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 407976001142 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 407976001143 ATP binding site [chemical binding]; other site 407976001144 putative Mg++ binding site [ion binding]; other site 407976001145 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 407976001146 nucleotide binding region [chemical binding]; other site 407976001147 ATP-binding site [chemical binding]; other site 407976001148 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 407976001149 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976001150 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976001151 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 407976001152 putative effector binding pocket; other site 407976001153 dimerization interface [polypeptide binding]; other site 407976001154 dUMP phosphatase; Provisional; Region: PRK09449 407976001155 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 407976001156 motif II; other site 407976001157 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 407976001158 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 407976001159 active site 407976001160 DNA binding site [nucleotide binding] 407976001161 Int/Topo IB signature motif; other site 407976001162 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 407976001163 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 407976001164 MPN+ (JAMM) motif; other site 407976001165 Zinc-binding site [ion binding]; other site 407976001166 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 407976001167 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 407976001168 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 407976001169 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976001170 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 407976001171 salt bridge; other site 407976001172 non-specific DNA binding site [nucleotide binding]; other site 407976001173 sequence-specific DNA binding site [nucleotide binding]; other site 407976001174 Helix-turn-helix; Region: HTH_3; pfam01381 407976001175 non-specific DNA binding site [nucleotide binding]; other site 407976001176 salt bridge; other site 407976001177 sequence-specific DNA binding site [nucleotide binding]; other site 407976001178 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 407976001179 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 407976001180 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 407976001181 ATP binding site [chemical binding]; other site 407976001182 putative Mg++ binding site [ion binding]; other site 407976001183 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 407976001184 HsdM N-terminal domain; Region: HsdM_N; pfam12161 407976001185 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 407976001186 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 407976001187 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976001188 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976001189 Walker A/P-loop; other site 407976001190 ATP binding site [chemical binding]; other site 407976001191 integrase; Provisional; Region: PRK09692 407976001192 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 407976001193 active site 407976001194 Int/Topo IB signature motif; other site 407976001195 hypothetical protein; Provisional; Region: PRK11820 407976001196 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 407976001197 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 407976001198 ribonuclease PH; Reviewed; Region: rph; PRK00173 407976001199 Ribonuclease PH; Region: RNase_PH_bact; cd11362 407976001200 hexamer interface [polypeptide binding]; other site 407976001201 active site 407976001202 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976001203 active site 407976001204 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 407976001205 GTP cyclohydrolase I; Provisional; Region: PLN03044 407976001206 active site 407976001207 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976001208 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976001209 division inhibitor protein; Provisional; Region: slmA; PRK09480 407976001210 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976001211 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 407976001212 trimer interface [polypeptide binding]; other site 407976001213 active site 407976001214 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 407976001215 Flavoprotein; Region: Flavoprotein; pfam02441 407976001216 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 407976001217 hypothetical protein; Reviewed; Region: PRK00024 407976001218 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 407976001219 MPN+ (JAMM) motif; other site 407976001220 Zinc-binding site [ion binding]; other site 407976001221 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 407976001222 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 407976001223 N-acetylglutamate synthase; Validated; Region: PRK05279 407976001224 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 407976001225 putative feedback inhibition sensing region; other site 407976001226 putative nucleotide binding site [chemical binding]; other site 407976001227 putative substrate binding site [chemical binding]; other site 407976001228 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976001229 Coenzyme A binding pocket [chemical binding]; other site 407976001230 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 407976001231 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 407976001232 CoenzymeA binding site [chemical binding]; other site 407976001233 subunit interaction site [polypeptide binding]; other site 407976001234 PHB binding site; other site 407976001235 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 407976001236 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 407976001237 ATP binding site [chemical binding]; other site 407976001238 putative Mg++ binding site [ion binding]; other site 407976001239 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 407976001240 nucleotide binding region [chemical binding]; other site 407976001241 ATP-binding site [chemical binding]; other site 407976001242 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 407976001243 HRDC domain; Region: HRDC; pfam00570 407976001244 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976001245 I-site; other site 407976001246 active site 407976001247 metal binding site [ion binding]; metal-binding site 407976001248 2-isopropylmalate synthase; Validated; Region: PRK00915 407976001249 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 407976001250 active site 407976001251 catalytic residues [active] 407976001252 metal binding site [ion binding]; metal-binding site 407976001253 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 407976001254 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 407976001255 tartrate dehydrogenase; Region: TTC; TIGR02089 407976001256 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 407976001257 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 407976001258 substrate binding site [chemical binding]; other site 407976001259 ligand binding site [chemical binding]; other site 407976001260 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 407976001261 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 407976001262 substrate binding site [chemical binding]; other site 407976001263 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 407976001264 glycerol kinase; Provisional; Region: glpK; PRK00047 407976001265 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 407976001266 N- and C-terminal domain interface [polypeptide binding]; other site 407976001267 active site 407976001268 MgATP binding site [chemical binding]; other site 407976001269 catalytic site [active] 407976001270 metal binding site [ion binding]; metal-binding site 407976001271 glycerol binding site [chemical binding]; other site 407976001272 homotetramer interface [polypeptide binding]; other site 407976001273 homodimer interface [polypeptide binding]; other site 407976001274 FBP binding site [chemical binding]; other site 407976001275 protein IIAGlc interface [polypeptide binding]; other site 407976001276 cell division protein MraZ; Reviewed; Region: PRK00326 407976001277 MraZ protein; Region: MraZ; pfam02381 407976001278 MraZ protein; Region: MraZ; pfam02381 407976001279 MraW methylase family; Region: Methyltransf_5; pfam01795 407976001280 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 407976001281 Cell division protein FtsL; Region: FtsL; pfam04999 407976001282 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 407976001283 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 407976001284 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 407976001285 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 407976001286 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 407976001287 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 407976001288 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 407976001289 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 407976001290 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 407976001291 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 407976001292 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 407976001293 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 407976001294 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 407976001295 Mg++ binding site [ion binding]; other site 407976001296 putative catalytic motif [active] 407976001297 putative substrate binding site [chemical binding]; other site 407976001298 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 407976001299 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 407976001300 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 407976001301 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 407976001302 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 407976001303 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 407976001304 active site 407976001305 homodimer interface [polypeptide binding]; other site 407976001306 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 407976001307 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 407976001308 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 407976001309 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 407976001310 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 407976001311 Cell division protein FtsQ; Region: FtsQ; pfam03799 407976001312 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 407976001313 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 407976001314 nucleotide binding site [chemical binding]; other site 407976001315 Cell division protein FtsA; Region: FtsA; pfam14450 407976001316 cell division protein FtsZ; Validated; Region: PRK09330 407976001317 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 407976001318 nucleotide binding site [chemical binding]; other site 407976001319 SulA interaction site; other site 407976001320 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 407976001321 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 407976001322 Protein of unknown function (DUF721); Region: DUF721; cl02324 407976001323 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 407976001324 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976001325 preprotein translocase subunit SecA; Reviewed; Region: PRK13107 407976001326 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 407976001327 SEC-C motif; Region: SEC-C; pfam02810 407976001328 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 407976001329 dimer interface [polypeptide binding]; other site 407976001330 allosteric magnesium binding site [ion binding]; other site 407976001331 active site 407976001332 aspartate-rich active site metal binding site; other site 407976001333 Schiff base residues; other site 407976001334 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 407976001335 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 407976001336 hypothetical protein; Region: PHA02277 407976001337 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976001338 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976001339 metal binding site [ion binding]; metal-binding site 407976001340 active site 407976001341 I-site; other site 407976001342 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 407976001343 active site 407976001344 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 407976001345 sec-independent translocase; Provisional; Region: PRK01770 407976001346 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 407976001347 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 407976001348 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 407976001349 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 407976001350 SCP-2 sterol transfer family; Region: SCP2; pfam02036 407976001351 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 407976001352 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 407976001353 S-adenosylmethionine binding site [chemical binding]; other site 407976001354 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 407976001355 putative active site [active] 407976001356 putative metal binding site [ion binding]; other site 407976001357 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 407976001358 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 407976001359 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 407976001360 active site 407976001361 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 407976001362 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 407976001363 Lipase. 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 process of...; Region: Lipase; cl14883 407976001364 nucleophilic elbow; other site 407976001365 catalytic triad; other site 407976001366 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 407976001367 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 407976001368 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 407976001369 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 407976001370 DHHA2 domain; Region: DHHA2; pfam02833 407976001371 Domain of unknown function (DUF386); Region: DUF386; cl01047 407976001372 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976001373 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 407976001374 N-terminal plug; other site 407976001375 ligand-binding site [chemical binding]; other site 407976001376 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 407976001377 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976001378 Pseudouridine synthase, a subgroup of the RluA family; Region: PSRA_1; cd02558 407976001379 probable active site [active] 407976001380 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 407976001381 metal binding site [ion binding]; metal-binding site 407976001382 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 407976001383 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 407976001384 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 407976001385 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 407976001386 NADP binding site [chemical binding]; other site 407976001387 active site 407976001388 putative substrate binding site [chemical binding]; other site 407976001389 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976001390 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 407976001391 ATP binding site [chemical binding]; other site 407976001392 Mg2+ binding site [ion binding]; other site 407976001393 G-X-G motif; other site 407976001394 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 407976001395 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 407976001396 active site 407976001397 phosphorylation site [posttranslational modification] 407976001398 intermolecular recognition site; other site 407976001399 dimerization interface [polypeptide binding]; other site 407976001400 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976001401 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 407976001402 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 407976001403 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 407976001404 active site 407976001405 Zn binding site [ion binding]; other site 407976001406 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976001407 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 407976001408 C factor cell-cell signaling protein; Provisional; Region: PRK09009 407976001409 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 407976001410 NADP binding site [chemical binding]; other site 407976001411 homodimer interface [polypeptide binding]; other site 407976001412 active site 407976001413 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 407976001414 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 407976001415 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 407976001416 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 407976001417 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 407976001418 Walker A motif; other site 407976001419 ATP binding site [chemical binding]; other site 407976001420 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 407976001421 Walker B motif; other site 407976001422 arginine finger; other site 407976001423 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 407976001424 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 407976001425 active site 407976001426 HslU subunit interaction site [polypeptide binding]; other site 407976001427 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 407976001428 RibD C-terminal domain; Region: RibD_C; cl17279 407976001429 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 407976001430 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 407976001431 active site 407976001432 phosphorylation site [posttranslational modification] 407976001433 intermolecular recognition site; other site 407976001434 dimerization interface [polypeptide binding]; other site 407976001435 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 407976001436 DNA binding residues [nucleotide binding] 407976001437 dimerization interface [polypeptide binding]; other site 407976001438 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 407976001439 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 407976001440 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 407976001441 ATP binding site [chemical binding]; other site 407976001442 Mg2+ binding site [ion binding]; other site 407976001443 G-X-G motif; other site 407976001444 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 407976001445 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 407976001446 octaheme c-type cytochrome, tetrathionate reductase family; Region: octaheme_Shew; TIGR04315 407976001447 Cytochrome c bacterial; Region: Cytochrome_cB; pfam11783 407976001448 Protein of unknown function (DUF3373); Region: DUF3373; pfam11853 407976001449 Cytochrome c; Region: Cytochrom_C; cl11414 407976001450 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 407976001451 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 407976001452 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 407976001453 substrate binding pocket [chemical binding]; other site 407976001454 membrane-bound complex binding site; other site 407976001455 hinge residues; other site 407976001456 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 407976001457 Sel1-like repeats; Region: SEL1; smart00671 407976001458 Sel1-like repeats; Region: SEL1; smart00671 407976001459 Sel1-like repeats; Region: SEL1; smart00671 407976001460 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 407976001461 Mechanosensitive ion channel; Region: MS_channel; pfam00924 407976001462 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 407976001463 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 407976001464 dimer interface [polypeptide binding]; other site 407976001465 active site 407976001466 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 407976001467 catalytic residues [active] 407976001468 substrate binding site [chemical binding]; other site 407976001469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 407976001470 uridine phosphorylase; Provisional; Region: PRK11178 407976001471 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 407976001472 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 407976001473 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 407976001474 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 407976001475 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 407976001476 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 407976001477 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 407976001478 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 407976001479 Sporulation related domain; Region: SPOR; pfam05036 407976001480 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 407976001481 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 407976001482 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 407976001483 active site 407976001484 HIGH motif; other site 407976001485 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 407976001486 KMSK motif region; other site 407976001487 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 407976001488 tRNA binding surface [nucleotide binding]; other site 407976001489 anticodon binding site; other site 407976001490 primosome assembly protein PriA; Validated; Region: PRK05580 407976001491 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 407976001492 ATP binding site [chemical binding]; other site 407976001493 putative Mg++ binding site [ion binding]; other site 407976001494 helicase superfamily c-terminal domain; Region: HELICc; smart00490 407976001495 FimV N-terminal domain; Region: FimV_core; TIGR03505 407976001496 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 407976001497 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 407976001498 Malic enzyme, N-terminal domain; Region: malic; pfam00390 407976001499 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 407976001500 putative NAD(P) binding site [chemical binding]; other site 407976001501 regulatory protein CsrD; Provisional; Region: PRK11059 407976001502 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976001503 metal binding site [ion binding]; metal-binding site 407976001504 active site 407976001505 I-site; other site 407976001506 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 407976001507 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 407976001508 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 407976001509 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 407976001510 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 407976001511 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 407976001512 Walker A motif; other site 407976001513 ATP binding site [chemical binding]; other site 407976001514 Walker B motif; other site 407976001515 arginine finger; other site 407976001516 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 407976001517 TPR motif; other site 407976001518 binding surface 407976001519 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 407976001520 binding surface 407976001521 TPR motif; other site 407976001522 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 407976001523 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 407976001524 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 407976001525 Walker A motif; other site 407976001526 ATP binding site [chemical binding]; other site 407976001527 Walker B motif; other site 407976001528 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 407976001529 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 407976001530 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 407976001531 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 407976001532 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 407976001533 VcfQ bacterial pilus biogenesis protein, lectin domain; Region: lectin_VcfQ; cd06900 407976001534 putative metal binding site [ion binding]; other site 407976001535 rod shape-determining protein MreB; Provisional; Region: PRK13927 407976001536 MreB and similar proteins; Region: MreB_like; cd10225 407976001537 nucleotide binding site [chemical binding]; other site 407976001538 Mg binding site [ion binding]; other site 407976001539 putative protofilament interaction site [polypeptide binding]; other site 407976001540 RodZ interaction site [polypeptide binding]; other site 407976001541 rod shape-determining protein MreC; Region: mreC; TIGR00219 407976001542 rod shape-determining protein MreC; Region: MreC; pfam04085 407976001543 rod shape-determining protein MreD; Region: MreD; cl01087 407976001544 Maf-like protein; Region: Maf; pfam02545 407976001545 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 407976001546 active site 407976001547 dimer interface [polypeptide binding]; other site 407976001548 ribonuclease G; Provisional; Region: PRK11712 407976001549 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 407976001550 homodimer interface [polypeptide binding]; other site 407976001551 oligonucleotide binding site [chemical binding]; other site 407976001552 TIGR02099 family protein; Region: TIGR02099 407976001553 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 407976001554 nitrilase; Region: PLN02798 407976001555 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 407976001556 putative active site [active] 407976001557 catalytic triad [active] 407976001558 dimer interface [polypeptide binding]; other site 407976001559 protease TldD; Provisional; Region: tldD; PRK10735 407976001560 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 407976001561 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 407976001562 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976001563 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976001564 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 407976001565 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 407976001566 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 407976001567 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 407976001568 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 407976001569 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 407976001570 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 407976001571 hypothetical protein; Provisional; Region: PRK05255 407976001572 peptidase PmbA; Provisional; Region: PRK11040 407976001573 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 407976001574 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 407976001575 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976001576 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 407976001577 substrate binding pocket [chemical binding]; other site 407976001578 membrane-bound complex binding site; other site 407976001579 hinge residues; other site 407976001580 Domain of unknown function; Region: DUF331; pfam03889 407976001581 fumarate hydratase; Reviewed; Region: fumC; PRK00485 407976001582 Class II fumarases; Region: Fumarase_classII; cd01362 407976001583 active site 407976001584 tetramer interface [polypeptide binding]; other site 407976001585 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 407976001586 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 407976001587 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 407976001588 FeS/SAM binding site; other site 407976001589 Uncharacterized conserved protein [Function unknown]; Region: COG2968 407976001590 oxidative stress defense protein; Provisional; Region: PRK11087 407976001591 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 407976001592 Methyltransferase domain; Region: Methyltransf_23; pfam13489 407976001593 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 407976001594 S-adenosylmethionine binding site [chemical binding]; other site 407976001595 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976001596 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976001597 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001598 nicotinamide riboside transporter PnuC; Provisional; Region: PRK15397 407976001599 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 407976001600 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 407976001601 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 407976001602 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 407976001603 ligand binding site [chemical binding]; other site 407976001604 flexible hinge region; other site 407976001605 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 407976001606 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 407976001607 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 407976001608 ATP binding site [chemical binding]; other site 407976001609 active site 407976001610 substrate binding site [chemical binding]; other site 407976001611 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_3; cd08896 407976001612 putative hydrophobic ligand binding site [chemical binding]; other site 407976001613 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 407976001614 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 407976001615 thiosulfate reductase PhsA; Provisional; Region: PRK15488 407976001616 The MopB_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_Thiosulfate-R-like; cd02755 407976001617 putative [Fe4-S4] binding site [ion binding]; other site 407976001618 putative molybdopterin cofactor binding site [chemical binding]; other site 407976001619 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 407976001620 putative molybdopterin cofactor binding site; other site 407976001621 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 407976001622 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 407976001623 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 407976001624 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 407976001625 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976001626 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox'...; Region: Met_repressor_MetJ; cd00490 407976001627 dimerization interface [polypeptide binding]; other site 407976001628 DNA binding site [nucleotide binding] 407976001629 corepressor binding sites; other site 407976001630 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 407976001631 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 407976001632 homodimer interface [polypeptide binding]; other site 407976001633 substrate-cofactor binding pocket; other site 407976001634 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976001635 catalytic residue [active] 407976001636 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 407976001637 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 407976001638 nucleotide binding site [chemical binding]; other site 407976001639 substrate binding site [chemical binding]; other site 407976001640 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 407976001641 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 407976001642 FAD binding site [chemical binding]; other site 407976001643 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976001644 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 407976001645 dimerization interface [polypeptide binding]; other site 407976001646 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976001647 dimer interface [polypeptide binding]; other site 407976001648 putative CheW interface [polypeptide binding]; other site 407976001649 transcriptional regulator SlyA; Provisional; Region: PRK03573 407976001650 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 407976001651 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 407976001652 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976001653 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976001654 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 407976001655 Cytochrome c; Region: Cytochrom_C; cl11414 407976001656 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 407976001657 Cytochrome c; Region: Cytochrom_C; pfam00034 407976001658 Cytochrome c [Energy production and conversion]; Region: COG3258 407976001659 Cytochrome c; Region: Cytochrom_C; pfam00034 407976001660 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 407976001661 RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_I; cd01646 407976001662 putative active site [active] 407976001663 putative NTP binding site [chemical binding]; other site 407976001664 putative nucleic acid binding site [nucleotide binding]; other site 407976001665 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 407976001666 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 407976001667 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 407976001668 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976001669 EamA-like transporter family; Region: EamA; pfam00892 407976001670 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 407976001671 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 407976001672 active site 407976001673 motif I; other site 407976001674 motif II; other site 407976001675 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 407976001676 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 407976001677 ATP binding site [chemical binding]; other site 407976001678 Mg++ binding site [ion binding]; other site 407976001679 motif III; other site 407976001680 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 407976001681 nucleotide binding region [chemical binding]; other site 407976001682 ATP-binding site [chemical binding]; other site 407976001683 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 407976001684 putative RNA binding site [nucleotide binding]; other site 407976001685 M28 Zn-Peptidases; Region: M28_like_2; cd05662 407976001686 Peptidase family M28; Region: Peptidase_M28; pfam04389 407976001687 metal binding site [ion binding]; metal-binding site 407976001688 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 407976001689 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 407976001690 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 407976001691 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 407976001692 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 407976001693 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976001694 putative substrate translocation pore; other site 407976001695 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 407976001696 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 407976001697 dimer interface [polypeptide binding]; other site 407976001698 ssDNA binding site [nucleotide binding]; other site 407976001699 tetramer (dimer of dimers) interface [polypeptide binding]; other site 407976001700 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 407976001701 DNA binding site [nucleotide binding] 407976001702 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 407976001703 active site 407976001704 catalytic residues [active] 407976001705 DNA binding site [nucleotide binding] 407976001706 Int/Topo IB signature motif; other site 407976001707 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4688 407976001708 chromosome segregation protein; Provisional; Region: PRK03918 407976001709 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 407976001710 AAA domain; Region: AAA_30; pfam13604 407976001711 Family description; Region: UvrD_C_2; pfam13538 407976001712 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976001713 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976001714 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001715 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 407976001716 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 407976001717 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 407976001718 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; cl17747 407976001719 Domain of unknown function (DUF1835); Region: DUF1835; pfam08874 407976001720 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976001721 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976001722 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001723 Domain of unknown function (DUF4354); Region: DUF4354; pfam14263 407976001724 Salmonella virulence plasmid 28.1kDa A protein; Region: VRP1; pfam03538 407976001725 Salmonella virulence plasmid 65kDa B protein; Region: SpvB; pfam03534 407976001726 Family description; Region: VCBS; pfam13517 407976001727 Insecticide toxin TcdB middle/N-terminal region; Region: TcdB_toxin_midN; pfam12256 407976001728 Insecticide toxin TcdB middle/C-terminal region; Region: TcdB_toxin_midC; pfam12255 407976001729 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 407976001730 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 407976001731 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 407976001732 Archaebacterial flagellin; Region: Arch_flagellin; cl00732 407976001733 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 407976001734 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 407976001735 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 407976001736 catalytic residues [active] 407976001737 catalytic nucleophile [active] 407976001738 Presynaptic Site I dimer interface [polypeptide binding]; other site 407976001739 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 407976001740 Synaptic Flat tetramer interface [polypeptide binding]; other site 407976001741 Synaptic Site I dimer interface [polypeptide binding]; other site 407976001742 DNA binding site [nucleotide binding] 407976001743 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 407976001744 DNA-binding interface [nucleotide binding]; DNA binding site 407976001745 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 407976001746 DNA binding site [nucleotide binding] 407976001747 Bacterial Ig-like domain (group 1); Region: BID_1; smart00634 407976001748 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 407976001749 Salmonella repeat of unknown function (DUF823); Region: DUF823; pfam05689 407976001750 Bacterial Ig-like domain (group 1); Region: BID_1; smart00634 407976001751 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976001752 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976001753 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001754 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001755 Bacterial Ig-like domain (group 1); Region: BID_1; smart00634 407976001756 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 407976001757 Salmonella repeat of unknown function (DUF823); Region: DUF823; pfam05689 407976001758 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 407976001759 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976001760 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976001761 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001762 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976001763 Walker A/P-loop; other site 407976001764 ATP binding site [chemical binding]; other site 407976001765 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 407976001766 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 407976001767 eyelet of channel; other site 407976001768 trimer interface [polypeptide binding]; other site 407976001769 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 407976001770 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 407976001771 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 407976001772 L-aspartate oxidase; Provisional; Region: PRK06175 407976001773 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 407976001774 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13554 407976001775 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 407976001776 Iron-sulfur protein interface; other site 407976001777 proximal heme binding site [chemical binding]; other site 407976001778 distal heme binding site [chemical binding]; other site 407976001779 dimer interface [polypeptide binding]; other site 407976001780 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 407976001781 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 407976001782 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 407976001783 Aspartase; Region: Aspartase; cd01357 407976001784 active sites [active] 407976001785 tetramer interface [polypeptide binding]; other site 407976001786 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 407976001787 active site 407976001788 homodimer interface [polypeptide binding]; other site 407976001789 homotetramer interface [polypeptide binding]; other site 407976001790 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976001791 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976001792 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976001793 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976001794 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976001795 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976001796 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976001797 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976001798 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 407976001799 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 407976001800 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 407976001801 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 407976001802 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976001803 catalytic residue [active] 407976001804 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976001805 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976001806 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 407976001807 Leucine rich repeat; Region: LRR_8; pfam13855 407976001808 Substrate binding site [chemical binding]; other site 407976001809 Leucine rich repeat; Region: LRR_8; pfam13855 407976001810 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 407976001811 Protein kinase domain; Region: Pkinase; pfam00069 407976001812 active site 407976001813 ATP binding site [chemical binding]; other site 407976001814 substrate binding site [chemical binding]; other site 407976001815 activation loop (A-loop); other site 407976001816 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976001817 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976001818 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976001819 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 407976001820 Sel1-like repeats; Region: SEL1; smart00671 407976001821 Peptidase family M9 N-terminal; Region: Peptidase_M9_N; pfam08453 407976001822 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 407976001823 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976001824 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976001825 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976001826 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 407976001827 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 407976001828 NAD(P) binding site [chemical binding]; other site 407976001829 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 407976001830 active site 407976001831 catalytic residues [active] 407976001832 galactokinase; Provisional; Region: PRK05101 407976001833 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 407976001834 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 407976001835 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 407976001836 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 407976001837 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 407976001838 TrkA-N domain; Region: TrkA_N; pfam02254 407976001839 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 407976001840 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 407976001841 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 407976001842 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 407976001843 DsbD alpha interface [polypeptide binding]; other site 407976001844 catalytic residues [active] 407976001845 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 407976001846 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 407976001847 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976001848 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976001849 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976001850 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976001851 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976001852 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 407976001853 putative effector binding pocket; other site 407976001854 dimerization interface [polypeptide binding]; other site 407976001855 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 407976001856 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 407976001857 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 407976001858 oligomerisation interface [polypeptide binding]; other site 407976001859 mobile loop; other site 407976001860 roof hairpin; other site 407976001861 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 407976001862 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 407976001863 ring oligomerisation interface [polypeptide binding]; other site 407976001864 ATP/Mg binding site [chemical binding]; other site 407976001865 stacking interactions; other site 407976001866 hinge regions; other site 407976001867 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976001868 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 407976001869 non-specific DNA binding site [nucleotide binding]; other site 407976001870 salt bridge; other site 407976001871 sequence-specific DNA binding site [nucleotide binding]; other site 407976001872 HipA N-terminal domain; Region: Couple_hipA; pfam13657 407976001873 HipA-like N-terminal domain; Region: HipA_N; pfam07805 407976001874 HipA-like C-terminal domain; Region: HipA_C; pfam07804 407976001875 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 407976001876 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 407976001877 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 407976001878 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976001879 ATP binding site [chemical binding]; other site 407976001880 Q-loop/lid; other site 407976001881 ABC transporter signature motif; other site 407976001882 Walker B; other site 407976001883 D-loop; other site 407976001884 H-loop/switch region; other site 407976001885 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976001886 Walker A/P-loop; other site 407976001887 ATP binding site [chemical binding]; other site 407976001888 Q-loop/lid; other site 407976001889 ABC transporter signature motif; other site 407976001890 Walker B; other site 407976001891 D-loop; other site 407976001892 H-loop/switch region; other site 407976001893 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 407976001894 Zn binding site [ion binding]; other site 407976001895 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 407976001896 catalytic residues [active] 407976001897 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 407976001898 DNA-binding site [nucleotide binding]; DNA binding site 407976001899 RNA-binding motif; other site 407976001900 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 407976001901 Predicted transcriptional regulators [Transcription]; Region: COG1695 407976001902 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 407976001903 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 407976001904 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 407976001905 putative active site [active] 407976001906 heme pocket [chemical binding]; other site 407976001907 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 407976001908 putative active site [active] 407976001909 heme pocket [chemical binding]; other site 407976001910 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976001911 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976001912 metal binding site [ion binding]; metal-binding site 407976001913 active site 407976001914 I-site; other site 407976001915 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 407976001916 dimer interface [polypeptide binding]; other site 407976001917 Alkaline phosphatase homologues; Region: alkPPc; smart00098 407976001918 active site 407976001919 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 407976001920 dimer interface [polypeptide binding]; other site 407976001921 Alkaline phosphatase homologues; Region: alkPPc; smart00098 407976001922 active site 407976001923 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 407976001924 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976001925 Helix-turn-helix domain; Region: HTH_18; pfam12833 407976001926 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976001927 LysE type translocator; Region: LysE; cl00565 407976001928 GAF domain; Region: GAF; pfam01590 407976001929 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976001930 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976001931 metal binding site [ion binding]; metal-binding site 407976001932 active site 407976001933 I-site; other site 407976001934 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 407976001935 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 407976001936 active site 407976001937 lipoprotein; Provisional; Region: PRK11443 407976001938 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 407976001939 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 407976001940 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 407976001941 ATP binding site [chemical binding]; other site 407976001942 Transposase; Region: HTH_Tnp_1; cl17663 407976001943 putative outer membrane lipoprotein; Provisional; Region: PRK10510 407976001944 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976001945 ligand binding site [chemical binding]; other site 407976001946 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 407976001947 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional; Region: PRK03537 407976001948 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 407976001949 MgtE intracellular N domain; Region: MgtE_N; smart00924 407976001950 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 407976001951 Divalent cation transporter; Region: MgtE; pfam01769 407976001952 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 407976001953 dimerization domain swap beta strand [polypeptide binding]; other site 407976001954 regulatory protein interface [polypeptide binding]; other site 407976001955 active site 407976001956 regulatory phosphorylation site [posttranslational modification]; other site 407976001957 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 407976001958 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG1102 407976001959 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 407976001960 active site 407976001961 phosphorylation site [posttranslational modification] 407976001962 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 407976001963 30S subunit binding site; other site 407976001964 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 407976001965 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 407976001966 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 407976001967 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 407976001968 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 407976001969 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 407976001970 Walker A/P-loop; other site 407976001971 ATP binding site [chemical binding]; other site 407976001972 Q-loop/lid; other site 407976001973 ABC transporter signature motif; other site 407976001974 Walker B; other site 407976001975 D-loop; other site 407976001976 H-loop/switch region; other site 407976001977 OstA-like protein; Region: OstA; cl00844 407976001978 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 407976001979 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 407976001980 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 407976001981 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 407976001982 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 407976001983 active site 407976001984 motif I; other site 407976001985 motif II; other site 407976001986 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 407976001987 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 407976001988 putative active site [active] 407976001989 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 407976001990 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 407976001991 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 407976001992 Walker A/P-loop; other site 407976001993 ATP binding site [chemical binding]; other site 407976001994 Q-loop/lid; other site 407976001995 ABC transporter signature motif; other site 407976001996 Walker B; other site 407976001997 D-loop; other site 407976001998 H-loop/switch region; other site 407976001999 conserved hypothetical integral membrane protein; Region: TIGR00056 407976002000 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 407976002001 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 407976002002 mce related protein; Region: MCE; pfam02470 407976002003 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 407976002004 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 407976002005 anti sigma factor interaction site; other site 407976002006 regulatory phosphorylation site [posttranslational modification]; other site 407976002007 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 407976002008 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 407976002009 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 407976002010 hinge; other site 407976002011 active site 407976002012 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 407976002013 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 407976002014 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 407976002015 protein binding site [polypeptide binding]; other site 407976002016 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 407976002017 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 407976002018 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 407976002019 protein binding site [polypeptide binding]; other site 407976002020 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 407976002021 Predicted ATPase [General function prediction only]; Region: COG1485 407976002022 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 407976002023 23S rRNA interface [nucleotide binding]; other site 407976002024 L3 interface [polypeptide binding]; other site 407976002025 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 407976002026 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 407976002027 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 407976002028 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 407976002029 GDP-binding site [chemical binding]; other site 407976002030 ACT binding site; other site 407976002031 IMP binding site; other site 407976002032 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 407976002033 Sel1-like repeats; Region: SEL1; smart00671 407976002034 exoribonuclease R; Provisional; Region: PRK11642 407976002035 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 407976002036 RNB domain; Region: RNB; pfam00773 407976002037 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 407976002038 RNA binding site [nucleotide binding]; other site 407976002039 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 407976002040 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 407976002041 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 407976002042 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 407976002043 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976002044 putative substrate translocation pore; other site 407976002045 Protein of unknown function, DUF481; Region: DUF481; pfam04338 407976002046 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 407976002047 primosomal replication protein N; Provisional; Region: PRK02801 407976002048 generic binding surface II; other site 407976002049 generic binding surface I; other site 407976002050 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 407976002051 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 407976002052 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 407976002053 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 407976002054 Peptidase S46; Region: Peptidase_S46; pfam10459 407976002055 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 407976002056 replicative DNA helicase; Provisional; Region: PRK08006 407976002057 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 407976002058 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 407976002059 Walker A motif; other site 407976002060 ATP binding site [chemical binding]; other site 407976002061 Walker B motif; other site 407976002062 DNA binding loops [nucleotide binding] 407976002063 alanine racemase; Reviewed; Region: alr; PRK00053 407976002064 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 407976002065 active site 407976002066 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 407976002067 substrate binding site [chemical binding]; other site 407976002068 catalytic residues [active] 407976002069 dimer interface [polypeptide binding]; other site 407976002070 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 407976002071 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 407976002072 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 407976002073 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 407976002074 N-terminal plug; other site 407976002075 ligand-binding site [chemical binding]; other site 407976002076 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 407976002077 Gram-negative bacterial tonB protein; Region: TonB; cl10048 407976002078 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 407976002079 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976002080 Coenzyme A binding pocket [chemical binding]; other site 407976002081 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 407976002082 Ead/Ea22-like protein; Region: Ead_Ea22; pfam13935 407976002083 Protein of unknown function (DUF1317); Region: DUF1317; pfam07026 407976002084 Pyocin activator protein PrtN; Region: PyocinActivator; pfam11112 407976002085 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cd00350 407976002086 iron binding site [ion binding]; other site 407976002087 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 407976002088 active site 407976002089 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976002090 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976002091 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976002092 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 407976002093 non-specific DNA binding site [nucleotide binding]; other site 407976002094 salt bridge; other site 407976002095 Predicted transcriptional regulator [Transcription]; Region: COG2932 407976002096 sequence-specific DNA binding site [nucleotide binding]; other site 407976002097 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 407976002098 Catalytic site [active] 407976002099 DNA-binding transcriptional regulator DicC; Provisional; Region: PRK09744 407976002100 Helix-turn-helix domain; Region: HTH_36; pfam13730 407976002101 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 407976002102 Replication protein P; Region: Phage_lambda_P; pfam06992 407976002103 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 407976002104 active site 407976002105 DNA binding site [nucleotide binding] 407976002106 Int/Topo IB signature motif; other site 407976002107 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976002108 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 407976002109 non-specific DNA binding site [nucleotide binding]; other site 407976002110 salt bridge; other site 407976002111 sequence-specific DNA binding site [nucleotide binding]; other site 407976002112 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 407976002113 catalytic site [active] 407976002114 putative active site [active] 407976002115 putative substrate binding site [chemical binding]; other site 407976002116 dimer interface [polypeptide binding]; other site 407976002117 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 407976002118 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 407976002119 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 407976002120 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 407976002121 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 407976002122 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 407976002123 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 407976002124 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 407976002125 oligomer interface [polypeptide binding]; other site 407976002126 active site residues [active] 407976002127 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 407976002128 Uncharacterized conserved protein (DUF2190); Region: DUF2190; pfam09956 407976002129 tape measure domain; Region: tape_meas_nterm; TIGR02675 407976002130 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976002131 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 407976002132 active site 407976002133 DNA binding site [nucleotide binding] 407976002134 Int/Topo IB signature motif; other site 407976002135 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 407976002136 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 407976002137 FMN binding site [chemical binding]; other site 407976002138 active site 407976002139 catalytic residues [active] 407976002140 substrate binding site [chemical binding]; other site 407976002141 PspC domain; Region: PspC; pfam04024 407976002142 enoyl-CoA hydratase; Provisional; Region: PRK06688 407976002143 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 407976002144 substrate binding site [chemical binding]; other site 407976002145 oxyanion hole (OAH) forming residues; other site 407976002146 trimer interface [polypeptide binding]; other site 407976002147 Protein of unknown function (DUF461); Region: DUF461; pfam04314 407976002148 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; pfam10095 407976002149 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 407976002150 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 407976002151 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 407976002152 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 407976002153 dimer interface [polypeptide binding]; other site 407976002154 ADP-ribose binding site [chemical binding]; other site 407976002155 active site 407976002156 nudix motif; other site 407976002157 metal binding site [ion binding]; metal-binding site 407976002158 Protein of unknown function (DUF1249); Region: DUF1249; pfam06853 407976002159 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 407976002160 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 407976002161 active site 407976002162 metal binding site [ion binding]; metal-binding site 407976002163 hexamer interface [polypeptide binding]; other site 407976002164 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 407976002165 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 407976002166 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 407976002167 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 407976002168 ATP binding site [chemical binding]; other site 407976002169 Mg2+ binding site [ion binding]; other site 407976002170 G-X-G motif; other site 407976002171 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 407976002172 anchoring element; other site 407976002173 dimer interface [polypeptide binding]; other site 407976002174 ATP binding site [chemical binding]; other site 407976002175 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 407976002176 active site 407976002177 metal binding site [ion binding]; metal-binding site 407976002178 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 407976002179 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 407976002180 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 407976002181 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 407976002182 CAP-like domain; other site 407976002183 active site 407976002184 primary dimer interface [polypeptide binding]; other site 407976002185 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 407976002186 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 407976002187 eyelet of channel; other site 407976002188 trimer interface [polypeptide binding]; other site 407976002189 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 407976002190 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 407976002191 eyelet of channel; other site 407976002192 trimer interface [polypeptide binding]; other site 407976002193 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 407976002194 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 407976002195 putative ATP binding site [chemical binding]; other site 407976002196 putative substrate interface [chemical binding]; other site 407976002197 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 407976002198 ATP binding site [chemical binding]; other site 407976002199 Mg2+ binding site [ion binding]; other site 407976002200 G-X-G motif; other site 407976002201 Superinfection exclusion protein B; Region: SieB; pfam14163 407976002202 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 407976002203 HAMP domain; Region: HAMP; pfam00672 407976002204 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976002205 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976002206 dimer interface [polypeptide binding]; other site 407976002207 putative CheW interface [polypeptide binding]; other site 407976002208 Hemerythrin; Region: Hemerythrin; cd12107 407976002209 Fe binding site [ion binding]; other site 407976002210 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 407976002211 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976002212 Walker A/P-loop; other site 407976002213 ATP binding site [chemical binding]; other site 407976002214 Q-loop/lid; other site 407976002215 ABC transporter signature motif; other site 407976002216 Walker B; other site 407976002217 D-loop; other site 407976002218 H-loop/switch region; other site 407976002219 TOBE domain; Region: TOBE; cl01440 407976002220 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 407976002221 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 407976002222 dimer interface [polypeptide binding]; other site 407976002223 conserved gate region; other site 407976002224 putative PBP binding loops; other site 407976002225 ABC-ATPase subunit interface; other site 407976002226 molybdate transporter periplasmic protein; Provisional; Region: modA; PRK10677 407976002227 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 407976002228 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 407976002229 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 407976002230 molybdenum-pterin binding domain; Region: Mop; TIGR00638 407976002231 TOBE domain; Region: TOBE; cl01440 407976002232 macrolide transporter subunit MacA; Provisional; Region: PRK11578 407976002233 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976002234 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976002235 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 407976002236 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 407976002237 Walker A/P-loop; other site 407976002238 ATP binding site [chemical binding]; other site 407976002239 Q-loop/lid; other site 407976002240 ABC transporter signature motif; other site 407976002241 Walker B; other site 407976002242 D-loop; other site 407976002243 H-loop/switch region; other site 407976002244 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 407976002245 FtsX-like permease family; Region: FtsX; pfam02687 407976002246 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 407976002247 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_2; cd06160 407976002248 Peptidase family M50; Region: Peptidase_M50; pfam02163 407976002249 active site 407976002250 putative substrate binding region [chemical binding]; other site 407976002251 protein structure with unknown function; Region: DUF4144; pfam13642 407976002252 Protein of unknown function (DUF342); Region: DUF342; pfam03961 407976002253 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 407976002254 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 407976002255 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 407976002256 S-adenosylmethionine binding site [chemical binding]; other site 407976002257 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 407976002258 dimer interface [polypeptide binding]; other site 407976002259 Alkaline phosphatase homologues; Region: alkPPc; smart00098 407976002260 active site 407976002261 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 407976002262 glutathione synthetase; Provisional; Region: PRK05246 407976002263 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 407976002264 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 407976002265 RNA methyltransferase, RsmE family; Region: TIGR00046 407976002266 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 407976002267 Endonuclease I [DNA replication, recombination, and repair]; Region: EndA; COG2356 407976002268 hypothetical protein; Provisional; Region: PRK04860 407976002269 Zn-dependent metalloprotease, SprT family [General function prediction only]; Region: SprT; COG3091 407976002270 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cl00237 407976002271 putative substrate binding pocket [chemical binding]; other site 407976002272 AC domain interface; other site 407976002273 catalytic triad [active] 407976002274 AB domain interface; other site 407976002275 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 407976002276 LysR family transcriptional regulator; Provisional; Region: PRK14997 407976002277 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976002278 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 407976002279 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 407976002280 putative effector binding pocket; other site 407976002281 dimerization interface [polypeptide binding]; other site 407976002282 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 407976002283 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 407976002284 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 407976002285 ATP-grasp domain; Region: ATP-grasp_4; cl17255 407976002286 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 407976002287 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 407976002288 carboxyltransferase (CT) interaction site; other site 407976002289 biotinylation site [posttranslational modification]; other site 407976002290 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976002291 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976002292 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976002293 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 407976002294 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 407976002295 substrate binding pocket [chemical binding]; other site 407976002296 membrane-bound complex binding site; other site 407976002297 hinge residues; other site 407976002298 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976002299 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976002300 metal binding site [ion binding]; metal-binding site 407976002301 active site 407976002302 I-site; other site 407976002303 elongation factor G; Reviewed; Region: PRK00007 407976002304 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 407976002305 G1 box; other site 407976002306 putative GEF interaction site [polypeptide binding]; other site 407976002307 GTP/Mg2+ binding site [chemical binding]; other site 407976002308 Switch I region; other site 407976002309 G2 box; other site 407976002310 G3 box; other site 407976002311 Switch II region; other site 407976002312 G4 box; other site 407976002313 G5 box; other site 407976002314 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 407976002315 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cl02789 407976002316 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 407976002317 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976002318 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976002319 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 407976002320 putative dimerization interface [polypeptide binding]; other site 407976002321 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 407976002322 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 407976002323 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 407976002324 [4Fe-4S] binding site [ion binding]; other site 407976002325 molybdopterin cofactor binding site; other site 407976002326 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 407976002327 molybdopterin cofactor binding site; other site 407976002328 NapD protein; Region: NapD; pfam03927 407976002329 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 407976002330 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 407976002331 hypothetical protein; Provisional; Region: PRK10506 407976002332 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 407976002333 Type II transport protein GspH; Region: GspH; pfam12019 407976002334 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 407976002335 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 407976002336 FtsX-like permease family; Region: FtsX; pfam02687 407976002337 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 407976002338 FtsX-like permease family; Region: FtsX; pfam02687 407976002339 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 407976002340 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 407976002341 Walker A/P-loop; other site 407976002342 ATP binding site [chemical binding]; other site 407976002343 Q-loop/lid; other site 407976002344 ABC transporter signature motif; other site 407976002345 Walker B; other site 407976002346 D-loop; other site 407976002347 H-loop/switch region; other site 407976002348 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 407976002349 amino acid carrier protein; Region: agcS; TIGR00835 407976002350 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 407976002351 PAS domain; Region: PAS_9; pfam13426 407976002352 PAS domain S-box; Region: sensory_box; TIGR00229 407976002353 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 407976002354 putative active site [active] 407976002355 heme pocket [chemical binding]; other site 407976002356 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 407976002357 PAS fold; Region: PAS_3; pfam08447 407976002358 putative active site [active] 407976002359 heme pocket [chemical binding]; other site 407976002360 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 407976002361 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 407976002362 putative active site [active] 407976002363 heme pocket [chemical binding]; other site 407976002364 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 407976002365 putative active site [active] 407976002366 heme pocket [chemical binding]; other site 407976002367 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 407976002368 dimer interface [polypeptide binding]; other site 407976002369 phosphorylation site [posttranslational modification] 407976002370 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 407976002371 ATP binding site [chemical binding]; other site 407976002372 Mg2+ binding site [ion binding]; other site 407976002373 G-X-G motif; other site 407976002374 Response regulator receiver domain; Region: Response_reg; pfam00072 407976002375 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 407976002376 active site 407976002377 phosphorylation site [posttranslational modification] 407976002378 intermolecular recognition site; other site 407976002379 dimerization interface [polypeptide binding]; other site 407976002380 Response regulator receiver domain; Region: Response_reg; pfam00072 407976002381 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 407976002382 active site 407976002383 phosphorylation site [posttranslational modification] 407976002384 intermolecular recognition site; other site 407976002385 dimerization interface [polypeptide binding]; other site 407976002386 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 407976002387 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 407976002388 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 407976002389 active site 407976002390 phosphorylation site [posttranslational modification] 407976002391 intermolecular recognition site; other site 407976002392 dimerization interface [polypeptide binding]; other site 407976002393 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976002394 Zn2+ binding site [ion binding]; other site 407976002395 Mg2+ binding site [ion binding]; other site 407976002396 putative global regulator; Reviewed; Region: PRK09559 407976002397 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 407976002398 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 407976002399 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 407976002400 ligand binding site [chemical binding]; other site 407976002401 NAD binding site [chemical binding]; other site 407976002402 tetramer interface [polypeptide binding]; other site 407976002403 catalytic site [active] 407976002404 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 407976002405 L-serine binding site [chemical binding]; other site 407976002406 ACT domain interface; other site 407976002407 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 407976002408 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976002409 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 407976002410 DNA binding residues [nucleotide binding] 407976002411 dimerization interface [polypeptide binding]; other site 407976002412 major curlin subunit; Provisional; Region: csgA; PRK10051 407976002413 Curlin associated repeat; Region: Curlin_rpt; pfam07012 407976002414 Curlin associated repeat; Region: Curlin_rpt; pfam07012 407976002415 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 407976002416 Curlin associated repeat; Region: Curlin_rpt; pfam07012 407976002417 Curlin associated repeat; Region: Curlin_rpt; pfam07012 407976002418 Curlin associated repeat; Region: Curlin_rpt; pfam07012 407976002419 Curlin associated repeat; Region: Curlin_rpt; pfam07012 407976002420 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 407976002421 Pantoate-beta-alanine ligase; Region: PanC; cd00560 407976002422 pantoate--beta-alanine ligase; Region: panC; TIGR00018 407976002423 active site 407976002424 ATP-binding site [chemical binding]; other site 407976002425 pantoate-binding site; other site 407976002426 HXXH motif; other site 407976002427 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 407976002428 oligomerization interface [polypeptide binding]; other site 407976002429 active site 407976002430 metal binding site [ion binding]; metal-binding site 407976002431 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 407976002432 catalytic center binding site [active] 407976002433 ATP binding site [chemical binding]; other site 407976002434 poly(A) polymerase; Region: pcnB; TIGR01942 407976002435 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 407976002436 active site 407976002437 NTP binding site [chemical binding]; other site 407976002438 metal binding triad [ion binding]; metal-binding site 407976002439 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 407976002440 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 407976002441 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 407976002442 active site 407976002443 nucleotide binding site [chemical binding]; other site 407976002444 HIGH motif; other site 407976002445 KMSKS motif; other site 407976002446 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 407976002447 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 407976002448 aminopeptidase B; Provisional; Region: PRK05015 407976002449 Peptidase; Region: DUF3663; pfam12404 407976002450 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; cl08294 407976002451 interface (dimer of trimers) [polypeptide binding]; other site 407976002452 Substrate-binding/catalytic site; other site 407976002453 Zn-binding sites [ion binding]; other site 407976002454 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976002455 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976002456 Coenzyme A binding pocket [chemical binding]; other site 407976002457 phosphoribulokinase; Provisional; Region: PRK15453 407976002458 active site 407976002459 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 407976002460 putative hydrolase; Provisional; Region: PRK10985 407976002461 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 407976002462 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 407976002463 Transcriptional activator [Transcription]; Region: ChrR; COG3806 407976002464 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 407976002465 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 407976002466 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 407976002467 classical (c) SDRs; Region: SDR_c; cd05233 407976002468 NAD(P) binding site [chemical binding]; other site 407976002469 active site 407976002470 Predicted transcriptional regulators [Transcription]; Region: COG1733 407976002471 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 407976002472 Uncharacterized conserved protein [Function unknown]; Region: COG3791 407976002473 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 407976002474 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 407976002475 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976002476 Walker A/P-loop; other site 407976002477 ATP binding site [chemical binding]; other site 407976002478 Q-loop/lid; other site 407976002479 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976002480 ABC transporter; Region: ABC_tran_2; pfam12848 407976002481 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976002482 Probable metal-binding protein (DUF2387); Region: DUF2387; pfam09526 407976002483 short chain dehydrogenase; Provisional; Region: PRK07478 407976002484 classical (c) SDRs; Region: SDR_c; cd05233 407976002485 NAD(P) binding site [chemical binding]; other site 407976002486 active site 407976002487 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 407976002488 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976002489 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 407976002490 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 407976002491 DNA binding site [nucleotide binding] 407976002492 active site 407976002493 Pirin-related protein [General function prediction only]; Region: COG1741 407976002494 Pirin; Region: Pirin; pfam02678 407976002495 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 407976002496 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 407976002497 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 407976002498 ATP binding site [chemical binding]; other site 407976002499 Mg++ binding site [ion binding]; other site 407976002500 motif III; other site 407976002501 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 407976002502 nucleotide binding region [chemical binding]; other site 407976002503 ATP-binding site [chemical binding]; other site 407976002504 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 407976002505 putative RNA binding site [nucleotide binding]; other site 407976002506 putative transposase OrfB; Reviewed; Region: PHA02517 407976002507 Integrase core domain; Region: rve; pfam00665 407976002508 Integrase core domain; Region: rve_3; pfam13683 407976002509 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 407976002510 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 407976002511 ATP binding site [chemical binding]; other site 407976002512 Mg++ binding site [ion binding]; other site 407976002513 motif III; other site 407976002514 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 407976002515 nucleotide binding region [chemical binding]; other site 407976002516 ATP-binding site [chemical binding]; other site 407976002517 Protein of unknown function (DUF3626); Region: DUF3626; pfam12294 407976002518 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 407976002519 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976002520 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976002521 Walker A/P-loop; other site 407976002522 ATP binding site [chemical binding]; other site 407976002523 Q-loop/lid; other site 407976002524 ABC transporter signature motif; other site 407976002525 Walker B; other site 407976002526 D-loop; other site 407976002527 H-loop/switch region; other site 407976002528 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 407976002529 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976002530 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976002531 Walker A/P-loop; other site 407976002532 ATP binding site [chemical binding]; other site 407976002533 Q-loop/lid; other site 407976002534 ABC transporter signature motif; other site 407976002535 Walker B; other site 407976002536 D-loop; other site 407976002537 H-loop/switch region; other site 407976002538 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 407976002539 putative active site [active] 407976002540 putative metal binding residues [ion binding]; other site 407976002541 signature motif; other site 407976002542 putative triphosphate binding site [ion binding]; other site 407976002543 dimer interface [polypeptide binding]; other site 407976002544 Helix-turn-helix domain; Region: HTH_17; pfam12728 407976002545 Protein of unknown function, DUF599; Region: DUF599; pfam04654 407976002546 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 407976002547 Proline dehydrogenase; Region: Pro_dh; pfam01619 407976002548 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 407976002549 Glutamate binding site [chemical binding]; other site 407976002550 NAD binding site [chemical binding]; other site 407976002551 catalytic residues [active] 407976002552 Bacterial SH3 domain homologues; Region: SH3b; smart00287 407976002553 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 407976002554 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 407976002555 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 407976002556 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 407976002557 Uncharacterized conserved protein [Function unknown]; Region: COG3025 407976002558 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 407976002559 putative active site [active] 407976002560 putative metal binding residues [ion binding]; other site 407976002561 signature motif; other site 407976002562 putative triphosphate binding site [ion binding]; other site 407976002563 Ion channel; Region: Ion_trans_2; pfam07885 407976002564 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 407976002565 Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]; Region: PspA; COG1842 407976002566 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; pfam09938 407976002567 spermidine synthase; Provisional; Region: PRK03612 407976002568 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 407976002569 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 407976002570 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 407976002571 metal binding triad; other site 407976002572 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 407976002573 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 407976002574 metal binding triad; other site 407976002575 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976002576 GAF domain; Region: GAF; pfam01590 407976002577 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976002578 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976002579 metal binding site [ion binding]; metal-binding site 407976002580 active site 407976002581 I-site; other site 407976002582 Domain of unknown function (DUF897); Region: DUF897; pfam05982 407976002583 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976002584 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976002585 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 407976002586 dimerization interface [polypeptide binding]; other site 407976002587 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 407976002588 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976002589 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 407976002590 dimerization interface [polypeptide binding]; other site 407976002591 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976002592 dimer interface [polypeptide binding]; other site 407976002593 putative CheW interface [polypeptide binding]; other site 407976002594 Predicted ATPase [General function prediction only]; Region: COG1485 407976002595 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976002596 Walker A/P-loop; other site 407976002597 ATP binding site [chemical binding]; other site 407976002598 ABC transporter signature motif; other site 407976002599 Walker B; other site 407976002600 D-loop; other site 407976002601 H-loop/switch region; other site 407976002602 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 407976002603 Phosphate-selective porin [Inorganic ion transport and metabolism]; Region: OprP; COG3746 407976002604 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 407976002605 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 407976002606 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 407976002607 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 407976002608 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 407976002609 PAS domain; Region: PAS; smart00091 407976002610 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 407976002611 ATP binding site [chemical binding]; other site 407976002612 Mg2+ binding site [ion binding]; other site 407976002613 G-X-G motif; other site 407976002614 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 407976002615 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 407976002616 active site 407976002617 phosphorylation site [posttranslational modification] 407976002618 intermolecular recognition site; other site 407976002619 dimerization interface [polypeptide binding]; other site 407976002620 Transcriptional regulator; Region: CitT; pfam12431 407976002621 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 407976002622 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976002623 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976002624 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976002625 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976002626 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 407976002627 putative active site [active] 407976002628 Zn binding site [ion binding]; other site 407976002629 L,D-transpeptidase; Provisional; Region: PRK10260 407976002630 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976002631 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 407976002632 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 407976002633 potassium/proton antiporter; Reviewed; Region: PRK05326 407976002634 TrkA-C domain; Region: TrkA_C; pfam02080 407976002635 Transporter associated domain; Region: CorC_HlyC; smart01091 407976002636 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 407976002637 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 407976002638 putative acyl-acceptor binding pocket; other site 407976002639 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 407976002640 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 407976002641 putative ribose interaction site [chemical binding]; other site 407976002642 putative ADP binding site [chemical binding]; other site 407976002643 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 407976002644 active site 407976002645 HIGH motif; other site 407976002646 nucleotide binding site [chemical binding]; other site 407976002647 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976002648 Transcription factor zinc-finger; Region: zf-TFIIB; pfam13453 407976002649 Transcription factor zinc-finger; Region: zf-TFIIB; pfam13453 407976002650 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 407976002651 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 407976002652 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 407976002653 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 407976002654 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 407976002655 ligand binding site [chemical binding]; other site 407976002656 homodimer interface [polypeptide binding]; other site 407976002657 NAD(P) binding site [chemical binding]; other site 407976002658 trimer interface B [polypeptide binding]; other site 407976002659 trimer interface A [polypeptide binding]; other site 407976002660 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 407976002661 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 407976002662 Flavodoxin; Region: Flavodoxin_1; pfam00258 407976002663 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 407976002664 FAD binding pocket [chemical binding]; other site 407976002665 FAD binding motif [chemical binding]; other site 407976002666 catalytic residues [active] 407976002667 NAD binding pocket [chemical binding]; other site 407976002668 phosphate binding motif [ion binding]; other site 407976002669 beta-alpha-beta structure motif; other site 407976002670 sulfite reductase subunit beta; Provisional; Region: PRK13504 407976002671 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 407976002672 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 407976002673 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 407976002674 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 407976002675 Active Sites [active] 407976002676 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 407976002677 Transglycosylase; Region: Transgly; cl17702 407976002678 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 407976002679 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 407976002680 Active site serine [active] 407976002681 Phage endonuclease I; Region: Phage_endo_I; cl11622 407976002682 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 407976002683 dimerization interface [polypeptide binding]; other site 407976002684 substrate binding site [chemical binding]; other site 407976002685 active site 407976002686 calcium binding site [ion binding]; other site 407976002687 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 407976002688 active site 407976002689 SAM binding site [chemical binding]; other site 407976002690 homodimer interface [polypeptide binding]; other site 407976002691 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 407976002692 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 407976002693 Active Sites [active] 407976002694 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 407976002695 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 407976002696 CysD dimerization site [polypeptide binding]; other site 407976002697 G1 box; other site 407976002698 putative GEF interaction site [polypeptide binding]; other site 407976002699 GTP/Mg2+ binding site [chemical binding]; other site 407976002700 Switch I region; other site 407976002701 G2 box; other site 407976002702 G3 box; other site 407976002703 Switch II region; other site 407976002704 G4 box; other site 407976002705 G5 box; other site 407976002706 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 407976002707 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 407976002708 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 407976002709 TrkA-C domain; Region: TrkA_C; pfam02080 407976002710 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 407976002711 TrkA-C domain; Region: TrkA_C; pfam02080 407976002712 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 407976002713 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 407976002714 ligand-binding site [chemical binding]; other site 407976002715 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976002716 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 407976002717 ATP binding site [chemical binding]; other site 407976002718 Mg2+ binding site [ion binding]; other site 407976002719 G-X-G motif; other site 407976002720 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976002721 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 407976002722 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976002723 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976002724 metal binding site [ion binding]; metal-binding site 407976002725 active site 407976002726 I-site; other site 407976002727 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 407976002728 TIGR03899 family protein; Region: TIGR03899 407976002729 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 407976002730 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976002731 putative substrate translocation pore; other site 407976002732 Flavodoxin domain; Region: Flavodoxin_5; cl17428 407976002733 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 407976002734 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 407976002735 catalytic residues [active] 407976002736 hinge region; other site 407976002737 alpha helical domain; other site 407976002738 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 407976002739 DNA-J related protein; Region: DNAJ_related; pfam12339 407976002740 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 407976002741 HSP70 interaction site [polypeptide binding]; other site 407976002742 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 407976002743 FMN binding site [chemical binding]; other site 407976002744 dimer interface [polypeptide binding]; other site 407976002745 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 407976002746 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 407976002747 Walker A/P-loop; other site 407976002748 ATP binding site [chemical binding]; other site 407976002749 Q-loop/lid; other site 407976002750 ABC transporter signature motif; other site 407976002751 Walker B; other site 407976002752 D-loop; other site 407976002753 H-loop/switch region; other site 407976002754 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 407976002755 dimer interface [polypeptide binding]; other site 407976002756 conserved gate region; other site 407976002757 putative PBP binding loops; other site 407976002758 ABC-ATPase subunit interface; other site 407976002759 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 407976002760 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976002761 substrate binding pocket [chemical binding]; other site 407976002762 membrane-bound complex binding site; other site 407976002763 hinge residues; other site 407976002764 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976002765 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976002766 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 407976002767 putative dimerization interface [polypeptide binding]; other site 407976002768 LrgA family; Region: LrgA; cl00608 407976002769 LrgB-like family; Region: LrgB; pfam04172 407976002770 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976002771 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976002772 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 407976002773 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 407976002774 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 407976002775 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 407976002776 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976002777 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976002778 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976002779 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976002780 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976002781 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 407976002782 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 407976002783 Nucleoside recognition; Region: Gate; pfam07670 407976002784 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 407976002785 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976002786 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976002787 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 407976002788 putative effector binding pocket; other site 407976002789 dimerization interface [polypeptide binding]; other site 407976002790 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 407976002791 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976002792 Cytochrome c; Region: Cytochrom_C; pfam00034 407976002793 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 407976002794 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 407976002795 Cytochrome c; Region: Cytochrom_C; pfam00034 407976002796 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 407976002797 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 407976002798 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 407976002799 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 407976002800 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 407976002801 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 407976002802 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 407976002803 Transposase; Region: HTH_Tnp_1; pfam01527 407976002804 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 407976002805 putative transposase OrfB; Reviewed; Region: PHA02517 407976002806 HTH-like domain; Region: HTH_21; pfam13276 407976002807 Integrase core domain; Region: rve; pfam00665 407976002808 Integrase core domain; Region: rve_2; pfam13333 407976002809 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976002810 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976002811 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976002812 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 407976002813 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 407976002814 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 407976002815 substrate binding pocket [chemical binding]; other site 407976002816 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 407976002817 B12 binding site [chemical binding]; other site 407976002818 cobalt ligand [ion binding]; other site 407976002819 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 407976002820 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 407976002821 catalytic core [active] 407976002822 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 407976002823 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 407976002824 Walker A/P-loop; other site 407976002825 ATP binding site [chemical binding]; other site 407976002826 Q-loop/lid; other site 407976002827 ABC transporter signature motif; other site 407976002828 Walker B; other site 407976002829 D-loop; other site 407976002830 H-loop/switch region; other site 407976002831 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 407976002832 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 407976002833 putative dimer interface [polypeptide binding]; other site 407976002834 active site pocket [active] 407976002835 putative cataytic base [active] 407976002836 cobalamin synthase; Reviewed; Region: cobS; PRK00235 407976002837 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 407976002838 homotrimer interface [polypeptide binding]; other site 407976002839 Walker A motif; other site 407976002840 GTP binding site [chemical binding]; other site 407976002841 Walker B motif; other site 407976002842 cobyric acid synthase; Provisional; Region: PRK00784 407976002843 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 407976002844 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 407976002845 catalytic triad [active] 407976002846 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 407976002847 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 407976002848 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 407976002849 homodimer interface [polypeptide binding]; other site 407976002850 Walker A motif; other site 407976002851 ATP binding site [chemical binding]; other site 407976002852 hydroxycobalamin binding site [chemical binding]; other site 407976002853 Walker B motif; other site 407976002854 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 407976002855 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 407976002856 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 407976002857 cobalamin binding residues [chemical binding]; other site 407976002858 putative BtuC binding residues; other site 407976002859 dimer interface [polypeptide binding]; other site 407976002860 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 407976002861 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 407976002862 NAD(P) binding site [chemical binding]; other site 407976002863 catalytic residues [active] 407976002864 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 407976002865 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 407976002866 dimer interface [polypeptide binding]; other site 407976002867 active site 407976002868 metal binding site [ion binding]; metal-binding site 407976002869 AAA domain; Region: AAA_33; pfam13671 407976002870 AAA domain; Region: AAA_17; pfam13207 407976002871 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976002872 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976002873 Coenzyme A binding pocket [chemical binding]; other site 407976002874 MAPEG family; Region: MAPEG; cl09190 407976002875 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 407976002876 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976002877 DNA-binding site [nucleotide binding]; DNA binding site 407976002878 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 407976002879 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976002880 homodimer interface [polypeptide binding]; other site 407976002881 catalytic residue [active] 407976002882 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976002883 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976002884 Coenzyme A binding pocket [chemical binding]; other site 407976002885 NACHT domain; Region: NACHT; pfam05729 407976002886 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 407976002887 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 407976002888 active site 407976002889 substrate binding pocket [chemical binding]; other site 407976002890 dimer interface [polypeptide binding]; other site 407976002891 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976002892 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976002893 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976002894 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 407976002895 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 407976002896 Walker A/P-loop; other site 407976002897 ATP binding site [chemical binding]; other site 407976002898 Q-loop/lid; other site 407976002899 ABC transporter signature motif; other site 407976002900 Walker B; other site 407976002901 D-loop; other site 407976002902 H-loop/switch region; other site 407976002903 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 407976002904 FtsX-like permease family; Region: FtsX; pfam02687 407976002905 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 407976002906 FtsX-like permease family; Region: FtsX; pfam02687 407976002907 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 407976002908 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 407976002909 active site 407976002910 phosphorylation site [posttranslational modification] 407976002911 intermolecular recognition site; other site 407976002912 dimerization interface [polypeptide binding]; other site 407976002913 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 407976002914 Walker A motif; other site 407976002915 ATP binding site [chemical binding]; other site 407976002916 Walker B motif; other site 407976002917 arginine finger; other site 407976002918 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976002919 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 407976002920 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 407976002921 ATP binding site [chemical binding]; other site 407976002922 Mg2+ binding site [ion binding]; other site 407976002923 G-X-G motif; other site 407976002924 Curli assembly protein CsgE; Region: CsgE; pfam10627 407976002925 Type VIII secretion system (T8SS), CsgF protein; Region: CsgF; cl08082 407976002926 Curli production assembly/transport component CsgG; Region: CsgG; pfam03783 407976002927 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976002928 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976002929 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 407976002930 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 407976002931 NAD(P) binding site [chemical binding]; other site 407976002932 catalytic residues [active] 407976002933 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 407976002934 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 407976002935 Ligand Binding Site [chemical binding]; other site 407976002936 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 407976002937 Ligand Binding Site [chemical binding]; other site 407976002938 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 407976002939 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976002940 substrate binding pocket [chemical binding]; other site 407976002941 membrane-bound complex binding site; other site 407976002942 hinge residues; other site 407976002943 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 407976002944 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; pfam09904 407976002945 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 407976002946 gamma-glutamyl kinase; Provisional; Region: PRK05429 407976002947 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 407976002948 nucleotide binding site [chemical binding]; other site 407976002949 homotetrameric interface [polypeptide binding]; other site 407976002950 putative phosphate binding site [ion binding]; other site 407976002951 putative allosteric binding site; other site 407976002952 PUA domain; Region: PUA; pfam01472 407976002953 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 407976002954 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 407976002955 putative catalytic cysteine [active] 407976002956 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 407976002957 putative deacylase active site [active] 407976002958 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976002959 EamA-like transporter family; Region: EamA; pfam00892 407976002960 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 407976002961 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 407976002962 nucleotide binding site [chemical binding]; other site 407976002963 chaperone protein DnaJ; Provisional; Region: PRK10767 407976002964 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 407976002965 HSP70 interaction site [polypeptide binding]; other site 407976002966 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 407976002967 substrate binding site [polypeptide binding]; other site 407976002968 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 407976002969 Zn binding sites [ion binding]; other site 407976002970 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 407976002971 dimer interface [polypeptide binding]; other site 407976002972 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 407976002973 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 407976002974 ATP binding site [chemical binding]; other site 407976002975 Mg++ binding site [ion binding]; other site 407976002976 motif III; other site 407976002977 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 407976002978 nucleotide binding region [chemical binding]; other site 407976002979 ATP-binding site [chemical binding]; other site 407976002980 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 407976002981 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976002982 Peptidase family M48; Region: Peptidase_M48; pfam01435 407976002983 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 407976002984 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 407976002985 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976002986 dihydrodipicolinate reductase; Provisional; Region: PRK00048 407976002987 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 407976002988 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 407976002989 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 407976002990 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 407976002991 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 407976002992 catalytic site [active] 407976002993 subunit interface [polypeptide binding]; other site 407976002994 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 407976002995 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 407976002996 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 407976002997 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 407976002998 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 407976002999 ATP-grasp domain; Region: ATP-grasp_4; cl17255 407976003000 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 407976003001 IMP binding site; other site 407976003002 dimer interface [polypeptide binding]; other site 407976003003 interdomain contacts; other site 407976003004 partial ornithine binding site; other site 407976003005 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976003006 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976003007 active site 407976003008 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976003009 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 407976003010 substrate binding pocket [chemical binding]; other site 407976003011 membrane-bound complex binding site; other site 407976003012 hinge residues; other site 407976003013 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976003014 dimer interface [polypeptide binding]; other site 407976003015 putative CheW interface [polypeptide binding]; other site 407976003016 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 407976003017 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 407976003018 MgtE intracellular N domain; Region: MgtE_N; pfam03448 407976003019 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 407976003020 Divalent cation transporter; Region: MgtE; pfam01769 407976003021 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 407976003022 putative metal binding site [ion binding]; other site 407976003023 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 407976003024 putative catalytic site [active] 407976003025 putative phosphate binding site [ion binding]; other site 407976003026 putative metal binding site [ion binding]; other site 407976003027 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 407976003028 hypothetical protein; Provisional; Region: PRK05409 407976003029 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 407976003030 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 407976003031 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 407976003032 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 407976003033 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 407976003034 putative RNA binding site [nucleotide binding]; other site 407976003035 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 407976003036 S-adenosylmethionine binding site [chemical binding]; other site 407976003037 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 407976003038 tetramer (dimer of dimers) interface [polypeptide binding]; other site 407976003039 active site 407976003040 dimer interface [polypeptide binding]; other site 407976003041 Protein of unknown function (DUF808); Region: DUF808; pfam05661 407976003042 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 407976003043 catalytic site [active] 407976003044 putative active site [active] 407976003045 putative substrate binding site [chemical binding]; other site 407976003046 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family; Region: SWIM_PBPRA1643; TIGR04102 407976003047 SEC-C motif; Region: SEC-C; pfam02810 407976003048 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976003049 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 407976003050 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 407976003051 ligand-binding site [chemical binding]; other site 407976003052 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 407976003053 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 407976003054 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 407976003055 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 407976003056 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 407976003057 dimer interface [polypeptide binding]; other site 407976003058 active site 407976003059 galactokinase; Provisional; Region: PRK05101 407976003060 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 407976003061 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 407976003062 Vibrio parahaemolyticus Na(+)/galactose cotransporter (vSGLT) and related proteins; solute binding domain; Region: SLC5sbd_vSGLT; cd10325 407976003063 putative transporter; Provisional; Region: PRK10484 407976003064 Na binding site [ion binding]; other site 407976003065 substrate binding site [chemical binding]; other site 407976003066 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 407976003067 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 407976003068 NAD binding site [chemical binding]; other site 407976003069 homodimer interface [polypeptide binding]; other site 407976003070 active site 407976003071 substrate binding site [chemical binding]; other site 407976003072 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 407976003073 Transcriptional regulators [Transcription]; Region: PurR; COG1609 407976003074 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976003075 DNA binding site [nucleotide binding] 407976003076 domain linker motif; other site 407976003077 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 407976003078 dimerization interface (closed form) [polypeptide binding]; other site 407976003079 ligand binding site [chemical binding]; other site 407976003080 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 407976003081 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 407976003082 N-terminal plug; other site 407976003083 ligand-binding site [chemical binding]; other site 407976003084 Predicted membrane protein [Function unknown]; Region: COG3503 407976003085 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 407976003086 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 407976003087 dimerization interface [polypeptide binding]; other site 407976003088 DPS ferroxidase diiron center [ion binding]; other site 407976003089 ion pore; other site 407976003090 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 407976003091 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 407976003092 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976003093 lipoyl synthase; Provisional; Region: PRK05481 407976003094 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 407976003095 FeS/SAM binding site; other site 407976003096 lipoate-protein ligase B; Provisional; Region: PRK14342 407976003097 hypothetical protein; Provisional; Region: PRK04998 407976003098 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 407976003099 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 407976003100 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 407976003101 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 407976003102 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 407976003103 Sporulation related domain; Region: SPOR; pfam05036 407976003104 Transglycosylase SLT domain; Region: SLT_2; pfam13406 407976003105 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 407976003106 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976003107 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 407976003108 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 407976003109 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 407976003110 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 407976003111 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 407976003112 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 407976003113 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 407976003114 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 407976003115 active site 407976003116 (T/H)XGH motif; other site 407976003117 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 407976003118 DNA polymerase III, delta subunit; Region: holA; TIGR01128 407976003119 Lipopolysaccharide-assembly; Region: LptE; cl01125 407976003120 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 407976003121 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 407976003122 HIGH motif; other site 407976003123 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 407976003124 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 407976003125 active site 407976003126 KMSKS motif; other site 407976003127 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 407976003128 tRNA binding surface [nucleotide binding]; other site 407976003129 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 407976003130 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 407976003131 S-adenosylmethionine binding site [chemical binding]; other site 407976003132 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 407976003133 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 407976003134 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 407976003135 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 407976003136 putative active site [active] 407976003137 catalytic triad [active] 407976003138 putative dimer interface [polypeptide binding]; other site 407976003139 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 407976003140 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 407976003141 Transporter associated domain; Region: CorC_HlyC; smart01091 407976003142 metal-binding heat shock protein; Provisional; Region: PRK00016 407976003143 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 407976003144 PhoH-like protein; Region: PhoH; pfam02562 407976003145 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 407976003146 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 407976003147 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 407976003148 FeS/SAM binding site; other site 407976003149 TRAM domain; Region: TRAM; pfam01938 407976003150 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 407976003151 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 407976003152 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 407976003153 putative active site [active] 407976003154 catalytic residue [active] 407976003155 GTP-binding protein YchF; Reviewed; Region: PRK09601 407976003156 YchF GTPase; Region: YchF; cd01900 407976003157 G1 box; other site 407976003158 GTP/Mg2+ binding site [chemical binding]; other site 407976003159 Switch I region; other site 407976003160 G2 box; other site 407976003161 Switch II region; other site 407976003162 G3 box; other site 407976003163 G4 box; other site 407976003164 G5 box; other site 407976003165 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 407976003166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 407976003167 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 407976003168 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 407976003169 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 407976003170 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 407976003171 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 407976003172 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 407976003173 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 407976003174 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 407976003175 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 407976003176 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 407976003177 Protein export membrane protein; Region: SecD_SecF; pfam02355 407976003178 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 407976003179 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 407976003180 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 407976003181 S-adenosylmethionine binding site [chemical binding]; other site 407976003182 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 407976003183 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 407976003184 Walker A motif; other site 407976003185 ATP binding site [chemical binding]; other site 407976003186 Walker B motif; other site 407976003187 arginine finger; other site 407976003188 Peptidase family M41; Region: Peptidase_M41; pfam01434 407976003189 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 407976003190 dihydropteroate synthase; Region: DHPS; TIGR01496 407976003191 substrate binding pocket [chemical binding]; other site 407976003192 dimer interface [polypeptide binding]; other site 407976003193 inhibitor binding site; inhibition site 407976003194 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 407976003195 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 407976003196 active site 407976003197 substrate binding site [chemical binding]; other site 407976003198 metal binding site [ion binding]; metal-binding site 407976003199 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 407976003200 triosephosphate isomerase; Provisional; Region: PRK14567 407976003201 substrate binding site [chemical binding]; other site 407976003202 dimer interface [polypeptide binding]; other site 407976003203 catalytic triad [active] 407976003204 Preprotein translocase SecG subunit; Region: SecG; pfam03840 407976003205 ribosome maturation protein RimP; Reviewed; Region: PRK00092 407976003206 Sm and related proteins; Region: Sm_like; cl00259 407976003207 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 407976003208 putative oligomer interface [polypeptide binding]; other site 407976003209 putative RNA binding site [nucleotide binding]; other site 407976003210 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 407976003211 NusA N-terminal domain; Region: NusA_N; pfam08529 407976003212 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 407976003213 RNA binding site [nucleotide binding]; other site 407976003214 homodimer interface [polypeptide binding]; other site 407976003215 NusA-like KH domain; Region: KH_5; pfam13184 407976003216 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 407976003217 G-X-X-G motif; other site 407976003218 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 407976003219 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 407976003220 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 407976003221 translation initiation factor IF-2; Region: IF-2; TIGR00487 407976003222 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 407976003223 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 407976003224 G1 box; other site 407976003225 putative GEF interaction site [polypeptide binding]; other site 407976003226 GTP/Mg2+ binding site [chemical binding]; other site 407976003227 Switch I region; other site 407976003228 G2 box; other site 407976003229 G3 box; other site 407976003230 Switch II region; other site 407976003231 G4 box; other site 407976003232 G5 box; other site 407976003233 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 407976003234 Translation-initiation factor 2; Region: IF-2; pfam11987 407976003235 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 407976003236 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 407976003237 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 407976003238 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 407976003239 RNA binding site [nucleotide binding]; other site 407976003240 active site 407976003241 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 407976003242 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 407976003243 16S/18S rRNA binding site [nucleotide binding]; other site 407976003244 S13e-L30e interaction site [polypeptide binding]; other site 407976003245 25S rRNA binding site [nucleotide binding]; other site 407976003246 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976003247 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976003248 metal binding site [ion binding]; metal-binding site 407976003249 active site 407976003250 I-site; other site 407976003251 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 407976003252 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 407976003253 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 407976003254 RNase E interface [polypeptide binding]; other site 407976003255 trimer interface [polypeptide binding]; other site 407976003256 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 407976003257 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 407976003258 RNase E interface [polypeptide binding]; other site 407976003259 trimer interface [polypeptide binding]; other site 407976003260 active site 407976003261 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 407976003262 putative nucleic acid binding region [nucleotide binding]; other site 407976003263 G-X-X-G motif; other site 407976003264 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 407976003265 RNA binding site [nucleotide binding]; other site 407976003266 domain interface; other site 407976003267 lipoprotein NlpI; Provisional; Region: PRK11189 407976003268 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 407976003269 binding surface 407976003270 TPR motif; other site 407976003271 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 407976003272 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 407976003273 G1 box; other site 407976003274 putative GEF interaction site [polypeptide binding]; other site 407976003275 GTP/Mg2+ binding site [chemical binding]; other site 407976003276 Switch I region; other site 407976003277 G2 box; other site 407976003278 G3 box; other site 407976003279 Switch II region; other site 407976003280 G4 box; other site 407976003281 G5 box; other site 407976003282 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 407976003283 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 407976003284 active site 407976003285 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 407976003286 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 407976003287 Nucleoside recognition; Region: Gate; pfam07670 407976003288 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 407976003289 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; pfam03502 407976003290 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 407976003291 intersubunit interface [polypeptide binding]; other site 407976003292 active site 407976003293 catalytic residue [active] 407976003294 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 407976003295 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 407976003296 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 407976003297 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 407976003298 phosphopentomutase; Provisional; Region: PRK05362 407976003299 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 407976003300 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 407976003301 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 407976003302 phosphoserine phosphatase SerB; Region: serB; TIGR00338 407976003303 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 407976003304 motif II; other site 407976003305 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 407976003306 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 407976003307 PilZ domain; Region: PilZ; pfam07238 407976003308 PilZ domain; Region: PilZ; pfam07238 407976003309 DNA repair protein RadA; Provisional; Region: PRK11823 407976003310 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 407976003311 Walker A motif/ATP binding site; other site 407976003312 ATP binding site [chemical binding]; other site 407976003313 Walker B motif; other site 407976003314 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 407976003315 PilZ domain; Region: PilZ; pfam07238 407976003316 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 407976003317 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 407976003318 active site 407976003319 phosphorylation site [posttranslational modification] 407976003320 intermolecular recognition site; other site 407976003321 dimerization interface [polypeptide binding]; other site 407976003322 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 407976003323 DNA binding site [nucleotide binding] 407976003324 TMAO reductase system periplasmic protein TorT; Provisional; Region: PRK10936 407976003325 TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; Region: PBP1_TorT-like; cd06306 407976003326 putative ligand binding site [chemical binding]; other site 407976003327 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 407976003328 HAMP domain; Region: HAMP; pfam00672 407976003329 dimerization interface [polypeptide binding]; other site 407976003330 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 407976003331 dimer interface [polypeptide binding]; other site 407976003332 phosphorylation site [posttranslational modification] 407976003333 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 407976003334 ATP binding site [chemical binding]; other site 407976003335 Mg2+ binding site [ion binding]; other site 407976003336 G-X-G motif; other site 407976003337 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 407976003338 active site 407976003339 phosphorylation site [posttranslational modification] 407976003340 intermolecular recognition site; other site 407976003341 dimerization interface [polypeptide binding]; other site 407976003342 chaperone protein TorD; Validated; Region: torD; PRK04976 407976003343 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 407976003344 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 407976003345 molybdopterin cofactor binding site [chemical binding]; other site 407976003346 substrate binding site [chemical binding]; other site 407976003347 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 407976003348 molybdopterin cofactor binding site; other site 407976003349 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 407976003350 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 407976003351 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 407976003352 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 407976003353 FOG: CBS domain [General function prediction only]; Region: COG0517 407976003354 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_24; cd04637 407976003355 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 407976003356 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 407976003357 putative acyl-acceptor binding pocket; other site 407976003358 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 407976003359 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 407976003360 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 407976003361 putative active site [active] 407976003362 putative metal binding site [ion binding]; other site 407976003363 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 407976003364 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 407976003365 Int/Topo IB signature motif; other site 407976003366 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 407976003367 Putative transposase; Region: Y2_Tnp; pfam04986 407976003368 DUF based on E. rectale Gene description (DUF3880); Region: DUF3880; pfam12996 407976003369 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 407976003370 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 407976003371 Nucleoside recognition; Region: Gate; pfam07670 407976003372 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 407976003373 putative protease; Provisional; Region: PRK15447 407976003374 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 407976003375 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 407976003376 Peptidase family U32; Region: Peptidase_U32; pfam01136 407976003377 SCP-2 sterol transfer family; Region: SCP2; cl01225 407976003378 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 407976003379 Peptidase S8 family domain in ProteinaseK-like proteins; Region: Peptidases_S8_PCSK9_ProteinaseK_like; cd04077 407976003380 calcium binding site 2 [ion binding]; other site 407976003381 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 407976003382 active site 407976003383 catalytic triad [active] 407976003384 calcium binding site 1 [ion binding]; other site 407976003385 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976003386 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976003387 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 407976003388 putative protease; Provisional; Region: PRK15452 407976003389 Peptidase family U32; Region: Peptidase_U32; pfam01136 407976003390 HDOD domain; Region: HDOD; pfam08668 407976003391 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976003392 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976003393 metal binding site [ion binding]; metal-binding site 407976003394 active site 407976003395 I-site; other site 407976003396 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 407976003397 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 407976003398 active site 407976003399 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 407976003400 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976003401 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 407976003402 active site 407976003403 phosphorylation site [posttranslational modification] 407976003404 intermolecular recognition site; other site 407976003405 dimerization interface [polypeptide binding]; other site 407976003406 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 407976003407 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 407976003408 GDP-binding site [chemical binding]; other site 407976003409 ACT binding site; other site 407976003410 IMP binding site; other site 407976003411 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976003412 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003413 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 407976003414 dimerization interface [polypeptide binding]; other site 407976003415 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976003416 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 407976003417 substrate binding pocket [chemical binding]; other site 407976003418 membrane-bound complex binding site; other site 407976003419 hinge residues; other site 407976003420 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976003421 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976003422 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976003423 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976003424 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 407976003425 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 407976003426 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976003427 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003428 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 407976003429 dimerization interface [polypeptide binding]; other site 407976003430 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976003431 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976003432 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976003433 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976003434 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976003435 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 407976003436 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976003437 Zn2+ binding site [ion binding]; other site 407976003438 Mg2+ binding site [ion binding]; other site 407976003439 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976003440 Zn2+ binding site [ion binding]; other site 407976003441 Mg2+ binding site [ion binding]; other site 407976003442 Cna protein B-type domain; Region: Cna_B; pfam05738 407976003443 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976003444 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976003445 metal binding site [ion binding]; metal-binding site 407976003446 active site 407976003447 I-site; other site 407976003448 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 407976003449 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 407976003450 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 407976003451 apolar tunnel; other site 407976003452 heme binding site [chemical binding]; other site 407976003453 dimerization interface [polypeptide binding]; other site 407976003454 Uncharacterized conserved protein [Function unknown]; Region: COG1432 407976003455 LabA_like proteins; Region: LabA_like/DUF88; cl10034 407976003456 putative metal binding site [ion binding]; other site 407976003457 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 407976003458 EamA-like transporter family; Region: EamA; pfam00892 407976003459 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 407976003460 EamA-like transporter family; Region: EamA; pfam00892 407976003461 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 407976003462 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 407976003463 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976003464 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 407976003465 putative substrate translocation pore; other site 407976003466 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976003467 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976003468 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976003469 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976003470 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 407976003471 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976003472 substrate binding pocket [chemical binding]; other site 407976003473 membrane-bound complex binding site; other site 407976003474 hinge residues; other site 407976003475 Shewanella-like phosphatases, metallophosphatase domain; Region: MPP_Shelphs; cd07425 407976003476 active site 407976003477 metal binding site [ion binding]; metal-binding site 407976003478 Ketosteroid isomerase-related protein [General function prediction only]; Region: COG3631 407976003479 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 407976003480 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 407976003481 catalytic residues [active] 407976003482 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 407976003483 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976003484 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003485 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 407976003486 putative effector binding pocket; other site 407976003487 dimerization interface [polypeptide binding]; other site 407976003488 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 407976003489 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976003490 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976003491 ABC transporter; Region: ABC_tran_2; pfam12848 407976003492 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976003493 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 407976003494 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 407976003495 dimer interface [polypeptide binding]; other site 407976003496 active site 407976003497 glycine-pyridoxal phosphate binding site [chemical binding]; other site 407976003498 folate binding site [chemical binding]; other site 407976003499 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 407976003500 ATP cone domain; Region: ATP-cone; pfam03477 407976003501 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 407976003502 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 407976003503 catalytic motif [active] 407976003504 Zn binding site [ion binding]; other site 407976003505 RibD C-terminal domain; Region: RibD_C; cl17279 407976003506 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 407976003507 Lumazine binding domain; Region: Lum_binding; pfam00677 407976003508 Lumazine binding domain; Region: Lum_binding; pfam00677 407976003509 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 407976003510 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 407976003511 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 407976003512 dimerization interface [polypeptide binding]; other site 407976003513 active site 407976003514 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 407976003515 homopentamer interface [polypeptide binding]; other site 407976003516 active site 407976003517 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 407976003518 putative RNA binding site [nucleotide binding]; other site 407976003519 thiamine monophosphate kinase; Provisional; Region: PRK05731 407976003520 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 407976003521 ATP binding site [chemical binding]; other site 407976003522 dimerization interface [polypeptide binding]; other site 407976003523 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 407976003524 tetramer interfaces [polypeptide binding]; other site 407976003525 binuclear metal-binding site [ion binding]; other site 407976003526 recombination and repair protein; Provisional; Region: PRK10869 407976003527 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 407976003528 Walker A/P-loop; other site 407976003529 ATP binding site [chemical binding]; other site 407976003530 Q-loop/lid; other site 407976003531 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 407976003532 ABC transporter signature motif; other site 407976003533 Walker B; other site 407976003534 D-loop; other site 407976003535 H-loop/switch region; other site 407976003536 Membrane transport protein; Region: Mem_trans; cl09117 407976003537 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976003538 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003539 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 407976003540 putative effector binding pocket; other site 407976003541 dimerization interface [polypeptide binding]; other site 407976003542 Protein of unknown function (DUF3319); Region: DUF3319; pfam11782 407976003543 Protein of unknown function (DUF416); Region: DUF416; pfam04222 407976003544 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 407976003545 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 407976003546 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 407976003547 dimerization interface [polypeptide binding]; other site 407976003548 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 407976003549 dimer interface [polypeptide binding]; other site 407976003550 phosphorylation site [posttranslational modification] 407976003551 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 407976003552 ATP binding site [chemical binding]; other site 407976003553 Mg2+ binding site [ion binding]; other site 407976003554 G-X-G motif; other site 407976003555 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 407976003556 active site 407976003557 phosphorylation site [posttranslational modification] 407976003558 intermolecular recognition site; other site 407976003559 dimerization interface [polypeptide binding]; other site 407976003560 Hpt domain; Region: Hpt; pfam01627 407976003561 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 407976003562 TRAM domain; Region: TRAM; pfam01938 407976003563 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 407976003564 S-adenosylmethionine binding site [chemical binding]; other site 407976003565 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 407976003566 HD domain; Region: HD_4; pfam13328 407976003567 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 407976003568 synthetase active site [active] 407976003569 NTP binding site [chemical binding]; other site 407976003570 metal binding site [ion binding]; metal-binding site 407976003571 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 407976003572 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 407976003573 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional; Region: PRK14844 407976003574 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 407976003575 AAA domain; Region: AAA_11; pfam13086 407976003576 Part of AAA domain; Region: AAA_19; pfam13245 407976003577 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 407976003578 AAA domain; Region: AAA_12; pfam13087 407976003579 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 407976003580 putative active site [active] 407976003581 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 407976003582 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976003583 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976003584 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976003585 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 407976003586 substrate binding site [chemical binding]; other site 407976003587 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional; Region: PRK08575 407976003588 THF binding site; other site 407976003589 zinc-binding site [ion binding]; other site 407976003590 amidase; Validated; Region: PRK06565 407976003591 Amidase; Region: Amidase; cl11426 407976003592 Amidase; Region: Amidase; cl11426 407976003593 agmatine deiminase; Provisional; Region: PRK13551 407976003594 agmatine deiminase; Region: agmatine_aguA; TIGR03380 407976003595 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 407976003596 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 407976003597 homodimer interface [polypeptide binding]; other site 407976003598 metal binding site [ion binding]; metal-binding site 407976003599 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 407976003600 homodimer interface [polypeptide binding]; other site 407976003601 active site 407976003602 putative chemical substrate binding site [chemical binding]; other site 407976003603 metal binding site [ion binding]; metal-binding site 407976003604 CTP synthetase; Validated; Region: pyrG; PRK05380 407976003605 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 407976003606 Catalytic site [active] 407976003607 active site 407976003608 UTP binding site [chemical binding]; other site 407976003609 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 407976003610 active site 407976003611 putative oxyanion hole; other site 407976003612 catalytic triad [active] 407976003613 enolase; Provisional; Region: eno; PRK00077 407976003614 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 407976003615 dimer interface [polypeptide binding]; other site 407976003616 metal binding site [ion binding]; metal-binding site 407976003617 substrate binding pocket [chemical binding]; other site 407976003618 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 407976003619 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 407976003620 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 407976003621 substrate binding site; other site 407976003622 dimer interface; other site 407976003623 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 407976003624 homotrimer interaction site [polypeptide binding]; other site 407976003625 zinc binding site [ion binding]; other site 407976003626 CDP-binding sites; other site 407976003627 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 407976003628 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 407976003629 Permutation of conserved domain; other site 407976003630 active site 407976003631 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 407976003632 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 407976003633 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 407976003634 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 407976003635 S-adenosylmethionine binding site [chemical binding]; other site 407976003636 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 407976003637 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976003638 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976003639 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 407976003640 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 407976003641 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976003642 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 407976003643 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 407976003644 DNA binding residues [nucleotide binding] 407976003645 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 407976003646 MutS domain I; Region: MutS_I; pfam01624 407976003647 MutS domain II; Region: MutS_II; pfam05188 407976003648 MutS domain III; Region: MutS_III; pfam05192 407976003649 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 407976003650 Walker A/P-loop; other site 407976003651 ATP binding site [chemical binding]; other site 407976003652 Q-loop/lid; other site 407976003653 ABC transporter signature motif; other site 407976003654 Walker B; other site 407976003655 D-loop; other site 407976003656 H-loop/switch region; other site 407976003657 recombinase A; Provisional; Region: recA; PRK09354 407976003658 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 407976003659 hexamer interface [polypeptide binding]; other site 407976003660 Walker A motif; other site 407976003661 ATP binding site [chemical binding]; other site 407976003662 Walker B motif; other site 407976003663 recombination regulator RecX; Reviewed; Region: recX; PRK00117 407976003664 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 407976003665 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 407976003666 motif 1; other site 407976003667 active site 407976003668 motif 2; other site 407976003669 motif 3; other site 407976003670 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 407976003671 DHHA1 domain; Region: DHHA1; pfam02272 407976003672 aspartate kinase; Reviewed; Region: PRK06635 407976003673 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 407976003674 putative nucleotide binding site [chemical binding]; other site 407976003675 putative catalytic residues [active] 407976003676 putative Mg ion binding site [ion binding]; other site 407976003677 putative aspartate binding site [chemical binding]; other site 407976003678 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 407976003679 putative allosteric regulatory residue; other site 407976003680 carbon storage regulator; Provisional; Region: PRK01712 407976003681 potential protein location (hypothetical protein Sbal223_1253 [Shewanella baltica OS223]) that overlaps RNA (tRNA-S) 407976003682 potential protein location (hypothetical protein Sbal223_1254 [Shewanella baltica OS223]) that overlaps RNA (tRNA-R) 407976003683 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 407976003684 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 407976003685 HIGH motif; other site 407976003686 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 407976003687 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 407976003688 active site 407976003689 KMSKS motif; other site 407976003690 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 407976003691 tRNA binding surface [nucleotide binding]; other site 407976003692 anticodon binding site; other site 407976003693 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 407976003694 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 407976003695 multifunctional aminopeptidase A; Provisional; Region: PRK00913 407976003696 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 407976003697 interface (dimer of trimers) [polypeptide binding]; other site 407976003698 Substrate-binding/catalytic site; other site 407976003699 Zn-binding sites [ion binding]; other site 407976003700 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 407976003701 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 407976003702 lipopolysaccharide ABC transporter permease; Provisional; Region: PRK15071 407976003703 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 407976003704 RDD family; Region: RDD; pfam06271 407976003705 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 407976003706 Protein of unknown function, DUF486; Region: DUF486; pfam04342 407976003707 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 407976003708 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 407976003709 active site 407976003710 Zn binding site [ion binding]; other site 407976003711 DsrE/DsrF-like family; Region: DrsE; pfam02635 407976003712 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 407976003713 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 407976003714 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 407976003715 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 407976003716 hypothetical protein; Provisional; Region: PRK09898 407976003717 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 407976003718 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976003719 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976003720 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976003721 hypothetical protein; Provisional; Region: PRK09947 407976003722 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976003723 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 407976003724 membrane-bound complex binding site; other site 407976003725 hinge residues; other site 407976003726 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 407976003727 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 407976003728 putative catalytic residues [active] 407976003729 Tryptophan-rich protein (DUF2389); Region: DUF2389; pfam09493 407976003730 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; COG2040 407976003731 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 407976003732 putrescine transporter; Provisional; Region: potE; PRK10655 407976003733 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 407976003734 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 407976003735 ATP binding site [chemical binding]; other site 407976003736 Mg++ binding site [ion binding]; other site 407976003737 motif III; other site 407976003738 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 407976003739 nucleotide binding region [chemical binding]; other site 407976003740 ATP-binding site [chemical binding]; other site 407976003741 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 407976003742 PAS fold; Region: PAS_3; pfam08447 407976003743 putative active site [active] 407976003744 heme pocket [chemical binding]; other site 407976003745 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976003746 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976003747 dimer interface [polypeptide binding]; other site 407976003748 putative CheW interface [polypeptide binding]; other site 407976003749 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 407976003750 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976003751 Zn2+ binding site [ion binding]; other site 407976003752 Mg2+ binding site [ion binding]; other site 407976003753 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 407976003754 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 407976003755 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 407976003756 active site 407976003757 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 407976003758 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 407976003759 N-terminal Early set domain associated with the catalytic domain of chitinase; Region: E_set_Chitinase_N; cd02848 407976003760 Glyco_18 domain; Region: Glyco_18; smart00636 407976003761 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 407976003762 active site 407976003763 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 407976003764 aromatic chitin/cellulose binding site residues [chemical binding]; other site 407976003765 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 407976003766 aromatic chitin/cellulose binding site residues [chemical binding]; other site 407976003767 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 407976003768 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 407976003769 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976003770 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 407976003771 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 407976003772 Predicted membrane protein [Function unknown]; Region: COG2311 407976003773 Protein of unknown function (DUF418); Region: DUF418; cl12135 407976003774 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 407976003775 nucleoside/Zn binding site; other site 407976003776 dimer interface [polypeptide binding]; other site 407976003777 catalytic motif [active] 407976003778 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 407976003779 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003780 The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_XapR; cd08449 407976003781 putative dimerization interface [polypeptide binding]; other site 407976003782 putative substrate binding pocket [chemical binding]; other site 407976003783 purine nucleoside phosphorylase; Provisional; Region: PRK08202 407976003784 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 407976003785 CoenzymeA binding site [chemical binding]; other site 407976003786 subunit interaction site [polypeptide binding]; other site 407976003787 PHB binding site; other site 407976003788 Domain of unknown function (DUF368); Region: DUF368; pfam04018 407976003789 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 407976003790 YheO-like PAS domain; Region: PAS_6; pfam08348 407976003791 HTH domain; Region: HTH_22; pfam13309 407976003792 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 407976003793 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 407976003794 homotrimer interaction site [polypeptide binding]; other site 407976003795 putative active site [active] 407976003796 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 407976003797 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 407976003798 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976003799 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976003800 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976003801 PBP superfamily domain; Region: PBP_like_2; cl17296 407976003802 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 407976003803 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 407976003804 MerT mercuric transport protein; Region: MerT; cl03578 407976003805 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 407976003806 metal-binding site [ion binding] 407976003807 Adenylosuccinate lyase C-terminus; Region: ADSL_C; cl17237 407976003808 Protein of unknown function (DUF523); Region: DUF523; pfam04463 407976003809 Uncharacterized conserved protein [Function unknown]; Region: COG3272 407976003810 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 407976003811 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 407976003812 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 407976003813 DNA binding residues [nucleotide binding] 407976003814 DNA photolyase; Region: DNA_photolyase; pfam00875 407976003815 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 407976003816 SnoaL-like domain; Region: SnoaL_2; pfam12680 407976003817 short chain dehydrogenase; Provisional; Region: PRK06101 407976003818 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976003819 NAD(P) binding site [chemical binding]; other site 407976003820 active site 407976003821 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 407976003822 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 407976003823 hydroxyglutarate oxidase; Provisional; Region: PRK11728 407976003824 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 407976003825 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 407976003826 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 407976003827 S-adenosylmethionine binding site [chemical binding]; other site 407976003828 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 407976003829 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 407976003830 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 407976003831 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 407976003832 hypothetical protein; Provisional; Region: PRK03757 407976003833 oxidative damage protection protein; Provisional; Region: PRK05408 407976003834 adenine DNA glycosylase; Provisional; Region: PRK10880 407976003835 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 407976003836 minor groove reading motif; other site 407976003837 helix-hairpin-helix signature motif; other site 407976003838 substrate binding pocket [chemical binding]; other site 407976003839 active site 407976003840 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 407976003841 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 407976003842 DNA binding and oxoG recognition site [nucleotide binding] 407976003843 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 407976003844 S-adenosylmethionine binding site [chemical binding]; other site 407976003845 hypothetical protein; Provisional; Region: PRK11702 407976003846 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 407976003847 glutaminase; Provisional; Region: PRK00971 407976003848 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 407976003849 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976003850 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003851 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 407976003852 putative effector binding pocket; other site 407976003853 dimerization interface [polypeptide binding]; other site 407976003854 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 407976003855 HemN family oxidoreductase; Provisional; Region: PRK05660 407976003856 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 407976003857 FeS/SAM binding site; other site 407976003858 HemN C-terminal domain; Region: HemN_C; pfam06969 407976003859 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 407976003860 active site 407976003861 dimerization interface [polypeptide binding]; other site 407976003862 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 407976003863 hypothetical protein; Validated; Region: PRK05090 407976003864 YGGT family; Region: YGGT; pfam02325 407976003865 YGGT family; Region: YGGT; pfam02325 407976003866 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 407976003867 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 407976003868 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 407976003869 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 407976003870 catalytic residue [active] 407976003871 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 407976003872 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 407976003873 Walker A motif; other site 407976003874 ATP binding site [chemical binding]; other site 407976003875 Walker B motif; other site 407976003876 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 407976003877 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 407976003878 Walker A motif; other site 407976003879 ATP binding site [chemical binding]; other site 407976003880 Walker B motif; other site 407976003881 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 407976003882 catalytic residues [active] 407976003883 dimer interface [polypeptide binding]; other site 407976003884 ferrochelatase; Reviewed; Region: hemH; PRK00035 407976003885 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 407976003886 C-terminal domain interface [polypeptide binding]; other site 407976003887 active site 407976003888 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 407976003889 active site 407976003890 N-terminal domain interface [polypeptide binding]; other site 407976003891 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 407976003892 Uncharacterized ACR, COG1678; Region: DUF179; pfam02622 407976003893 translation initiation factor Sui1; Validated; Region: PRK06824 407976003894 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 407976003895 putative rRNA binding site [nucleotide binding]; other site 407976003896 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 407976003897 Predicted membrane protein [Function unknown]; Region: COG2860 407976003898 UPF0126 domain; Region: UPF0126; pfam03458 407976003899 UPF0126 domain; Region: UPF0126; pfam03458 407976003900 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 407976003901 dimer interface [polypeptide binding]; other site 407976003902 catalytic triad [active] 407976003903 peroxidatic and resolving cysteines [active] 407976003904 Conserved TM helix; Region: TM_helix; pfam05552 407976003905 mechanosensitive channel MscS; Provisional; Region: PRK10334 407976003906 Mechanosensitive ion channel; Region: MS_channel; pfam00924 407976003907 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 407976003908 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976003909 ligand binding site [chemical binding]; other site 407976003910 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 407976003911 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 407976003912 tetramer interface [polypeptide binding]; other site 407976003913 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976003914 catalytic residue [active] 407976003915 HDOD domain; Region: HDOD; pfam08668 407976003916 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 407976003917 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 407976003918 SnoaL-like domain; Region: SnoaL_3; pfam13474 407976003919 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 407976003920 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976003921 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976003922 metal binding site [ion binding]; metal-binding site 407976003923 active site 407976003924 I-site; other site 407976003925 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 407976003926 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 407976003927 ParA-like protein; Provisional; Region: PHA02518 407976003928 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 407976003929 P-loop; other site 407976003930 Magnesium ion binding site [ion binding]; other site 407976003931 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 407976003932 Coenzyme A binding pocket [chemical binding]; other site 407976003933 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 407976003934 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976003935 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976003936 Coenzyme A binding pocket [chemical binding]; other site 407976003937 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976003938 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976003939 Coenzyme A binding pocket [chemical binding]; other site 407976003940 Pirin-related protein [General function prediction only]; Region: COG1741 407976003941 Pirin; Region: Pirin; pfam02678 407976003942 DoxX; Region: DoxX; pfam07681 407976003943 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976003944 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 407976003945 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 407976003946 putative dimerization interface [polypeptide binding]; other site 407976003947 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 407976003948 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 407976003949 active site 407976003950 metal binding site [ion binding]; metal-binding site 407976003951 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 407976003952 Domain of unknown function DUF21; Region: DUF21; pfam01595 407976003953 FOG: CBS domain [General function prediction only]; Region: COG0517 407976003954 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 407976003955 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 407976003956 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 407976003957 FeS/SAM binding site; other site 407976003958 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 407976003959 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 407976003960 TPR motif; other site 407976003961 binding surface 407976003962 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 407976003963 binding surface 407976003964 TPR motif; other site 407976003965 cytoskeletal protein RodZ; Provisional; Region: PRK10856 407976003966 Helix-turn-helix domain; Region: HTH_25; pfam13413 407976003967 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 407976003968 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 407976003969 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 407976003970 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 407976003971 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 407976003972 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 407976003973 dimer interface [polypeptide binding]; other site 407976003974 motif 1; other site 407976003975 active site 407976003976 motif 2; other site 407976003977 motif 3; other site 407976003978 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 407976003979 anticodon binding site; other site 407976003980 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 407976003981 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 407976003982 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 407976003983 TPR motif; other site 407976003984 binding surface 407976003985 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 407976003986 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 407976003987 Trp docking motif [polypeptide binding]; other site 407976003988 active site 407976003989 GTP-binding protein Der; Reviewed; Region: PRK00093 407976003990 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 407976003991 G1 box; other site 407976003992 GTP/Mg2+ binding site [chemical binding]; other site 407976003993 Switch I region; other site 407976003994 G2 box; other site 407976003995 Switch II region; other site 407976003996 G3 box; other site 407976003997 G4 box; other site 407976003998 G5 box; other site 407976003999 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 407976004000 G1 box; other site 407976004001 GTP/Mg2+ binding site [chemical binding]; other site 407976004002 Switch I region; other site 407976004003 G2 box; other site 407976004004 G3 box; other site 407976004005 Switch II region; other site 407976004006 G4 box; other site 407976004007 G5 box; other site 407976004008 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 407976004009 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 407976004010 generic binding surface II; other site 407976004011 generic binding surface I; other site 407976004012 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 407976004013 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 407976004014 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 407976004015 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 407976004016 active site 407976004017 GMP synthase; Reviewed; Region: guaA; PRK00074 407976004018 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 407976004019 AMP/PPi binding site [chemical binding]; other site 407976004020 candidate oxyanion hole; other site 407976004021 catalytic triad [active] 407976004022 potential glutamine specificity residues [chemical binding]; other site 407976004023 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 407976004024 ATP Binding subdomain [chemical binding]; other site 407976004025 Ligand Binding sites [chemical binding]; other site 407976004026 Dimerization subdomain; other site 407976004027 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 407976004028 nucleoside/Zn binding site; other site 407976004029 dimer interface [polypeptide binding]; other site 407976004030 catalytic motif [active] 407976004031 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 407976004032 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 407976004033 substrate binding pocket [chemical binding]; other site 407976004034 membrane-bound complex binding site; other site 407976004035 hinge residues; other site 407976004036 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 407976004037 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976004038 catalytic residue [active] 407976004039 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 407976004040 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 407976004041 dimerization interface [polypeptide binding]; other site 407976004042 ATP binding site [chemical binding]; other site 407976004043 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 407976004044 dimerization interface [polypeptide binding]; other site 407976004045 ATP binding site [chemical binding]; other site 407976004046 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 407976004047 putative active site [active] 407976004048 catalytic triad [active] 407976004049 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 407976004050 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 407976004051 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 407976004052 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 407976004053 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 407976004054 Cache domain; Region: Cache_1; pfam02743 407976004055 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 407976004056 dimerization interface [polypeptide binding]; other site 407976004057 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976004058 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976004059 dimer interface [polypeptide binding]; other site 407976004060 putative CheW interface [polypeptide binding]; other site 407976004061 Protein of unknown function (DUF465); Region: DUF465; pfam04325 407976004062 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976004063 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976004064 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976004065 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976004066 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976004067 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 407976004068 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 407976004069 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 407976004070 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 407976004071 binding surface 407976004072 TPR motif; other site 407976004073 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 407976004074 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 407976004075 NAD(P) binding site [chemical binding]; other site 407976004076 homodimer interface [polypeptide binding]; other site 407976004077 substrate binding site [chemical binding]; other site 407976004078 active site 407976004079 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976004080 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976004081 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976004082 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 407976004083 active site 407976004084 N-terminal catalytic domain of alpha-galactosidase; glycoside hydrolase family 57 (GH57); Region: GH57N_PfGalA_like; cd10794 407976004085 putative active site [active] 407976004086 catalytic site [active] 407976004087 Biotin carboxylase [Lipid metabolism]; Region: AccC; COG0439 407976004088 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 407976004089 Methyltransferase domain; Region: Methyltransf_23; pfam13489 407976004090 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 407976004091 S-adenosylmethionine binding site [chemical binding]; other site 407976004092 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 407976004093 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976004094 NAD(P) binding site [chemical binding]; other site 407976004095 active site 407976004096 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 407976004097 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 407976004098 PYR/PP interface [polypeptide binding]; other site 407976004099 dimer interface [polypeptide binding]; other site 407976004100 TPP binding site [chemical binding]; other site 407976004101 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 407976004102 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 407976004103 TPP-binding site [chemical binding]; other site 407976004104 dimer interface [polypeptide binding]; other site 407976004105 NeuB family; Region: NeuB; pfam03102 407976004106 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 407976004107 LPP20 lipoprotein; Region: LPP20; pfam02169 407976004108 FlgN protein; Region: FlgN; pfam05130 407976004109 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 407976004110 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 407976004111 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 407976004112 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 407976004113 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976004114 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 407976004115 active site 407976004116 phosphorylation site [posttranslational modification] 407976004117 intermolecular recognition site; other site 407976004118 dimerization interface [polypeptide binding]; other site 407976004119 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 407976004120 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 407976004121 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 407976004122 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 407976004123 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 407976004124 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 407976004125 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 407976004126 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 407976004127 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 407976004128 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 407976004129 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 407976004130 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 407976004131 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 407976004132 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 407976004133 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 407976004134 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 407976004135 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 407976004136 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 407976004137 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 407976004138 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 407976004139 Flagellar L-ring protein; Region: FlgH; pfam02107 407976004140 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 407976004141 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 407976004142 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 407976004143 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 407976004144 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 407976004145 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08871 407976004146 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 407976004147 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 407976004148 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 407976004149 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 407976004150 flagellin; Provisional; Region: PRK12802 407976004151 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 407976004152 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 407976004153 flagellin; Provisional; Region: PRK12802 407976004154 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 407976004155 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 407976004156 FlaG protein; Region: FlaG; pfam03646 407976004157 flagellar capping protein; Reviewed; Region: fliD; PRK08032 407976004158 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 407976004159 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 407976004160 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 407976004161 flagellar protein FliS; Validated; Region: fliS; PRK05685 407976004162 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 407976004163 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 407976004164 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 407976004165 Walker A motif; other site 407976004166 ATP binding site [chemical binding]; other site 407976004167 Walker B motif; other site 407976004168 arginine finger; other site 407976004169 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976004170 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 407976004171 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 407976004172 putative active site [active] 407976004173 heme pocket [chemical binding]; other site 407976004174 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 407976004175 dimer interface [polypeptide binding]; other site 407976004176 phosphorylation site [posttranslational modification] 407976004177 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 407976004178 ATP binding site [chemical binding]; other site 407976004179 Mg2+ binding site [ion binding]; other site 407976004180 G-X-G motif; other site 407976004181 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 407976004182 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 407976004183 active site 407976004184 phosphorylation site [posttranslational modification] 407976004185 intermolecular recognition site; other site 407976004186 dimerization interface [polypeptide binding]; other site 407976004187 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 407976004188 Walker A motif; other site 407976004189 ATP binding site [chemical binding]; other site 407976004190 Walker B motif; other site 407976004191 arginine finger; other site 407976004192 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976004193 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 407976004194 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 407976004195 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 407976004196 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 407976004197 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 407976004198 MgtE intracellular N domain; Region: MgtE_N; smart00924 407976004199 FliG C-terminal domain; Region: FliG_C; pfam01706 407976004200 flagellar assembly protein H; Validated; Region: fliH; PRK05687 407976004201 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 407976004202 Flagellar assembly protein FliH; Region: FliH; pfam02108 407976004203 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 407976004204 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 407976004205 Walker A motif/ATP binding site; other site 407976004206 Walker B motif; other site 407976004207 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 407976004208 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 407976004209 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 407976004210 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK05696 407976004211 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 407976004212 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 407976004213 flagellar motor switch protein; Validated; Region: fliN; PRK08983 407976004214 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 407976004215 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 407976004216 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 407976004217 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 407976004218 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 407976004219 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 407976004220 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 407976004221 FHIPEP family; Region: FHIPEP; pfam00771 407976004222 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 407976004223 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 407976004224 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 407976004225 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 407976004226 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 407976004227 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 407976004228 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976004229 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 407976004230 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 407976004231 DNA binding residues [nucleotide binding] 407976004232 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 407976004233 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 407976004234 active site 407976004235 phosphorylation site [posttranslational modification] 407976004236 intermolecular recognition site; other site 407976004237 dimerization interface [polypeptide binding]; other site 407976004238 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 407976004239 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 407976004240 putative binding surface; other site 407976004241 active site 407976004242 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 407976004243 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 407976004244 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 407976004245 ATP binding site [chemical binding]; other site 407976004246 Mg2+ binding site [ion binding]; other site 407976004247 G-X-G motif; other site 407976004248 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 407976004249 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 407976004250 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 407976004251 active site 407976004252 phosphorylation site [posttranslational modification] 407976004253 intermolecular recognition site; other site 407976004254 CheB methylesterase; Region: CheB_methylest; pfam01339 407976004255 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 407976004256 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 407976004257 P-loop; other site 407976004258 Magnesium ion binding site [ion binding]; other site 407976004259 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 407976004260 Magnesium ion binding site [ion binding]; other site 407976004261 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 407976004262 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 407976004263 putative CheA interaction surface; other site 407976004264 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 407976004265 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 407976004266 Flagellar hook-length control protein FliK; Region: Flg_hook; cl17777 407976004267 VacJ like lipoprotein; Region: VacJ; cl01073 407976004268 Response regulator receiver domain; Region: Response_reg; pfam00072 407976004269 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 407976004270 active site 407976004271 phosphorylation site [posttranslational modification] 407976004272 intermolecular recognition site; other site 407976004273 dimerization interface [polypeptide binding]; other site 407976004274 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 407976004275 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 407976004276 putative substrate translocation pore; other site 407976004277 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 407976004278 transcriptional activator RfaH; Region: RfaH; TIGR01955 407976004279 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 407976004280 heterodimer interface [polypeptide binding]; other site 407976004281 homodimer interface [polypeptide binding]; other site 407976004282 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 407976004283 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 407976004284 SLBB domain; Region: SLBB; pfam10531 407976004285 SLBB domain; Region: SLBB; pfam10531 407976004286 SLBB domain; Region: SLBB; pfam10531 407976004287 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 407976004288 SLBB domain; Region: SLBB; pfam10531 407976004289 Chain length determinant protein; Region: Wzz; pfam02706 407976004290 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 407976004291 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 407976004292 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 407976004293 NAD binding site [chemical binding]; other site 407976004294 substrate binding site [chemical binding]; other site 407976004295 homodimer interface [polypeptide binding]; other site 407976004296 active site 407976004297 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 407976004298 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 407976004299 substrate binding site; other site 407976004300 tetramer interface; other site 407976004301 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 407976004302 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 407976004303 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 407976004304 trimer interface [polypeptide binding]; other site 407976004305 active site 407976004306 substrate binding site [chemical binding]; other site 407976004307 CoA binding site [chemical binding]; other site 407976004308 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 407976004309 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 407976004310 inhibitor-cofactor binding pocket; inhibition site 407976004311 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976004312 catalytic residue [active] 407976004313 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 407976004314 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 407976004315 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 407976004316 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 407976004317 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 407976004318 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 407976004319 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 407976004320 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 407976004321 NAD(P) binding site [chemical binding]; other site 407976004322 homodimer interface [polypeptide binding]; other site 407976004323 substrate binding site [chemical binding]; other site 407976004324 active site 407976004325 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 407976004326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976004327 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 407976004328 NAD(P) binding site [chemical binding]; other site 407976004329 active site 407976004330 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 407976004331 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 407976004332 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 407976004333 active site 407976004334 homodimer interface [polypeptide binding]; other site 407976004335 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 407976004336 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 407976004337 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 407976004338 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 407976004339 putative NAD(P) binding site [chemical binding]; other site 407976004340 active site 407976004341 putative substrate binding site [chemical binding]; other site 407976004342 Bacterial sugar transferase; Region: Bac_transf; pfam02397 407976004343 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 407976004344 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 407976004345 NAD(P) binding site [chemical binding]; other site 407976004346 homodimer interface [polypeptide binding]; other site 407976004347 substrate binding site [chemical binding]; other site 407976004348 active site 407976004349 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 407976004350 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 407976004351 active site 407976004352 substrate binding site [chemical binding]; other site 407976004353 metal binding site [ion binding]; metal-binding site 407976004354 HutD; Region: HutD; pfam05962 407976004355 NlpE N-terminal domain; Region: NlpE; pfam04170 407976004356 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976004357 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 407976004358 active site 407976004359 phosphorylation site [posttranslational modification] 407976004360 intermolecular recognition site; other site 407976004361 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 407976004362 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 407976004363 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976004364 Zn2+ binding site [ion binding]; other site 407976004365 Mg2+ binding site [ion binding]; other site 407976004366 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976004367 GAF domain; Region: GAF; pfam01590 407976004368 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976004369 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 407976004370 ATP binding site [chemical binding]; other site 407976004371 Mg2+ binding site [ion binding]; other site 407976004372 G-X-G motif; other site 407976004373 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 407976004374 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 407976004375 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 407976004376 active site 407976004377 FMN binding site [chemical binding]; other site 407976004378 substrate binding site [chemical binding]; other site 407976004379 homotetramer interface [polypeptide binding]; other site 407976004380 catalytic residue [active] 407976004381 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 407976004382 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 407976004383 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 407976004384 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 407976004385 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 407976004386 nucleophile elbow; other site 407976004387 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 407976004388 active site 407976004389 oligomerization interface [polypeptide binding]; other site 407976004390 metal binding site [ion binding]; metal-binding site 407976004391 Cupin domain; Region: Cupin_2; cl17218 407976004392 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976004393 Helix-turn-helix domain; Region: HTH_18; pfam12833 407976004394 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976004395 prolyl-tRNA synthetase; Provisional; Region: PRK09194 407976004396 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 407976004397 dimer interface [polypeptide binding]; other site 407976004398 motif 1; other site 407976004399 active site 407976004400 motif 2; other site 407976004401 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 407976004402 putative deacylase active site [active] 407976004403 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 407976004404 active site 407976004405 motif 3; other site 407976004406 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 407976004407 anticodon binding site; other site 407976004408 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 407976004409 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 407976004410 putative CoA binding site [chemical binding]; other site 407976004411 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 407976004412 trimer interface [polypeptide binding]; other site 407976004413 active site 407976004414 substrate binding site [chemical binding]; other site 407976004415 CoA binding site [chemical binding]; other site 407976004416 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 407976004417 homodimer interaction site [polypeptide binding]; other site 407976004418 cofactor binding site; other site 407976004419 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 407976004420 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 407976004421 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 407976004422 active site 407976004423 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 407976004424 active site 407976004425 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 407976004426 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 407976004427 active site 407976004428 Amidohydrolase; Region: Amidohydro_5; pfam13594 407976004429 H-NS histone family; Region: Histone_HNS; pfam00816 407976004430 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 407976004431 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 407976004432 Ligand binding site [chemical binding]; other site 407976004433 Electron transfer flavoprotein domain; Region: ETF; pfam01012 407976004434 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 407976004435 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 407976004436 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 407976004437 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 407976004438 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 407976004439 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 407976004440 active site 407976004441 Zn binding site [ion binding]; other site 407976004442 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 407976004443 thymidine kinase; Provisional; Region: PRK04296 407976004444 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 407976004445 Transglycosylase; Region: Transgly; cl17702 407976004446 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976004447 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976004448 Coenzyme A binding pocket [chemical binding]; other site 407976004449 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 407976004450 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 407976004451 hypothetical protein; Provisional; Region: PRK10621 407976004452 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976004453 Arginine repressor [Transcription]; Region: ArgR; COG1438 407976004454 Putative amidotransferase; Region: DUF4066; pfam13278 407976004455 conserved cys residue [active] 407976004456 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 407976004457 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 407976004458 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 407976004459 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 407976004460 active site 407976004461 catalytic residues [active] 407976004462 metal binding site [ion binding]; metal-binding site 407976004463 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 407976004464 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 407976004465 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 407976004466 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 407976004467 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 407976004468 carboxyltransferase (CT) interaction site; other site 407976004469 biotinylation site [posttranslational modification]; other site 407976004470 enoyl-CoA hydratase; Provisional; Region: PRK05995 407976004471 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 407976004472 substrate binding site [chemical binding]; other site 407976004473 oxyanion hole (OAH) forming residues; other site 407976004474 trimer interface [polypeptide binding]; other site 407976004475 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 407976004476 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 407976004477 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 407976004478 isovaleryl-CoA dehydrogenase; Region: PLN02519 407976004479 substrate binding site [chemical binding]; other site 407976004480 FAD binding site [chemical binding]; other site 407976004481 catalytic base [active] 407976004482 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 407976004483 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 407976004484 DNA binding residues [nucleotide binding] 407976004485 putative dimer interface [polypeptide binding]; other site 407976004486 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 407976004487 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 407976004488 acyl-activating enzyme (AAE) consensus motif; other site 407976004489 AMP binding site [chemical binding]; other site 407976004490 active site 407976004491 CoA binding site [chemical binding]; other site 407976004492 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 407976004493 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 407976004494 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 407976004495 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 407976004496 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976004497 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976004498 LysR substrate binding domain; Region: LysR_substrate; pfam03466 407976004499 dimerization interface [polypeptide binding]; other site 407976004500 DoxX-like family; Region: DoxX_2; pfam13564 407976004501 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 407976004502 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 407976004503 putative active site [active] 407976004504 metal binding site [ion binding]; metal-binding site 407976004505 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 407976004506 UbiA prenyltransferase family; Region: UbiA; pfam01040 407976004507 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 407976004508 classical (c) SDRs; Region: SDR_c; cd05233 407976004509 NAD(P) binding site [chemical binding]; other site 407976004510 active site 407976004511 acyl-CoA thioesterase II; Provisional; Region: PRK10526 407976004512 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 407976004513 active site 407976004514 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 407976004515 catalytic triad [active] 407976004516 dimer interface [polypeptide binding]; other site 407976004517 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 407976004518 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 407976004519 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 407976004520 active site 407976004521 catalytic triad [active] 407976004522 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 407976004523 PA/protease or protease-like domain interface [polypeptide binding]; other site 407976004524 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 407976004525 catalytic residues [active] 407976004526 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976004527 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976004528 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976004529 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 407976004530 dimerization interface [polypeptide binding]; other site 407976004531 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976004532 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 407976004533 putative substrate translocation pore; other site 407976004534 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976004535 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976004536 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 407976004537 putative effector binding pocket; other site 407976004538 dimerization interface [polypeptide binding]; other site 407976004539 Protein of unknown function, DUF606; Region: DUF606; pfam04657 407976004540 Protein of unknown function, DUF606; Region: DUF606; pfam04657 407976004541 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 407976004542 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 407976004543 active site 407976004544 phosphorylation site [posttranslational modification] 407976004545 intermolecular recognition site; other site 407976004546 dimerization interface [polypeptide binding]; other site 407976004547 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 407976004548 Walker A motif; other site 407976004549 ATP binding site [chemical binding]; other site 407976004550 Walker B motif; other site 407976004551 arginine finger; other site 407976004552 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976004553 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 407976004554 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 407976004555 dimer interface [polypeptide binding]; other site 407976004556 phosphorylation site [posttranslational modification] 407976004557 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 407976004558 ATP binding site [chemical binding]; other site 407976004559 Mg2+ binding site [ion binding]; other site 407976004560 G-X-G motif; other site 407976004561 DctM-like transporters; Region: DctM; pfam06808 407976004562 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 407976004563 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 407976004564 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 407976004565 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 407976004566 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 407976004567 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 407976004568 active site 407976004569 HIGH motif; other site 407976004570 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 407976004571 active site 407976004572 KMSKS motif; other site 407976004573 potential protein location (hypothetical protein Sbal223_1555 [Shewanella baltica OS223]) that overlaps RNA (tRNA-A) 407976004574 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 407976004575 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976004576 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 407976004577 Walker A/P-loop; other site 407976004578 ATP binding site [chemical binding]; other site 407976004579 Q-loop/lid; other site 407976004580 ABC transporter signature motif; other site 407976004581 Walker B; other site 407976004582 D-loop; other site 407976004583 H-loop/switch region; other site 407976004584 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 407976004585 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 407976004586 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976004587 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976004588 AlkA N-terminal domain; Region: AlkA_N; pfam06029 407976004589 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 407976004590 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 407976004591 minor groove reading motif; other site 407976004592 helix-hairpin-helix signature motif; other site 407976004593 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 407976004594 DNA binding site [nucleotide binding] 407976004595 active site 407976004596 helicase 45; Provisional; Region: PTZ00424 407976004597 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 407976004598 ATP binding site [chemical binding]; other site 407976004599 Mg++ binding site [ion binding]; other site 407976004600 motif III; other site 407976004601 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 407976004602 nucleotide binding region [chemical binding]; other site 407976004603 ATP-binding site [chemical binding]; other site 407976004604 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 407976004605 active site 407976004606 catalytic residues [active] 407976004607 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 407976004608 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976004609 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 407976004610 active site 407976004611 phosphorylation site [posttranslational modification] 407976004612 intermolecular recognition site; other site 407976004613 dimerization interface [polypeptide binding]; other site 407976004614 serine/threonine transporter SstT; Provisional; Region: PRK13628 407976004615 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976004616 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 407976004617 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 407976004618 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976004619 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976004620 active site 407976004621 Protein of unknown function, DUF479; Region: DUF479; pfam04336 407976004622 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 407976004623 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 407976004624 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 407976004625 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 407976004626 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 407976004627 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 407976004628 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 407976004629 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 407976004630 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 407976004631 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 407976004632 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 407976004633 Protein export membrane protein; Region: SecD_SecF; pfam02355 407976004634 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 407976004635 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 407976004636 active site residue [active] 407976004637 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 407976004638 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 407976004639 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 407976004640 YaeQ protein; Region: YaeQ; pfam07152 407976004641 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 407976004642 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 407976004643 active site 407976004644 catalytic residues [active] 407976004645 PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from...; Region: PA_VapT_like; cd04817 407976004646 PA/subtilisin-like domain interface [polypeptide binding]; other site 407976004647 Subtilase family; Region: Peptidase_S8; pfam00082 407976004648 catalytic residues [active] 407976004649 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 407976004650 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 407976004651 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976004652 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976004653 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 407976004654 Coenzyme A binding pocket [chemical binding]; other site 407976004655 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 407976004656 active site residue [active] 407976004657 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 407976004658 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976004659 Protein export membrane protein; Region: SecD_SecF; cl14618 407976004660 Protein export membrane protein; Region: SecD_SecF; cl14618 407976004661 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976004662 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976004663 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976004664 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 407976004665 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 407976004666 active site 407976004667 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 407976004668 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 407976004669 Na binding site [ion binding]; other site 407976004670 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 407976004671 RNA polymerase sigma factor; Provisional; Region: PRK12517 407976004672 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976004673 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 407976004674 DNA binding residues [nucleotide binding] 407976004675 Oxygen tolerance; Region: BatD; pfam13584 407976004676 von Willebrand factor type A domain; Region: VWA_2; pfam13519 407976004677 metal ion-dependent adhesion site (MIDAS); other site 407976004678 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 407976004679 binding surface 407976004680 TPR motif; other site 407976004681 Tetratricopeptide repeat; Region: TPR_16; pfam13432 407976004682 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 407976004683 VWA BatA type: 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_BatA_type; cd01467 407976004684 metal ion-dependent adhesion site (MIDAS); other site 407976004685 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 407976004686 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 407976004687 Protein of unknown function DUF58; Region: DUF58; pfam01882 407976004688 MoxR-like ATPases [General function prediction only]; Region: COG0714 407976004689 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 407976004690 Walker A motif; other site 407976004691 ATP binding site [chemical binding]; other site 407976004692 Walker B motif; other site 407976004693 arginine finger; other site 407976004694 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 407976004695 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 407976004696 dimer interface [polypeptide binding]; other site 407976004697 active site 407976004698 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 407976004699 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 407976004700 substrate binding site [chemical binding]; other site 407976004701 oxyanion hole (OAH) forming residues; other site 407976004702 trimer interface [polypeptide binding]; other site 407976004703 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 407976004704 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 407976004705 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 407976004706 Two component regulator propeller; Region: Reg_prop; pfam07494 407976004707 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 407976004708 PAS fold; Region: PAS_3; pfam08447 407976004709 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 407976004710 PAS domain; Region: PAS_9; pfam13426 407976004711 putative active site [active] 407976004712 heme pocket [chemical binding]; other site 407976004713 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976004714 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976004715 metal binding site [ion binding]; metal-binding site 407976004716 active site 407976004717 I-site; other site 407976004718 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 407976004719 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 407976004720 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976004721 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976004722 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976004723 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 407976004724 catalytic core [active] 407976004725 hypothetical protein; Provisional; Region: PRK04946 407976004726 Smr domain; Region: Smr; pfam01713 407976004727 HemK family putative methylases; Region: hemK_fam; TIGR00536 407976004728 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 407976004729 S-adenosylmethionine binding site [chemical binding]; other site 407976004730 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 407976004731 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 407976004732 Tetramer interface [polypeptide binding]; other site 407976004733 active site 407976004734 FMN-binding site [chemical binding]; other site 407976004735 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 407976004736 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 407976004737 putative substrate translocation pore; other site 407976004738 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 407976004739 YfcL protein; Region: YfcL; pfam08891 407976004740 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 407976004741 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 407976004742 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 407976004743 tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain; Region: MnmC_Cterm; TIGR03197 407976004744 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 407976004745 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 407976004746 dimer interface [polypeptide binding]; other site 407976004747 active site 407976004748 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 407976004749 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 407976004750 ligand binding site [chemical binding]; other site 407976004751 NAD binding site [chemical binding]; other site 407976004752 catalytic site [active] 407976004753 homodimer interface [polypeptide binding]; other site 407976004754 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 407976004755 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 407976004756 FimV N-terminal domain; Region: FimV_core; TIGR03505 407976004757 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 407976004758 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 407976004759 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 407976004760 dimerization interface 3.5A [polypeptide binding]; other site 407976004761 active site 407976004762 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 407976004763 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 407976004764 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 407976004765 Sporulation related domain; Region: SPOR; pfam05036 407976004766 Colicin V production protein; Region: Colicin_V; cl00567 407976004767 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 407976004768 amidophosphoribosyltransferase; Provisional; Region: PRK09246 407976004769 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 407976004770 active site 407976004771 tetramer interface [polypeptide binding]; other site 407976004772 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976004773 active site 407976004774 DNA topoisomerase III; Provisional; Region: PRK07726 407976004775 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 407976004776 active site 407976004777 putative interdomain interaction site [polypeptide binding]; other site 407976004778 putative metal-binding site [ion binding]; other site 407976004779 putative nucleotide binding site [chemical binding]; other site 407976004780 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 407976004781 domain I; other site 407976004782 DNA binding groove [nucleotide binding] 407976004783 phosphate binding site [ion binding]; other site 407976004784 domain II; other site 407976004785 domain III; other site 407976004786 nucleotide binding site [chemical binding]; other site 407976004787 catalytic site [active] 407976004788 domain IV; other site 407976004789 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 407976004790 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 407976004791 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976004792 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 407976004793 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976004794 dimer interface [polypeptide binding]; other site 407976004795 putative CheW interface [polypeptide binding]; other site 407976004796 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 407976004797 XdhC Rossmann domain; Region: XdhC_C; pfam13478 407976004798 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 407976004799 Ligand binding site; other site 407976004800 metal-binding site 407976004801 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 407976004802 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 407976004803 catalytic loop [active] 407976004804 iron binding site [ion binding]; other site 407976004805 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 407976004806 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 407976004807 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 407976004808 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 407976004809 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 407976004810 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 407976004811 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 407976004812 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 407976004813 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976004814 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976004815 dimer interface [polypeptide binding]; other site 407976004816 putative CheW interface [polypeptide binding]; other site 407976004817 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 407976004818 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 407976004819 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 407976004820 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 407976004821 ligand binding site [chemical binding]; other site 407976004822 flexible hinge region; other site 407976004823 non-specific DNA interactions [nucleotide binding]; other site 407976004824 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 407976004825 DNA binding site [nucleotide binding] 407976004826 sequence specific DNA binding site [nucleotide binding]; other site 407976004827 putative cAMP binding site [chemical binding]; other site 407976004828 PRC-barrel domain; Region: PRC; pfam05239 407976004829 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976004830 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976004831 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976004832 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 407976004833 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 407976004834 putative catalytic site [active] 407976004835 putative phosphate binding site [ion binding]; other site 407976004836 active site 407976004837 metal binding site A [ion binding]; metal-binding site 407976004838 DNA binding site [nucleotide binding] 407976004839 putative AP binding site [nucleotide binding]; other site 407976004840 putative metal binding site B [ion binding]; other site 407976004841 YciI-like protein; Reviewed; Region: PRK11370 407976004842 intracellular septation protein A; Reviewed; Region: PRK00259 407976004843 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 407976004844 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 407976004845 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 407976004846 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 407976004847 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 407976004848 N-terminal plug; other site 407976004849 ligand-binding site [chemical binding]; other site 407976004850 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 407976004851 IucA / IucC family; Region: IucA_IucC; pfam04183 407976004852 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 407976004853 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 407976004854 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 407976004855 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 407976004856 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976004857 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 407976004858 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 407976004859 substrate binding site [chemical binding]; other site 407976004860 active site 407976004861 catalytic residues [active] 407976004862 heterodimer interface [polypeptide binding]; other site 407976004863 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 407976004864 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 407976004865 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976004866 catalytic residue [active] 407976004867 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 407976004868 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 407976004869 active site 407976004870 ribulose/triose binding site [chemical binding]; other site 407976004871 phosphate binding site [ion binding]; other site 407976004872 substrate (anthranilate) binding pocket [chemical binding]; other site 407976004873 product (indole) binding pocket [chemical binding]; other site 407976004874 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 407976004875 active site 407976004876 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 407976004877 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 407976004878 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 407976004879 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 407976004880 glutamine binding [chemical binding]; other site 407976004881 catalytic triad [active] 407976004882 anthranilate synthase component I; Provisional; Region: PRK13564 407976004883 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 407976004884 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 407976004885 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 407976004886 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 407976004887 active site 407976004888 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 407976004889 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 407976004890 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 407976004891 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 407976004892 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 407976004893 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 407976004894 RNA binding surface [nucleotide binding]; other site 407976004895 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 407976004896 probable active site [active] 407976004897 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976004898 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976004899 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976004900 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 407976004901 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976004902 NAD(P) binding site [chemical binding]; other site 407976004903 active site 407976004904 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 407976004905 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 407976004906 putative inner membrane peptidase; Provisional; Region: PRK11778 407976004907 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 407976004908 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 407976004909 tandem repeat interface [polypeptide binding]; other site 407976004910 oligomer interface [polypeptide binding]; other site 407976004911 active site residues [active] 407976004912 Predicted integral membrane protein [Function unknown]; Region: COG0392 407976004913 Uncharacterized conserved protein [Function unknown]; Region: COG2898 407976004914 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 407976004915 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 407976004916 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 407976004917 Protein of unknown function (DUF3083); Region: DUF3083; pfam11281 407976004918 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 407976004919 active site 407976004920 catalytic triad [active] 407976004921 oxyanion hole [active] 407976004922 switch loop; other site 407976004923 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 407976004924 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 407976004925 Walker A/P-loop; other site 407976004926 ATP binding site [chemical binding]; other site 407976004927 Q-loop/lid; other site 407976004928 ABC transporter signature motif; other site 407976004929 Walker B; other site 407976004930 D-loop; other site 407976004931 H-loop/switch region; other site 407976004932 FtsX-like permease family; Region: FtsX; pfam02687 407976004933 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 407976004934 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 407976004935 Catalytic site [active] 407976004936 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 407976004937 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 407976004938 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 407976004939 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 407976004940 putative NAD(P) binding site [chemical binding]; other site 407976004941 putative active site [active] 407976004942 D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional; Region: folX; PRK11245 407976004943 active site 407976004944 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 407976004945 Domain of unknown function DUF20; Region: UPF0118; pfam01594 407976004946 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 407976004947 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 407976004948 S-adenosylmethionine binding site [chemical binding]; other site 407976004949 phosphate acetyltransferase; Reviewed; Region: PRK05632 407976004950 DRTGG domain; Region: DRTGG; pfam07085 407976004951 phosphate acetyltransferase; Region: pta; TIGR00651 407976004952 propionate/acetate kinase; Provisional; Region: PRK12379 407976004953 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 407976004954 nucleotide binding site [chemical binding]; other site 407976004955 butyrate kinase; Provisional; Region: PRK03011 407976004956 Protein of unknown function, DUF412; Region: DUF412; pfam04217 407976004957 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 407976004958 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 407976004959 FeS/SAM binding site; other site 407976004960 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 407976004961 Pyruvate formate lyase 1; Region: PFL1; cd01678 407976004962 coenzyme A binding site [chemical binding]; other site 407976004963 active site 407976004964 catalytic residues [active] 407976004965 glycine loop; other site 407976004966 formate transporter FocA; Region: formate_focA; TIGR04060 407976004967 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 407976004968 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 407976004969 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976004970 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 407976004971 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 407976004972 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 407976004973 gating phenylalanine in ion channel; other site 407976004974 Methyltransferase domain; Region: Methyltransf_18; pfam12847 407976004975 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 407976004976 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 407976004977 dimer interface [polypeptide binding]; other site 407976004978 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976004979 catalytic residue [active] 407976004980 RDD family; Region: RDD; pfam06271 407976004981 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 407976004982 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 407976004983 active site 407976004984 putative sulfate transport protein CysZ; Validated; Region: PRK04949 407976004985 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 407976004986 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 407976004987 Walker A/P-loop; other site 407976004988 ATP binding site [chemical binding]; other site 407976004989 Q-loop/lid; other site 407976004990 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 407976004991 ABC transporter signature motif; other site 407976004992 Walker B; other site 407976004993 D-loop; other site 407976004994 H-loop/switch region; other site 407976004995 Cell division protein [Cell division and chromosome partitioning]; Region: ZipA; COG3115 407976004996 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 407976004997 FtsZ protein binding site [polypeptide binding]; other site 407976004998 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 407976004999 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 407976005000 nucleotide binding pocket [chemical binding]; other site 407976005001 K-X-D-G motif; other site 407976005002 catalytic site [active] 407976005003 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 407976005004 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 407976005005 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 407976005006 Dimer interface [polypeptide binding]; other site 407976005007 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 407976005008 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 407976005009 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 407976005010 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976005011 Zn2+ binding site [ion binding]; other site 407976005012 Mg2+ binding site [ion binding]; other site 407976005013 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 407976005014 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 407976005015 putative NAD(P) binding site [chemical binding]; other site 407976005016 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 407976005017 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 407976005018 catalytic residues [active] 407976005019 hinge region; other site 407976005020 alpha helical domain; other site 407976005021 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 407976005022 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 407976005023 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 407976005024 Na binding site [ion binding]; other site 407976005025 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 407976005026 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 407976005027 ligand binding site [chemical binding]; other site 407976005028 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 407976005029 flexible hinge region; other site 407976005030 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 407976005031 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 407976005032 metal binding triad; other site 407976005033 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 407976005034 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 407976005035 active site 407976005036 catalytic site [active] 407976005037 substrate binding site [chemical binding]; other site 407976005038 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 407976005039 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 407976005040 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 407976005041 dimer interface [polypeptide binding]; other site 407976005042 active site 407976005043 CoA binding pocket [chemical binding]; other site 407976005044 Transcriptional regulators [Transcription]; Region: GntR; COG1802 407976005045 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976005046 DNA-binding site [nucleotide binding]; DNA binding site 407976005047 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 407976005048 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 407976005049 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 407976005050 active site 407976005051 motif I; other site 407976005052 motif II; other site 407976005053 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 407976005054 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 407976005055 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 407976005056 active site 407976005057 metal binding site [ion binding]; metal-binding site 407976005058 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 407976005059 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 407976005060 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 407976005061 active site 407976005062 Zn binding site [ion binding]; other site 407976005063 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976005064 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976005065 Coenzyme A binding pocket [chemical binding]; other site 407976005066 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 407976005067 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 407976005068 active site 407976005069 Zn binding site [ion binding]; other site 407976005070 hypothetical protein; Provisional; Region: PRK06156 407976005071 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 407976005072 active site 407976005073 metal binding site [ion binding]; metal-binding site 407976005074 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 407976005075 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 407976005076 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 407976005077 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 407976005078 Protein of unknown function, DUF482; Region: DUF482; pfam04339 407976005079 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 407976005080 maltose O-acetyltransferase; Provisional; Region: PRK10092 407976005081 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 407976005082 active site 407976005083 substrate binding site [chemical binding]; other site 407976005084 trimer interface [polypeptide binding]; other site 407976005085 CoA binding site [chemical binding]; other site 407976005086 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 407976005087 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 407976005088 dimer interface [polypeptide binding]; other site 407976005089 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 407976005090 active site 407976005091 Fe binding site [ion binding]; other site 407976005092 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 407976005093 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976005094 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976005095 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 407976005096 dimerization interface [polypeptide binding]; other site 407976005097 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 407976005098 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 407976005099 Polysaccharide biosynthesis protein; Region: Polysacc_synt_3; pfam13440 407976005100 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 407976005101 Uncharacterized conserved protein [Function unknown]; Region: COG2947 407976005102 AMP-binding domain protein; Validated; Region: PRK08315 407976005103 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 407976005104 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 407976005105 acyl-activating enzyme (AAE) consensus motif; other site 407976005106 putative AMP binding site [chemical binding]; other site 407976005107 putative active site [active] 407976005108 putative CoA binding site [chemical binding]; other site 407976005109 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 407976005110 membrane-bound complex binding site; other site 407976005111 hinge residues; other site 407976005112 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 407976005113 putative active site [active] 407976005114 Zn binding site [ion binding]; other site 407976005115 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 407976005116 hypothetical protein; Provisional; Region: PRK11770 407976005117 Domain of unknown function (DUF307); Region: DUF307; pfam03733 407976005118 Domain of unknown function (DUF307); Region: DUF307; pfam03733 407976005119 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 407976005120 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 407976005121 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 407976005122 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 407976005123 RNA polymerase sigma factor; Provisional; Region: PRK11924 407976005124 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976005125 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 407976005126 DNA binding residues [nucleotide binding] 407976005127 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 407976005128 Methyltransferase domain; Region: Methyltransf_31; pfam13847 407976005129 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 407976005130 S-adenosylmethionine binding site [chemical binding]; other site 407976005131 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 407976005132 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976005133 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 407976005134 active site 407976005135 phosphorylation site [posttranslational modification] 407976005136 intermolecular recognition site; other site 407976005137 dimerization interface [polypeptide binding]; other site 407976005138 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 407976005139 Transglycosylase SLT domain; Region: SLT_2; pfam13406 407976005140 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 407976005141 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976005142 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 407976005143 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 407976005144 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976005145 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 407976005146 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 407976005147 active site 407976005148 Zn binding site [ion binding]; other site 407976005149 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 407976005150 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 407976005151 putative hydrolase; Provisional; Region: PRK11460 407976005152 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 407976005153 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 407976005154 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 407976005155 active site 407976005156 metal binding site [ion binding]; metal-binding site 407976005157 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 407976005158 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 407976005159 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 407976005160 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 407976005161 FMN binding site [chemical binding]; other site 407976005162 active site 407976005163 catalytic residues [active] 407976005164 substrate binding site [chemical binding]; other site 407976005165 hypothetical protein; Provisional; Region: PRK05409 407976005166 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 407976005167 hypothetical protein; Provisional; Region: PRK10527 407976005168 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976005169 active site 407976005170 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14949 407976005171 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 407976005172 Walker A motif; other site 407976005173 ATP binding site [chemical binding]; other site 407976005174 Walker B motif; other site 407976005175 arginine finger; other site 407976005176 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 407976005177 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 407976005178 hypothetical protein; Validated; Region: PRK00153 407976005179 recombination protein RecR; Reviewed; Region: recR; PRK00076 407976005180 RecR protein; Region: RecR; pfam02132 407976005181 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 407976005182 putative active site [active] 407976005183 putative metal-binding site [ion binding]; other site 407976005184 tetramer interface [polypeptide binding]; other site 407976005185 putative acetyltransferase YhhY; Provisional; Region: PRK10140 407976005186 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976005187 Coenzyme A binding pocket [chemical binding]; other site 407976005188 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 407976005189 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 407976005190 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 407976005191 S-adenosylmethionine binding site [chemical binding]; other site 407976005192 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 407976005193 S-adenosylmethionine binding site [chemical binding]; other site 407976005194 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 407976005195 ABC transporter ATPase component; Reviewed; Region: PRK11147 407976005196 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976005197 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976005198 ABC transporter; Region: ABC_tran_2; pfam12848 407976005199 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976005200 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 407976005201 ribosome modulation factor; Provisional; Region: PRK14563 407976005202 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 407976005203 active site 1 [active] 407976005204 dimer interface [polypeptide binding]; other site 407976005205 active site 2 [active] 407976005206 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 407976005207 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 407976005208 Cache domain; Region: Cache_1; pfam02743 407976005209 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 407976005210 dimerization interface [polypeptide binding]; other site 407976005211 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976005212 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976005213 dimer interface [polypeptide binding]; other site 407976005214 putative CheW interface [polypeptide binding]; other site 407976005215 response regulator; Provisional; Region: PRK09483 407976005216 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 407976005217 active site 407976005218 phosphorylation site [posttranslational modification] 407976005219 intermolecular recognition site; other site 407976005220 dimerization interface [polypeptide binding]; other site 407976005221 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 407976005222 DNA binding residues [nucleotide binding] 407976005223 dimerization interface [polypeptide binding]; other site 407976005224 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 407976005225 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 407976005226 GIY-YIG motif/motif A; other site 407976005227 active site 407976005228 catalytic site [active] 407976005229 putative DNA binding site [nucleotide binding]; other site 407976005230 metal binding site [ion binding]; metal-binding site 407976005231 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 407976005232 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 407976005233 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 407976005234 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 407976005235 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 407976005236 active site pocket [active] 407976005237 oxyanion hole [active] 407976005238 catalytic triad [active] 407976005239 active site nucleophile [active] 407976005240 heat shock protein HtpX; Provisional; Region: PRK05457 407976005241 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 407976005242 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976005243 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 407976005244 putative dimerization interface [polypeptide binding]; other site 407976005245 Lysine efflux permease [General function prediction only]; Region: COG1279 407976005246 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 407976005247 catalytic triad [active] 407976005248 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 407976005249 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 407976005250 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 407976005251 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 407976005252 dihydrodipicolinate synthase; Region: dapA; TIGR00674 407976005253 dimer interface [polypeptide binding]; other site 407976005254 active site 407976005255 catalytic residue [active] 407976005256 lipoprotein; Provisional; Region: PRK11679 407976005257 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 407976005258 putative transposase OrfB; Reviewed; Region: PHA02517 407976005259 Integrase core domain; Region: rve; pfam00665 407976005260 Integrase core domain; Region: rve_3; pfam13683 407976005261 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976005262 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976005263 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976005264 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976005265 Protein export membrane protein; Region: SecD_SecF; cl14618 407976005266 heat shock protein 90; Provisional; Region: PRK05218 407976005267 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 407976005268 ATP binding site [chemical binding]; other site 407976005269 Mg2+ binding site [ion binding]; other site 407976005270 G-X-G motif; other site 407976005271 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 407976005272 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 407976005273 adenylate kinase; Reviewed; Region: adk; PRK00279 407976005274 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 407976005275 AMP-binding site [chemical binding]; other site 407976005276 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 407976005277 ferrochelatase; Reviewed; Region: hemH; PRK00035 407976005278 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 407976005279 C-terminal domain interface [polypeptide binding]; other site 407976005280 active site 407976005281 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 407976005282 active site 407976005283 N-terminal domain interface [polypeptide binding]; other site 407976005284 inosine/guanosine kinase; Provisional; Region: PRK15074 407976005285 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 407976005286 substrate binding site [chemical binding]; other site 407976005287 ATP binding site [chemical binding]; other site 407976005288 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 407976005289 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 407976005290 homodimer interface [polypeptide binding]; other site 407976005291 NAD binding pocket [chemical binding]; other site 407976005292 ATP binding pocket [chemical binding]; other site 407976005293 Mg binding site [ion binding]; other site 407976005294 active-site loop [active] 407976005295 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 407976005296 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 407976005297 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976005298 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976005299 metal binding site [ion binding]; metal-binding site 407976005300 active site 407976005301 I-site; other site 407976005302 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 407976005303 active site 407976005304 DNA binding site [nucleotide binding] 407976005305 Int/Topo IB signature motif; other site 407976005306 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 407976005307 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 407976005308 catalytic residues [active] 407976005309 catalytic nucleophile [active] 407976005310 Presynaptic Site I dimer interface [polypeptide binding]; other site 407976005311 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 407976005312 Synaptic Flat tetramer interface [polypeptide binding]; other site 407976005313 Synaptic Site I dimer interface [polypeptide binding]; other site 407976005314 DNA binding site [nucleotide binding] 407976005315 Homeodomain-like domain; Region: HTH_23; pfam13384 407976005316 hypothetical protein; Provisional; Region: PRK02135 407976005317 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976005318 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976005319 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 407976005320 dimerization interface [polypeptide binding]; other site 407976005321 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 407976005322 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 407976005323 active site 407976005324 FMN binding site [chemical binding]; other site 407976005325 substrate binding site [chemical binding]; other site 407976005326 homotetramer interface [polypeptide binding]; other site 407976005327 catalytic residue [active] 407976005328 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 407976005329 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 407976005330 Sulfatase; Region: Sulfatase; cl17466 407976005331 hypothetical protein; Provisional; Region: PRK13689 407976005332 Nucleoid-associated protein [General function prediction only]; Region: COG3081 407976005333 nucleoid-associated protein NdpA; Validated; Region: PRK00378 407976005334 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 407976005335 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 407976005336 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 407976005337 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976005338 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_4; cd07268 407976005339 putative metal binding site [ion binding]; other site 407976005340 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 407976005341 Ion transport protein; Region: Ion_trans; pfam00520 407976005342 Ion channel; Region: Ion_trans_2; pfam07885 407976005343 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 407976005344 putative efflux protein, MATE family; Region: matE; TIGR00797 407976005345 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 407976005346 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as...; Region: ASCH_yqfb_like; cd06552 407976005347 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976005348 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976005349 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976005350 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976005351 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976005352 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 407976005353 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 407976005354 dimer interface [polypeptide binding]; other site 407976005355 active site 407976005356 citrylCoA binding site [chemical binding]; other site 407976005357 NADH binding [chemical binding]; other site 407976005358 cationic pore residues; other site 407976005359 oxalacetate/citrate binding site [chemical binding]; other site 407976005360 coenzyme A binding site [chemical binding]; other site 407976005361 catalytic triad [active] 407976005362 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 407976005363 Iron-sulfur protein interface; other site 407976005364 proximal quinone binding site [chemical binding]; other site 407976005365 SdhD (CybS) interface [polypeptide binding]; other site 407976005366 proximal heme binding site [chemical binding]; other site 407976005367 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 407976005368 SdhC subunit interface [polypeptide binding]; other site 407976005369 proximal heme binding site [chemical binding]; other site 407976005370 cardiolipin binding site; other site 407976005371 Iron-sulfur protein interface; other site 407976005372 proximal quinone binding site [chemical binding]; other site 407976005373 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 407976005374 L-aspartate oxidase; Provisional; Region: PRK06175 407976005375 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 407976005376 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 407976005377 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 407976005378 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 407976005379 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 407976005380 TPP-binding site [chemical binding]; other site 407976005381 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 407976005382 PYR/PP interface [polypeptide binding]; other site 407976005383 dimer interface [polypeptide binding]; other site 407976005384 TPP binding site [chemical binding]; other site 407976005385 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 407976005386 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 407976005387 E3 interaction surface; other site 407976005388 lipoyl attachment site [posttranslational modification]; other site 407976005389 e3 binding domain; Region: E3_binding; pfam02817 407976005390 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 407976005391 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 407976005392 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 407976005393 CoA-ligase; Region: Ligase_CoA; pfam00549 407976005394 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 407976005395 CoA binding domain; Region: CoA_binding; pfam02629 407976005396 CoA-ligase; Region: Ligase_CoA; pfam00549 407976005397 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 407976005398 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 407976005399 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976005400 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976005401 ferric uptake regulator; Provisional; Region: fur; PRK09462 407976005402 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 407976005403 metal binding site 2 [ion binding]; metal-binding site 407976005404 putative DNA binding helix; other site 407976005405 metal binding site 1 [ion binding]; metal-binding site 407976005406 dimer interface [polypeptide binding]; other site 407976005407 structural Zn2+ binding site [ion binding]; other site 407976005408 NAD-dependent deacetylase; Provisional; Region: PRK00481 407976005409 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 407976005410 NAD+ binding site [chemical binding]; other site 407976005411 substrate binding site [chemical binding]; other site 407976005412 Zn binding site [ion binding]; other site 407976005413 AAA domain; Region: AAA_33; pfam13671 407976005414 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 407976005415 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 407976005416 Cl binding site [ion binding]; other site 407976005417 oligomer interface [polypeptide binding]; other site 407976005418 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 407976005419 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976005420 Zn2+ binding site [ion binding]; other site 407976005421 Mg2+ binding site [ion binding]; other site 407976005422 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 407976005423 sensor protein PhoQ; Provisional; Region: PRK10815 407976005424 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 407976005425 ATP binding site [chemical binding]; other site 407976005426 Mg2+ binding site [ion binding]; other site 407976005427 G-X-G motif; other site 407976005428 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 407976005429 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 407976005430 active site 407976005431 phosphorylation site [posttranslational modification] 407976005432 intermolecular recognition site; other site 407976005433 dimerization interface [polypeptide binding]; other site 407976005434 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 407976005435 DNA binding site [nucleotide binding] 407976005436 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976005437 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 407976005438 succinylarginine dihydrolase; Provisional; Region: PRK13281 407976005439 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 407976005440 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 407976005441 active site 407976005442 interdomain interaction site; other site 407976005443 putative metal-binding site [ion binding]; other site 407976005444 nucleotide binding site [chemical binding]; other site 407976005445 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 407976005446 domain I; other site 407976005447 DNA binding groove [nucleotide binding] 407976005448 phosphate binding site [ion binding]; other site 407976005449 domain II; other site 407976005450 domain III; other site 407976005451 nucleotide binding site [chemical binding]; other site 407976005452 catalytic site [active] 407976005453 domain IV; other site 407976005454 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 407976005455 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 407976005456 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 407976005457 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 407976005458 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 407976005459 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976005460 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 407976005461 substrate binding site [chemical binding]; other site 407976005462 dimerization interface [polypeptide binding]; other site 407976005463 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976005464 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 407976005465 active site 407976005466 phosphorylation site [posttranslational modification] 407976005467 intermolecular recognition site; other site 407976005468 dimerization interface [polypeptide binding]; other site 407976005469 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 407976005470 DNA binding residues [nucleotide binding] 407976005471 dimerization interface [polypeptide binding]; other site 407976005472 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 407976005473 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 407976005474 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 407976005475 aromatic chitin/cellulose binding site residues [chemical binding]; other site 407976005476 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 407976005477 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 407976005478 active site 407976005479 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 407976005480 Chitinase C; Region: ChiC; pfam06483 407976005481 Cellulose-binding domain, chitinase and related proteins; Region: CBD_like; cd12204 407976005482 aromatic chitin/cellulose binding site residues [chemical binding]; other site 407976005483 ligand binding site [chemical binding]; other site 407976005484 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12756 407976005485 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 407976005486 PEP synthetase regulatory protein; Provisional; Region: PRK05339 407976005487 phosphoenolpyruvate synthase; Validated; Region: PRK06464 407976005488 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 407976005489 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 407976005490 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 407976005491 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 407976005492 FAD binding domain; Region: FAD_binding_4; pfam01565 407976005493 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 407976005494 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 407976005495 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 407976005496 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 407976005497 MarR family; Region: MarR; pfam01047 407976005498 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 407976005499 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 407976005500 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 407976005501 NAD binding site [chemical binding]; other site 407976005502 Phe binding site; other site 407976005503 Cupin superfamily protein; Region: Cupin_4; pfam08007 407976005504 Cupin-like domain; Region: Cupin_8; pfam13621 407976005505 adenylosuccinate lyase; Provisional; Region: PRK09285 407976005506 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 407976005507 tetramer interface [polypeptide binding]; other site 407976005508 active site 407976005509 putative lysogenization regulator; Reviewed; Region: PRK00218 407976005510 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 407976005511 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 407976005512 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 407976005513 nudix motif; other site 407976005514 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 407976005515 pseudouridine synthase; Region: TIGR00093 407976005516 probable active site [active] 407976005517 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 407976005518 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 407976005519 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 407976005520 DNA-binding site [nucleotide binding]; DNA binding site 407976005521 RNA-binding motif; other site 407976005522 Uncharacterized conserved protein [Function unknown]; Region: COG2127 407976005523 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 407976005524 Clp amino terminal domain; Region: Clp_N; pfam02861 407976005525 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 407976005526 Walker A motif; other site 407976005527 ATP binding site [chemical binding]; other site 407976005528 Walker B motif; other site 407976005529 arginine finger; other site 407976005530 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 407976005531 Walker A motif; other site 407976005532 ATP binding site [chemical binding]; other site 407976005533 Walker B motif; other site 407976005534 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 407976005535 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 407976005536 rRNA binding site [nucleotide binding]; other site 407976005537 predicted 30S ribosome binding site; other site 407976005538 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 407976005539 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 407976005540 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 407976005541 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 407976005542 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 407976005543 Uncharacterized conserved protein [Function unknown]; Region: COG0327 407976005544 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 407976005545 Predicted permeases [General function prediction only]; Region: COG0679 407976005546 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 407976005547 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 407976005548 active site 407976005549 HIGH motif; other site 407976005550 KMSKS motif; other site 407976005551 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 407976005552 tRNA binding surface [nucleotide binding]; other site 407976005553 anticodon binding site; other site 407976005554 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 407976005555 dimer interface [polypeptide binding]; other site 407976005556 putative tRNA-binding site [nucleotide binding]; other site 407976005557 antiporter inner membrane protein; Provisional; Region: PRK11670 407976005558 Domain of unknown function DUF59; Region: DUF59; cl00941 407976005559 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 407976005560 Walker A motif; other site 407976005561 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 407976005562 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 407976005563 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 407976005564 Sugar specificity; other site 407976005565 Pyrimidine base specificity; other site 407976005566 ATP-binding site [chemical binding]; other site 407976005567 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 407976005568 trimer interface [polypeptide binding]; other site 407976005569 active site 407976005570 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 407976005571 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 407976005572 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976005573 catalytic residue [active] 407976005574 YceG-like family; Region: YceG; pfam02618 407976005575 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 407976005576 dimerization interface [polypeptide binding]; other site 407976005577 thymidylate kinase; Validated; Region: tmk; PRK00698 407976005578 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 407976005579 TMP-binding site; other site 407976005580 ATP-binding site [chemical binding]; other site 407976005581 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 407976005582 DNA polymerase III subunit delta'; Validated; Region: PRK08485 407976005583 PilZ domain; Region: PilZ; cl01260 407976005584 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 407976005585 active site 407976005586 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 407976005587 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 407976005588 S-adenosylmethionine binding site [chemical binding]; other site 407976005589 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 407976005590 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 407976005591 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 407976005592 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 407976005593 mce related protein; Region: MCE; pfam02470 407976005594 mce related protein; Region: MCE; pfam02470 407976005595 mce related protein; Region: MCE; pfam02470 407976005596 mce related protein; Region: MCE; pfam02470 407976005597 mce related protein; Region: MCE; pfam02470 407976005598 mce related protein; Region: MCE; pfam02470 407976005599 Paraquat-inducible protein A; Region: PqiA; pfam04403 407976005600 Paraquat-inducible protein A; Region: PqiA; pfam04403 407976005601 YebG protein; Region: YebG; pfam07130 407976005602 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 407976005603 GAF domain; Region: GAF_2; pfam13185 407976005604 ProP expression regulator; Provisional; Region: PRK04950 407976005605 ProQ/FINO family; Region: ProQ; smart00945 407976005606 carboxy-terminal protease; Provisional; Region: PRK11186 407976005607 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 407976005608 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 407976005609 protein binding site [polypeptide binding]; other site 407976005610 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 407976005611 Catalytic dyad [active] 407976005612 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 407976005613 aminopeptidase N; Provisional; Region: pepN; PRK14015 407976005614 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 407976005615 active site 407976005616 Zn binding site [ion binding]; other site 407976005617 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 407976005618 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 407976005619 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 407976005620 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 407976005621 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 407976005622 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 407976005623 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 407976005624 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 407976005625 quinone interaction residues [chemical binding]; other site 407976005626 active site 407976005627 catalytic residues [active] 407976005628 FMN binding site [chemical binding]; other site 407976005629 substrate binding site [chemical binding]; other site 407976005630 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 407976005631 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976005632 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976005633 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 407976005634 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 407976005635 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 407976005636 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 407976005637 aromatic amino acid transport protein; Region: araaP; TIGR00837 407976005638 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 407976005639 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 407976005640 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 407976005641 metal binding site [ion binding]; metal-binding site 407976005642 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 407976005643 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 407976005644 substrate binding site [chemical binding]; other site 407976005645 glutamase interaction surface [polypeptide binding]; other site 407976005646 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 407976005647 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 407976005648 catalytic residues [active] 407976005649 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 407976005650 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 407976005651 putative active site [active] 407976005652 oxyanion strand; other site 407976005653 catalytic triad [active] 407976005654 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 407976005655 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 407976005656 active site 407976005657 motif I; other site 407976005658 motif II; other site 407976005659 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 407976005660 putative active site pocket [active] 407976005661 4-fold oligomerization interface [polypeptide binding]; other site 407976005662 metal binding residues [ion binding]; metal-binding site 407976005663 3-fold/trimer interface [polypeptide binding]; other site 407976005664 histidinol-phosphate aminotransferase; Provisional; Region: PRK04635 407976005665 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 407976005666 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976005667 homodimer interface [polypeptide binding]; other site 407976005668 catalytic residue [active] 407976005669 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 407976005670 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 407976005671 NAD binding site [chemical binding]; other site 407976005672 dimerization interface [polypeptide binding]; other site 407976005673 product binding site; other site 407976005674 substrate binding site [chemical binding]; other site 407976005675 zinc binding site [ion binding]; other site 407976005676 catalytic residues [active] 407976005677 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 407976005678 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 407976005679 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 407976005680 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 407976005681 DEAD/DEAH box helicase; Region: DEAD; pfam00270 407976005682 DEAD_2; Region: DEAD_2; pfam06733 407976005683 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 407976005684 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 407976005685 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 407976005686 N-terminal plug; other site 407976005687 ligand-binding site [chemical binding]; other site 407976005688 Protein of unknown function (DUF938); Region: DUF938; pfam06080 407976005689 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 407976005690 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 407976005691 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976005692 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976005693 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 407976005694 putative effector binding pocket; other site 407976005695 putative dimerization interface [polypeptide binding]; other site 407976005696 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 407976005697 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 407976005698 substrate binding site [chemical binding]; other site 407976005699 catalytic Zn binding site [ion binding]; other site 407976005700 NAD binding site [chemical binding]; other site 407976005701 structural Zn binding site [ion binding]; other site 407976005702 dimer interface [polypeptide binding]; other site 407976005703 S-formylglutathione hydrolase; Region: PLN02442 407976005704 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 407976005705 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 407976005706 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 407976005707 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 407976005708 beta-hexosaminidase; Provisional; Region: PRK05337 407976005709 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 407976005710 hypothetical protein; Provisional; Region: PRK04940 407976005711 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976005712 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976005713 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976005714 acylphosphatase; Provisional; Region: PRK14429 407976005715 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 407976005716 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 407976005717 transcription-repair coupling factor; Provisional; Region: PRK10689 407976005718 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 407976005719 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 407976005720 ATP binding site [chemical binding]; other site 407976005721 putative Mg++ binding site [ion binding]; other site 407976005722 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 407976005723 nucleotide binding region [chemical binding]; other site 407976005724 ATP-binding site [chemical binding]; other site 407976005725 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 407976005726 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 407976005727 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 407976005728 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 407976005729 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 407976005730 Walker A/P-loop; other site 407976005731 ATP binding site [chemical binding]; other site 407976005732 Q-loop/lid; other site 407976005733 ABC transporter signature motif; other site 407976005734 Walker B; other site 407976005735 D-loop; other site 407976005736 H-loop/switch region; other site 407976005737 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 407976005738 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 407976005739 FtsX-like permease family; Region: FtsX; pfam02687 407976005740 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 407976005741 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 407976005742 active site 407976005743 dimerization interface [polypeptide binding]; other site 407976005744 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 407976005745 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 407976005746 serine O-acetyltransferase; Region: cysE; TIGR01172 407976005747 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 407976005748 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 407976005749 trimer interface [polypeptide binding]; other site 407976005750 active site 407976005751 substrate binding site [chemical binding]; other site 407976005752 CoA binding site [chemical binding]; other site 407976005753 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 407976005754 Rrf2 family protein; Region: rrf2_super; TIGR00738 407976005755 cysteine desulfurase; Provisional; Region: PRK14012 407976005756 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 407976005757 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976005758 catalytic residue [active] 407976005759 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 407976005760 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 407976005761 trimerization site [polypeptide binding]; other site 407976005762 active site 407976005763 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 407976005764 co-chaperone HscB; Provisional; Region: hscB; PRK05014 407976005765 DnaJ domain; Region: DnaJ; pfam00226 407976005766 HSP70 interaction site [polypeptide binding]; other site 407976005767 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 407976005768 chaperone protein HscA; Provisional; Region: hscA; PRK05183 407976005769 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 407976005770 nucleotide binding site [chemical binding]; other site 407976005771 putative NEF/HSP70 interaction site [polypeptide binding]; other site 407976005772 SBD interface [polypeptide binding]; other site 407976005773 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 407976005774 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 407976005775 catalytic loop [active] 407976005776 iron binding site [ion binding]; other site 407976005777 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 407976005778 ATP-grasp domain; Region: ATP-grasp_4; cl17255 407976005779 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 407976005780 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 407976005781 active site 407976005782 multimer interface [polypeptide binding]; other site 407976005783 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 407976005784 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 407976005785 putative dimer interface [polypeptide binding]; other site 407976005786 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 407976005787 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 407976005788 putative valine binding site [chemical binding]; other site 407976005789 dimer interface [polypeptide binding]; other site 407976005790 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 407976005791 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08979 407976005792 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 407976005793 PYR/PP interface [polypeptide binding]; other site 407976005794 dimer interface [polypeptide binding]; other site 407976005795 TPP binding site [chemical binding]; other site 407976005796 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 407976005797 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 407976005798 TPP-binding site [chemical binding]; other site 407976005799 dimer interface [polypeptide binding]; other site 407976005800 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 407976005801 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 407976005802 putative substrate translocation pore; other site 407976005803 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 407976005804 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976005805 DNA-binding site [nucleotide binding]; DNA binding site 407976005806 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 407976005807 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976005808 homodimer interface [polypeptide binding]; other site 407976005809 catalytic residue [active] 407976005810 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 407976005811 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 407976005812 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 407976005813 Sulfate transporter family; Region: Sulfate_transp; pfam00916 407976005814 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 407976005815 GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_Omega_like; cd03060 407976005816 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976005817 putative GSH binding site (G-site) [chemical binding]; other site 407976005818 active site cysteine [active] 407976005819 putative C-terminal domain interface [polypeptide binding]; other site 407976005820 putative dimer interface [polypeptide binding]; other site 407976005821 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 407976005822 putative N-terminal domain interface [polypeptide binding]; other site 407976005823 putative dimer interface [polypeptide binding]; other site 407976005824 putative substrate binding pocket (H-site) [chemical binding]; other site 407976005825 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 407976005826 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 407976005827 active site residue [active] 407976005828 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 407976005829 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 407976005830 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 407976005831 Ligand binding site; other site 407976005832 oligomer interface; other site 407976005833 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 407976005834 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 407976005835 active site 407976005836 NAD binding site [chemical binding]; other site 407976005837 metal binding site [ion binding]; metal-binding site 407976005838 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 407976005839 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 407976005840 inhibitor-cofactor binding pocket; inhibition site 407976005841 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976005842 catalytic residue [active] 407976005843 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 407976005844 active site clefts [active] 407976005845 zinc binding site [ion binding]; other site 407976005846 dimer interface [polypeptide binding]; other site 407976005847 PBP superfamily domain; Region: PBP_like_2; cl17296 407976005848 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 407976005849 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 407976005850 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 407976005851 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 407976005852 metal binding site [ion binding]; metal-binding site 407976005853 dimer interface [polypeptide binding]; other site 407976005854 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 407976005855 ArsC family; Region: ArsC; pfam03960 407976005856 putative catalytic residues [active] 407976005857 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 407976005858 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976005859 putative substrate translocation pore; other site 407976005860 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 407976005861 PTS system glucose-specific transporter subunit; Provisional; Region: PRK09439 407976005862 HPr interaction site; other site 407976005863 glycerol kinase (GK) interaction site [polypeptide binding]; other site 407976005864 active site 407976005865 phosphorylation site [posttranslational modification] 407976005866 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 407976005867 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 407976005868 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 407976005869 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 407976005870 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 407976005871 dimerization domain swap beta strand [polypeptide binding]; other site 407976005872 regulatory protein interface [polypeptide binding]; other site 407976005873 active site 407976005874 regulatory phosphorylation site [posttranslational modification]; other site 407976005875 Uncharacterized conserved protein [Function unknown]; Region: COG3603 407976005876 Family description; Region: ACT_7; pfam13840 407976005877 Cache domain; Region: Cache_2; pfam08269 407976005878 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976005879 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 407976005880 dimerization interface [polypeptide binding]; other site 407976005881 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976005882 dimer interface [polypeptide binding]; other site 407976005883 putative CheW interface [polypeptide binding]; other site 407976005884 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 407976005885 Transcriptional regulators [Transcription]; Region: PurR; COG1609 407976005886 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976005887 DNA binding site [nucleotide binding] 407976005888 domain linker motif; other site 407976005889 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 407976005890 putative dimerization interface [polypeptide binding]; other site 407976005891 putative ligand binding site [chemical binding]; other site 407976005892 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 407976005893 active site 407976005894 catalytic site [active] 407976005895 substrate binding site [chemical binding]; other site 407976005896 Uncharacterized conserved protein [Function unknown]; Region: COG2850 407976005897 Cupin-like domain; Region: Cupin_8; pfam13621 407976005898 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 407976005899 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 407976005900 active site 407976005901 DNA binding site [nucleotide binding] 407976005902 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 407976005903 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 407976005904 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 407976005905 Catalytic site [active] 407976005906 Citrate transporter; Region: CitMHS; pfam03600 407976005907 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; cd00625 407976005908 transmembrane helices; other site 407976005909 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 407976005910 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976005911 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 407976005912 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976005913 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 407976005914 Domain interface; other site 407976005915 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 407976005916 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 407976005917 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 407976005918 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976005919 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 407976005920 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976005921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2350 407976005922 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 407976005923 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 407976005924 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 407976005925 catalytic site [active] 407976005926 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 407976005927 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 407976005928 putative RNA binding site [nucleotide binding]; other site 407976005929 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 407976005930 Uncharacterized conserved protein [Function unknown]; Region: COG2128 407976005931 Helix-turn-helix domain; Region: HTH_18; pfam12833 407976005932 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976005933 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 407976005934 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 407976005935 Family of unknown function (DUF633); Region: DUF633; pfam04816 407976005936 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_27; cd04686 407976005937 nudix motif; other site 407976005938 DTW domain; Region: DTW; cl01221 407976005939 Haemolysin-III related; Region: HlyIII; cl03831 407976005940 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 407976005941 putative transposase OrfB; Reviewed; Region: PHA02517 407976005942 Integrase core domain; Region: rve; pfam00665 407976005943 Integrase core domain; Region: rve_3; pfam13683 407976005944 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 407976005945 ThiC-associated domain; Region: ThiC-associated; pfam13667 407976005946 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 407976005947 Phosphomethylpyrimidine kinase; Region: Phos_pyr_kin; pfam08543 407976005948 ATP binding site [chemical binding]; other site 407976005949 substrate binding site [chemical binding]; other site 407976005950 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 407976005951 thiamine phosphate binding site [chemical binding]; other site 407976005952 active site 407976005953 pyrophosphate binding site [ion binding]; other site 407976005954 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 407976005955 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 407976005956 ATP binding site [chemical binding]; other site 407976005957 substrate interface [chemical binding]; other site 407976005958 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 407976005959 thiS-thiF/thiG interaction site; other site 407976005960 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 407976005961 ThiS interaction site; other site 407976005962 putative active site [active] 407976005963 tetramer interface [polypeptide binding]; other site 407976005964 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 407976005965 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 407976005966 FeS/SAM binding site; other site 407976005967 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 407976005968 SprA-related family; Region: SprA-related; pfam12118 407976005969 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976005970 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976005971 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 407976005972 dimerization interface [polypeptide binding]; other site 407976005973 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 407976005974 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 407976005975 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 407976005976 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 407976005977 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 407976005978 Methyltransferase domain; Region: Methyltransf_23; pfam13489 407976005979 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 407976005980 S-adenosylmethionine binding site [chemical binding]; other site 407976005981 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 407976005982 S-adenosylmethionine binding site [chemical binding]; other site 407976005983 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976005984 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 407976005985 substrate binding pocket [chemical binding]; other site 407976005986 membrane-bound complex binding site; other site 407976005987 hinge residues; other site 407976005988 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976005989 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 407976005990 substrate binding pocket [chemical binding]; other site 407976005991 membrane-bound complex binding site; other site 407976005992 hinge residues; other site 407976005993 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 407976005994 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976005995 substrate binding pocket [chemical binding]; other site 407976005996 membrane-bound complex binding site; other site 407976005997 hinge residues; other site 407976005998 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976005999 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006000 metal binding site [ion binding]; metal-binding site 407976006001 active site 407976006002 I-site; other site 407976006003 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 407976006004 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 407976006005 dimer interface [polypeptide binding]; other site 407976006006 anticodon binding site; other site 407976006007 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 407976006008 homodimer interface [polypeptide binding]; other site 407976006009 motif 1; other site 407976006010 active site 407976006011 motif 2; other site 407976006012 GAD domain; Region: GAD; pfam02938 407976006013 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 407976006014 active site 407976006015 motif 3; other site 407976006016 hypothetical protein; Validated; Region: PRK00110 407976006017 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 407976006018 active site 407976006019 putative DNA-binding cleft [nucleotide binding]; other site 407976006020 dimer interface [polypeptide binding]; other site 407976006021 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 407976006022 RuvA N terminal domain; Region: RuvA_N; pfam01330 407976006023 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 407976006024 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 407976006025 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 407976006026 Walker A motif; other site 407976006027 ATP binding site [chemical binding]; other site 407976006028 Walker B motif; other site 407976006029 arginine finger; other site 407976006030 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 407976006031 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976006032 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 407976006033 N-terminal plug; other site 407976006034 ligand-binding site [chemical binding]; other site 407976006035 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976006036 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 407976006037 active site 407976006038 phosphorylation site [posttranslational modification] 407976006039 intermolecular recognition site; other site 407976006040 dimerization interface [polypeptide binding]; other site 407976006041 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 407976006042 DNA binding site [nucleotide binding] 407976006043 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 407976006044 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 407976006045 putative active site [active] 407976006046 Zn binding site [ion binding]; other site 407976006047 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 407976006048 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 407976006049 active site 407976006050 homodimer interface [polypeptide binding]; other site 407976006051 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 407976006052 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 407976006053 tandem repeat interface [polypeptide binding]; other site 407976006054 oligomer interface [polypeptide binding]; other site 407976006055 active site residues [active] 407976006056 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 407976006057 tandem repeat interface [polypeptide binding]; other site 407976006058 oligomer interface [polypeptide binding]; other site 407976006059 active site residues [active] 407976006060 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 407976006061 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 407976006062 active site 407976006063 FMN binding site [chemical binding]; other site 407976006064 2,4-decadienoyl-CoA binding site; other site 407976006065 catalytic residue [active] 407976006066 4Fe-4S cluster binding site [ion binding]; other site 407976006067 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 407976006068 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976006069 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 407976006070 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 407976006071 catalytic loop [active] 407976006072 iron binding site [ion binding]; other site 407976006073 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 407976006074 dimer interface [polypeptide binding]; other site 407976006075 putative radical transfer pathway; other site 407976006076 diiron center [ion binding]; other site 407976006077 tyrosyl radical; other site 407976006078 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 407976006079 ATP cone domain; Region: ATP-cone; pfam03477 407976006080 Class I ribonucleotide reductase; Region: RNR_I; cd01679 407976006081 active site 407976006082 dimer interface [polypeptide binding]; other site 407976006083 catalytic residues [active] 407976006084 effector binding site; other site 407976006085 R2 peptide binding site; other site 407976006086 phosphoglycolate phosphatase; Provisional; Region: PRK13222 407976006087 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 407976006088 motif II; other site 407976006089 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 407976006090 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 407976006091 S-adenosylmethionine binding site [chemical binding]; other site 407976006092 DNA gyrase subunit A; Validated; Region: PRK05560 407976006093 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 407976006094 CAP-like domain; other site 407976006095 active site 407976006096 primary dimer interface [polypeptide binding]; other site 407976006097 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 407976006098 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 407976006099 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 407976006100 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 407976006101 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 407976006102 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 407976006103 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 407976006104 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976006105 catalytic residue [active] 407976006106 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976006107 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976006108 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 407976006109 substrate binding pocket [chemical binding]; other site 407976006110 dimerization interface [polypeptide binding]; other site 407976006111 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 407976006112 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 407976006113 hypothetical protein; Provisional; Region: PRK10977 407976006114 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 407976006115 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 407976006116 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976006117 homodimer interface [polypeptide binding]; other site 407976006118 catalytic residue [active] 407976006119 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 407976006120 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 407976006121 hinge; other site 407976006122 active site 407976006123 cytidylate kinase; Provisional; Region: cmk; PRK00023 407976006124 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 407976006125 CMP-binding site; other site 407976006126 The sites determining sugar specificity; other site 407976006127 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 407976006128 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 407976006129 RNA binding site [nucleotide binding]; other site 407976006130 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 407976006131 RNA binding site [nucleotide binding]; other site 407976006132 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 407976006133 RNA binding site [nucleotide binding]; other site 407976006134 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 407976006135 RNA binding site [nucleotide binding]; other site 407976006136 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 407976006137 RNA binding site [nucleotide binding]; other site 407976006138 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 407976006139 RNA binding site [nucleotide binding]; other site 407976006140 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 407976006141 IHF dimer interface [polypeptide binding]; other site 407976006142 IHF - DNA interface [nucleotide binding]; other site 407976006143 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 407976006144 tetratricopeptide repeat protein; Provisional; Region: PRK11788 407976006145 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 407976006146 active site 407976006147 dimer interface [polypeptide binding]; other site 407976006148 short chain dehydrogenase; Provisional; Region: PRK07576 407976006149 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976006150 NAD(P) binding site [chemical binding]; other site 407976006151 active site 407976006152 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 407976006153 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 407976006154 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 407976006155 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 407976006156 active site 407976006157 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 407976006158 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 407976006159 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 407976006160 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 407976006161 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 407976006162 domain interface [polypeptide binding]; other site 407976006163 putative active site [active] 407976006164 catalytic site [active] 407976006165 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 407976006166 domain interface [polypeptide binding]; other site 407976006167 putative active site [active] 407976006168 catalytic site [active] 407976006169 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 407976006170 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 407976006171 putative substrate translocation pore; other site 407976006172 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 407976006173 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 407976006174 Uncharacterized conserved protein [Function unknown]; Region: COG3148 407976006175 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 407976006176 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 407976006177 active site 407976006178 DNA binding site [nucleotide binding] 407976006179 Int/Topo IB signature motif; other site 407976006180 DEAD-like helicases superfamily; Region: DEXDc; smart00487 407976006181 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 407976006182 ATP binding site [chemical binding]; other site 407976006183 putative Mg++ binding site [ion binding]; other site 407976006184 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 407976006185 nucleotide binding region [chemical binding]; other site 407976006186 ATP-binding site [chemical binding]; other site 407976006187 ecotin; Provisional; Region: PRK03719 407976006188 secondary substrate binding site; other site 407976006189 primary substrate binding site; other site 407976006190 inhibition loop; other site 407976006191 dimerization interface [polypeptide binding]; other site 407976006192 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 407976006193 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 407976006194 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 407976006195 MarR family; Region: MarR; pfam01047 407976006196 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 407976006197 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976006198 putative metal dependent hydrolase; Provisional; Region: PRK11598 407976006199 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 407976006200 Sulfatase; Region: Sulfatase; pfam00884 407976006201 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006202 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006203 metal binding site [ion binding]; metal-binding site 407976006204 active site 407976006205 I-site; other site 407976006206 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 407976006207 CoA binding domain; Region: CoA_binding_2; pfam13380 407976006208 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 407976006209 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 407976006210 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976006211 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976006212 dimer interface [polypeptide binding]; other site 407976006213 putative CheW interface [polypeptide binding]; other site 407976006214 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 407976006215 anti sigma factor interaction site; other site 407976006216 regulatory phosphorylation site [posttranslational modification]; other site 407976006217 Response regulator receiver domain; Region: Response_reg; pfam00072 407976006218 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 407976006219 active site 407976006220 phosphorylation site [posttranslational modification] 407976006221 intermolecular recognition site; other site 407976006222 dimerization interface [polypeptide binding]; other site 407976006223 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 407976006224 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 407976006225 Response regulator receiver domain; Region: Response_reg; pfam00072 407976006226 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 407976006227 active site 407976006228 phosphorylation site [posttranslational modification] 407976006229 intermolecular recognition site; other site 407976006230 dimerization interface [polypeptide binding]; other site 407976006231 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 407976006232 putative binding surface; other site 407976006233 active site 407976006234 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 407976006235 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 407976006236 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 407976006237 ATP binding site [chemical binding]; other site 407976006238 Mg2+ binding site [ion binding]; other site 407976006239 G-X-G motif; other site 407976006240 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 407976006241 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 407976006242 putative CheA interaction surface; other site 407976006243 PAS fold; Region: PAS; pfam00989 407976006244 PAS domain; Region: PAS; smart00091 407976006245 PAS domain; Region: PAS_9; pfam13426 407976006246 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976006247 dimer interface [polypeptide binding]; other site 407976006248 putative CheW interface [polypeptide binding]; other site 407976006249 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 407976006250 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 407976006251 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 407976006252 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 407976006253 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 407976006254 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 407976006255 active site 407976006256 phosphorylation site [posttranslational modification] 407976006257 intermolecular recognition site; other site 407976006258 dimerization interface [polypeptide binding]; other site 407976006259 CheB methylesterase; Region: CheB_methylest; pfam01339 407976006260 Hpt domain; Region: Hpt; pfam01627 407976006261 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 407976006262 active site 407976006263 phosphorylation site [posttranslational modification] 407976006264 intermolecular recognition site; other site 407976006265 dimerization interface [polypeptide binding]; other site 407976006266 Response regulator receiver domain; Region: Response_reg; pfam00072 407976006267 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 407976006268 active site 407976006269 phosphorylation site [posttranslational modification] 407976006270 intermolecular recognition site; other site 407976006271 dimerization interface [polypeptide binding]; other site 407976006272 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006273 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006274 metal binding site [ion binding]; metal-binding site 407976006275 active site 407976006276 I-site; other site 407976006277 Methyltransferase domain; Region: Methyltransf_25; pfam13649 407976006278 S-adenosylmethionine binding site [chemical binding]; other site 407976006279 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 407976006280 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 407976006281 active site 407976006282 Nuclease-related domain; Region: NERD; pfam08378 407976006283 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 407976006284 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976006285 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976006286 ABC transporter; Region: ABC_tran_2; pfam12848 407976006287 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976006288 Uncharacterized conserved protein [Function unknown]; Region: COG4628 407976006289 Phytase; Region: Phytase; cl17685 407976006290 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 407976006291 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976006292 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 407976006293 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 407976006294 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006295 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006296 metal binding site [ion binding]; metal-binding site 407976006297 active site 407976006298 I-site; other site 407976006299 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 407976006300 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 407976006301 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976006302 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 407976006303 non-specific DNA binding site [nucleotide binding]; other site 407976006304 salt bridge; other site 407976006305 sequence-specific DNA binding site [nucleotide binding]; other site 407976006306 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976006307 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 407976006308 active site 407976006309 phosphorylation site [posttranslational modification] 407976006310 intermolecular recognition site; other site 407976006311 dimerization interface [polypeptide binding]; other site 407976006312 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 407976006313 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976006314 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 407976006315 dimer interface [polypeptide binding]; other site 407976006316 phosphorylation site [posttranslational modification] 407976006317 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 407976006318 ATP binding site [chemical binding]; other site 407976006319 Mg2+ binding site [ion binding]; other site 407976006320 G-X-G motif; other site 407976006321 Response regulator receiver domain; Region: Response_reg; pfam00072 407976006322 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 407976006323 active site 407976006324 phosphorylation site [posttranslational modification] 407976006325 intermolecular recognition site; other site 407976006326 dimerization interface [polypeptide binding]; other site 407976006327 PAS fold; Region: PAS_7; pfam12860 407976006328 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 407976006329 putative active site [active] 407976006330 heme pocket [chemical binding]; other site 407976006331 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006332 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006333 metal binding site [ion binding]; metal-binding site 407976006334 active site 407976006335 I-site; other site 407976006336 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 407976006337 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 407976006338 N-terminal plug; other site 407976006339 ligand-binding site [chemical binding]; other site 407976006340 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 407976006341 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 407976006342 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 407976006343 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 407976006344 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 407976006345 N-terminal plug; other site 407976006346 ligand-binding site [chemical binding]; other site 407976006347 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 407976006348 Uncharacterized conserved protein [Function unknown]; Region: COG3461 407976006349 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 407976006350 active site 407976006351 catalytic residues [active] 407976006352 Int/Topo IB signature motif; other site 407976006353 DNA binding site [nucleotide binding] 407976006354 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976006355 Zn2+ binding site [ion binding]; other site 407976006356 Mg2+ binding site [ion binding]; other site 407976006357 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 407976006358 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976006359 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 407976006360 active site 407976006361 DNA binding site [nucleotide binding] 407976006362 Int/Topo IB signature motif; other site 407976006363 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 407976006364 non-specific DNA binding site [nucleotide binding]; other site 407976006365 salt bridge; other site 407976006366 sequence-specific DNA binding site [nucleotide binding]; other site 407976006367 ribulokinase; Provisional; Region: PRK04123 407976006368 Ribulokinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_RBK; cd07781 407976006369 N- and C-terminal domain interface [polypeptide binding]; other site 407976006370 active site 407976006371 MgATP binding site [chemical binding]; other site 407976006372 catalytic site [active] 407976006373 metal binding site [ion binding]; metal-binding site 407976006374 carbohydrate binding site [chemical binding]; other site 407976006375 homodimer interface [polypeptide binding]; other site 407976006376 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 407976006377 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 407976006378 intersubunit interface [polypeptide binding]; other site 407976006379 active site 407976006380 Zn2+ binding site [ion binding]; other site 407976006381 L-arabinose isomerase; Provisional; Region: PRK02929 407976006382 L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose...; Region: L-fuc_L-ara-isomerases; cl00947 407976006383 hexamer (dimer of trimers) interface [polypeptide binding]; other site 407976006384 trimer interface [polypeptide binding]; other site 407976006385 substrate binding site [chemical binding]; other site 407976006386 Mn binding site [ion binding]; other site 407976006387 fructose-1-P/6-phosphogluconate phosphatase; Provisional; Region: PRK10725 407976006388 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 407976006389 active site 407976006390 motif I; other site 407976006391 motif II; other site 407976006392 Transcriptional regulators [Transcription]; Region: FadR; COG2186 407976006393 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976006394 DNA-binding site [nucleotide binding]; DNA binding site 407976006395 FCD domain; Region: FCD; pfam07729 407976006396 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 407976006397 substrate binding site [chemical binding]; other site 407976006398 active site 407976006399 dihydroxy-acid dehydratase; Validated; Region: PRK06131 407976006400 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 407976006401 classical (c) SDRs; Region: SDR_c; cd05233 407976006402 NAD(P) binding site [chemical binding]; other site 407976006403 active site 407976006404 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 407976006405 active site 407976006406 catalytic residues [active] 407976006407 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 407976006408 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 407976006409 putative ligand binding site [chemical binding]; other site 407976006410 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 407976006411 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 407976006412 Walker A/P-loop; other site 407976006413 ATP binding site [chemical binding]; other site 407976006414 Q-loop/lid; other site 407976006415 ABC transporter signature motif; other site 407976006416 Walker B; other site 407976006417 D-loop; other site 407976006418 H-loop/switch region; other site 407976006419 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 407976006420 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 407976006421 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 407976006422 TM-ABC transporter signature motif; other site 407976006423 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 407976006424 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 407976006425 TM-ABC transporter signature motif; other site 407976006426 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 407976006427 active site 407976006428 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 407976006429 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 407976006430 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 407976006431 active site 407976006432 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 407976006433 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 407976006434 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 407976006435 substrate binding site [chemical binding]; other site 407976006436 active site 407976006437 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 407976006438 active site 407976006439 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 407976006440 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976006441 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 407976006442 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976006443 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 407976006444 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 407976006445 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 407976006446 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 407976006447 substrate binding site [chemical binding]; other site 407976006448 active site 407976006449 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 407976006450 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 407976006451 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 407976006452 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 407976006453 catalytic tetrad [active] 407976006454 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 407976006455 FeS/SAM binding site; other site 407976006456 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 407976006457 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 407976006458 N-terminal plug; other site 407976006459 ligand-binding site [chemical binding]; other site 407976006460 Acidobacterial duplicated orphan permease; Region: ADOP; TIGR03434 407976006461 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 407976006462 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 407976006463 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 407976006464 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 407976006465 DNA binding residues [nucleotide binding] 407976006466 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976006467 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976006468 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 407976006469 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 407976006470 FMN binding site [chemical binding]; other site 407976006471 active site 407976006472 substrate binding site [chemical binding]; other site 407976006473 catalytic residue [active] 407976006474 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 407976006475 classical (c) SDRs; Region: SDR_c; cd05233 407976006476 NAD(P) binding site [chemical binding]; other site 407976006477 active site 407976006478 short chain dehydrogenase; Provisional; Region: PRK06179 407976006479 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 407976006480 NADP binding site [chemical binding]; other site 407976006481 active site 407976006482 steroid binding site; other site 407976006483 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 407976006484 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 407976006485 multidrug efflux protein; Reviewed; Region: PRK01766 407976006486 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 407976006487 cation binding site [ion binding]; other site 407976006488 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 407976006489 Lumazine binding domain; Region: Lum_binding; pfam00677 407976006490 Lumazine binding domain; Region: Lum_binding; pfam00677 407976006491 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 407976006492 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 407976006493 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 407976006494 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 407976006495 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 407976006496 active site 407976006497 dimer interface [polypeptide binding]; other site 407976006498 motif 1; other site 407976006499 motif 2; other site 407976006500 motif 3; other site 407976006501 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 407976006502 anticodon binding site; other site 407976006503 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 407976006504 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 407976006505 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 407976006506 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 407976006507 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 407976006508 23S rRNA binding site [nucleotide binding]; other site 407976006509 L21 binding site [polypeptide binding]; other site 407976006510 L13 binding site [polypeptide binding]; other site 407976006511 thioredoxin reductase; Provisional; Region: PRK10262 407976006512 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976006513 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 407976006514 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 407976006515 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 407976006516 hexamer interface [polypeptide binding]; other site 407976006517 ligand binding site [chemical binding]; other site 407976006518 putative active site [active] 407976006519 NAD(P) binding site [chemical binding]; other site 407976006520 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 407976006521 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 407976006522 putative DNA binding site [nucleotide binding]; other site 407976006523 putative Zn2+ binding site [ion binding]; other site 407976006524 AsnC family; Region: AsnC_trans_reg; pfam01037 407976006525 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 407976006526 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 407976006527 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 407976006528 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 407976006529 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 407976006530 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 407976006531 recombination factor protein RarA; Reviewed; Region: PRK13342 407976006532 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 407976006533 Walker A motif; other site 407976006534 ATP binding site [chemical binding]; other site 407976006535 Walker B motif; other site 407976006536 arginine finger; other site 407976006537 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 407976006538 camphor resistance protein CrcB; Provisional; Region: PRK14197 407976006539 seryl-tRNA synthetase; Provisional; Region: PRK05431 407976006540 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 407976006541 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 407976006542 dimer interface [polypeptide binding]; other site 407976006543 active site 407976006544 motif 1; other site 407976006545 motif 2; other site 407976006546 motif 3; other site 407976006547 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 407976006548 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 407976006549 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 407976006550 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 407976006551 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 407976006552 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 407976006553 YccA-like proteins; Region: YccA_like; cd10433 407976006554 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 407976006555 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976006556 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 407976006557 dimerization interface [polypeptide binding]; other site 407976006558 putative transporter; Provisional; Region: PRK11043 407976006559 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 407976006560 putative substrate translocation pore; other site 407976006561 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 407976006562 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 407976006563 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 407976006564 PAS fold; Region: PAS_4; pfam08448 407976006565 PAS domain S-box; Region: sensory_box; TIGR00229 407976006566 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 407976006567 putative active site [active] 407976006568 heme pocket [chemical binding]; other site 407976006569 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006570 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006571 metal binding site [ion binding]; metal-binding site 407976006572 active site 407976006573 I-site; other site 407976006574 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 407976006575 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 407976006576 putative efflux protein, MATE family; Region: matE; TIGR00797 407976006577 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976006578 Probable pectinesterase/pectinesterase inhibitor; Region: PLN02698 407976006579 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 407976006580 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 407976006581 Int/Topo IB signature motif; other site 407976006582 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976006583 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 407976006584 active site 407976006585 phosphorylation site [posttranslational modification] 407976006586 intermolecular recognition site; other site 407976006587 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 407976006588 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 407976006589 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976006590 Zn2+ binding site [ion binding]; other site 407976006591 Mg2+ binding site [ion binding]; other site 407976006592 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 407976006593 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 407976006594 Low-spin heme binding site [chemical binding]; other site 407976006595 Putative water exit pathway; other site 407976006596 Binuclear center (active site) [active] 407976006597 Putative proton exit pathway; other site 407976006598 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 407976006599 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 407976006600 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 407976006601 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 407976006602 Cytochrome c; Region: Cytochrom_C; pfam00034 407976006603 Cytochrome c; Region: Cytochrom_C; pfam00034 407976006604 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 407976006605 FixH; Region: FixH; pfam05751 407976006606 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 407976006607 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 407976006608 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 407976006609 metal-binding site [ion binding] 407976006610 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 407976006611 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 407976006612 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 407976006613 Family description; Region: DsbD_2; pfam13386 407976006614 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 407976006615 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 407976006616 ligand binding site [chemical binding]; other site 407976006617 flexible hinge region; other site 407976006618 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 407976006619 putative switch regulator; other site 407976006620 non-specific DNA interactions [nucleotide binding]; other site 407976006621 DNA binding site [nucleotide binding] 407976006622 sequence specific DNA binding site [nucleotide binding]; other site 407976006623 putative cAMP binding site [chemical binding]; other site 407976006624 universal stress protein UspE; Provisional; Region: PRK11175 407976006625 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 407976006626 Ligand Binding Site [chemical binding]; other site 407976006627 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 407976006628 Ligand Binding Site [chemical binding]; other site 407976006629 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 407976006630 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 407976006631 Ligand Binding Site [chemical binding]; other site 407976006632 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 407976006633 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 407976006634 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 407976006635 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 407976006636 phosphate binding site [ion binding]; other site 407976006637 putative substrate binding pocket [chemical binding]; other site 407976006638 dimer interface [polypeptide binding]; other site 407976006639 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 407976006640 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 407976006641 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976006642 homodimer interface [polypeptide binding]; other site 407976006643 catalytic residue [active] 407976006644 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 407976006645 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 407976006646 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 407976006647 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 407976006648 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 407976006649 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 407976006650 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 407976006651 quinolinate synthetase; Provisional; Region: PRK09375 407976006652 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 407976006653 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 407976006654 E3 interaction surface; other site 407976006655 lipoyl attachment site [posttranslational modification]; other site 407976006656 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 407976006657 E3 interaction surface; other site 407976006658 lipoyl attachment site [posttranslational modification]; other site 407976006659 e3 binding domain; Region: E3_binding; pfam02817 407976006660 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 407976006661 3-methyl-2-oxobutanate dehydrogenase; Provisional; Region: PTZ00182 407976006662 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 407976006663 alpha subunit interface [polypeptide binding]; other site 407976006664 TPP binding site [chemical binding]; other site 407976006665 heterodimer interface [polypeptide binding]; other site 407976006666 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 407976006667 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 407976006668 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 407976006669 tetramer interface [polypeptide binding]; other site 407976006670 TPP-binding site [chemical binding]; other site 407976006671 heterodimer interface [polypeptide binding]; other site 407976006672 phosphorylation loop region [posttranslational modification] 407976006673 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 407976006674 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 407976006675 putative active site [active] 407976006676 Zn binding site [ion binding]; other site 407976006677 methionine sulfoxide reductase A; Provisional; Region: PRK14054 407976006678 phosphoglucomutase; Validated; Region: PRK07564 407976006679 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 407976006680 active site 407976006681 substrate binding site [chemical binding]; other site 407976006682 metal binding site [ion binding]; metal-binding site 407976006683 replication initiation regulator SeqA; Provisional; Region: PRK11187 407976006684 PGAP1-like protein; Region: PGAP1; pfam07819 407976006685 acyl-CoA esterase; Provisional; Region: PRK10673 407976006686 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 407976006687 LexA regulated protein; Provisional; Region: PRK11675 407976006688 flavodoxin FldA; Validated; Region: PRK09267 407976006689 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 407976006690 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 407976006691 elongation factor P; Validated; Region: PRK00529 407976006692 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 407976006693 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 407976006694 RNA binding site [nucleotide binding]; other site 407976006695 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 407976006696 RNA binding site [nucleotide binding]; other site 407976006697 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 407976006698 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 407976006699 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 407976006700 Short chain fatty acid transporter; Region: SCFA_trans; cl17380 407976006701 aminotransferase AlaT; Validated; Region: PRK09265 407976006702 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 407976006703 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976006704 homodimer interface [polypeptide binding]; other site 407976006705 catalytic residue [active] 407976006706 5'-nucleotidase; Provisional; Region: PRK03826 407976006707 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 407976006708 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 407976006709 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 407976006710 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 407976006711 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 407976006712 active site 407976006713 intersubunit interface [polypeptide binding]; other site 407976006714 catalytic residue [active] 407976006715 phosphogluconate dehydratase; Validated; Region: PRK09054 407976006716 6-phosphogluconate dehydratase; Region: edd; TIGR01196 407976006717 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 407976006718 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 407976006719 putative active site [active] 407976006720 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 407976006721 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 407976006722 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 407976006723 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 407976006724 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 407976006725 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 407976006726 putative active site [active] 407976006727 pyruvate kinase; Provisional; Region: PRK05826 407976006728 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 407976006729 domain interfaces; other site 407976006730 active site 407976006731 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 407976006732 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 407976006733 active site 407976006734 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 407976006735 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976006736 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976006737 Peptidase family M2 Angiotensin converting enzyme (ACE); Region: M2_ACE; cd06461 407976006738 active site 407976006739 Zn binding site [ion binding]; other site 407976006740 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 407976006741 Smr domain; Region: Smr; pfam01713 407976006742 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 407976006743 SEC-C motif; Region: SEC-C; pfam02810 407976006744 SEC-C motif; Region: SEC-C; pfam02810 407976006745 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976006746 GAF domain; Region: GAF; pfam01590 407976006747 PAS domain; Region: PAS_9; pfam13426 407976006748 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 407976006749 putative active site [active] 407976006750 heme pocket [chemical binding]; other site 407976006751 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006752 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006753 metal binding site [ion binding]; metal-binding site 407976006754 active site 407976006755 I-site; other site 407976006756 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 407976006757 Protein of unknown function (DUF406); Region: DUF406; pfam04175 407976006758 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 407976006759 potential protein location (hypothetical protein Sbal223_2266 [Shewanella baltica OS223]) that overlaps RNA (tRNA-Y) 407976006760 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 407976006761 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 407976006762 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976006763 catalytic residue [active] 407976006764 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 407976006765 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 407976006766 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 407976006767 Ligand Binding Site [chemical binding]; other site 407976006768 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 407976006769 excinuclease ABC subunit B; Provisional; Region: PRK05298 407976006770 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 407976006771 ATP binding site [chemical binding]; other site 407976006772 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 407976006773 nucleotide binding region [chemical binding]; other site 407976006774 ATP-binding site [chemical binding]; other site 407976006775 Ultra-violet resistance protein B; Region: UvrB; pfam12344 407976006776 UvrB/uvrC motif; Region: UVR; pfam02151 407976006777 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006778 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006779 active site 407976006780 I-site; other site 407976006781 metal binding site [ion binding]; metal-binding site 407976006782 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 407976006783 electron transport complex protein RsxA; Provisional; Region: PRK05151 407976006784 ferredoxin; Provisional; Region: PRK08764 407976006785 Putative Fe-S cluster; Region: FeS; pfam04060 407976006786 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 407976006787 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 407976006788 SLBB domain; Region: SLBB; pfam10531 407976006789 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 407976006790 electron transport complex protein RnfD; Reviewed; Region: rnfD; PRK00816 407976006791 electron transport complex protein RnfG; Validated; Region: PRK01908 407976006792 electron transport complex RsxE subunit; Provisional; Region: PRK12405 407976006793 endonuclease III; Provisional; Region: PRK10702 407976006794 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 407976006795 minor groove reading motif; other site 407976006796 helix-hairpin-helix signature motif; other site 407976006797 substrate binding pocket [chemical binding]; other site 407976006798 active site 407976006799 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 407976006800 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976006801 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 407976006802 dimer interface [polypeptide binding]; other site 407976006803 active site 407976006804 metal binding site [ion binding]; metal-binding site 407976006805 glutathione binding site [chemical binding]; other site 407976006806 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 407976006807 TMAO/DMSO reductase; Reviewed; Region: PRK05363 407976006808 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 407976006809 Moco binding site; other site 407976006810 metal coordination site [ion binding]; other site 407976006811 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 407976006812 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 407976006813 RmuC family; Region: RmuC; pfam02646 407976006814 lytic murein transglycosylase; Provisional; Region: PRK11619 407976006815 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 407976006816 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976006817 catalytic residue [active] 407976006818 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 407976006819 MoxR-like ATPases [General function prediction only]; Region: COG0714 407976006820 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 407976006821 Walker A motif; other site 407976006822 ATP binding site [chemical binding]; other site 407976006823 Walker B motif; other site 407976006824 arginine finger; other site 407976006825 Protein of unknown function DUF58; Region: DUF58; pfam01882 407976006826 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 407976006827 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 407976006828 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 407976006829 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 407976006830 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 407976006831 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 407976006832 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 407976006833 Part of AAA domain; Region: AAA_19; pfam13245 407976006834 Family description; Region: UvrD_C_2; pfam13538 407976006835 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 407976006836 AAA domain; Region: AAA_30; pfam13604 407976006837 Family description; Region: UvrD_C_2; pfam13538 407976006838 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976006839 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976006840 Coenzyme A binding pocket [chemical binding]; other site 407976006841 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 407976006842 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 407976006843 ATP-grasp domain; Region: ATP-grasp_4; cl17255 407976006844 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976006845 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976006846 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976006847 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976006848 GAF domain; Region: GAF; pfam01590 407976006849 PAS domain; Region: PAS_9; pfam13426 407976006850 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976006851 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976006852 metal binding site [ion binding]; metal-binding site 407976006853 active site 407976006854 I-site; other site 407976006855 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 407976006856 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 407976006857 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 407976006858 S-adenosylmethionine binding site [chemical binding]; other site 407976006859 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 407976006860 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 407976006861 putative substrate translocation pore; other site 407976006862 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 407976006863 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 407976006864 active site 407976006865 catalytic site [active] 407976006866 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976006867 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 407976006868 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 407976006869 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 407976006870 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 407976006871 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 407976006872 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 407976006873 Ca binding site [ion binding]; other site 407976006874 active site 407976006875 homodimer interface [polypeptide binding]; other site 407976006876 catalytic site [active] 407976006877 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 407976006878 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 407976006879 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 407976006880 active site 407976006881 catalytic site [active] 407976006882 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_1; cd08352 407976006883 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976006884 putative metal binding site [ion binding]; other site 407976006885 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 407976006886 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 407976006887 active site 407976006888 FMN binding site [chemical binding]; other site 407976006889 substrate binding site [chemical binding]; other site 407976006890 3Fe-4S cluster binding site [ion binding]; other site 407976006891 pyruvate dehydrogenase; Provisional; Region: PRK06546 407976006892 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 407976006893 PYR/PP interface [polypeptide binding]; other site 407976006894 dimer interface [polypeptide binding]; other site 407976006895 tetramer interface [polypeptide binding]; other site 407976006896 TPP binding site [chemical binding]; other site 407976006897 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 407976006898 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 407976006899 TPP-binding site [chemical binding]; other site 407976006900 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 407976006901 PRC-barrel domain; Region: PRC; pfam05239 407976006902 PRC-barrel domain; Region: PRC; pfam05239 407976006903 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 407976006904 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 407976006905 Walker A/P-loop; other site 407976006906 ATP binding site [chemical binding]; other site 407976006907 Q-loop/lid; other site 407976006908 ABC transporter signature motif; other site 407976006909 Walker B; other site 407976006910 D-loop; other site 407976006911 H-loop/switch region; other site 407976006912 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 407976006913 glycine betaine transporter membrane protein; Provisional; Region: PRK10952 407976006914 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 407976006915 dimer interface [polypeptide binding]; other site 407976006916 conserved gate region; other site 407976006917 ABC-ATPase subunit interface; other site 407976006918 glycine betaine transporter periplasmic subunit; Provisional; Region: proX; PRK11119 407976006919 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 407976006920 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 407976006921 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 407976006922 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 407976006923 active site 407976006924 catalytic residues [active] 407976006925 metal binding site [ion binding]; metal-binding site 407976006926 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 407976006927 active site 407976006928 DNA binding site [nucleotide binding] 407976006929 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 407976006930 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 407976006931 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 407976006932 putative active site [active] 407976006933 putative dimer interface [polypeptide binding]; other site 407976006934 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 407976006935 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 407976006936 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 407976006937 active site 407976006938 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 407976006939 Predicted acetamidase/formamidase [Energy production and conversion]; Region: COG2421 407976006940 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 407976006941 TrkA-N domain; Region: TrkA_N; pfam02254 407976006942 TIGR03503 family protein; Region: TIGR03503 407976006943 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 407976006944 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 407976006945 active site 407976006946 catalytic site [active] 407976006947 substrate binding site [chemical binding]; other site 407976006948 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 407976006949 RNA/DNA hybrid binding site [nucleotide binding]; other site 407976006950 active site 407976006951 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 407976006952 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976006953 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 407976006954 putative dimerization interface [polypeptide binding]; other site 407976006955 Methyltransferase domain; Region: Methyltransf_11; pfam08241 407976006956 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 407976006957 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 407976006958 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 407976006959 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976006960 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976006961 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976006962 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 407976006963 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976006964 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976006965 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976006966 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976006967 Intracellular proteinase inhibitor; Region: BsuPI; pfam12690 407976006968 AsmA family; Region: AsmA; pfam05170 407976006969 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 407976006970 ribonuclease activity regulator protein RraA; Reviewed; Region: PRK12487 407976006971 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 407976006972 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 407976006973 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 407976006974 ATP binding site [chemical binding]; other site 407976006975 Mg++ binding site [ion binding]; other site 407976006976 motif III; other site 407976006977 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 407976006978 nucleotide binding region [chemical binding]; other site 407976006979 ATP-binding site [chemical binding]; other site 407976006980 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 407976006981 substrate binding site [chemical binding]; other site 407976006982 Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase; Region: GAT1_cyanophycinase; cd03145 407976006983 proposed catalytic triad [active] 407976006984 active site nucleophile [active] 407976006985 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976006986 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 407976006987 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 407976006988 ligand-binding site [chemical binding]; other site 407976006989 hypothetical protein; Provisional; Region: PRK11588 407976006990 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 407976006991 isoaspartyl dipeptidase; Provisional; Region: PRK10657 407976006992 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 407976006993 active site 407976006994 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976006995 EamA-like transporter family; Region: EamA; pfam00892 407976006996 HAD superfamily, subfamily IIIB (Acid phosphatase); Region: Acid_phosphat_B; cl17236 407976006997 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 407976006998 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 407976006999 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976007000 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976007001 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976007002 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 407976007003 Transposase; Region: HTH_Tnp_1; pfam01527 407976007004 putative transposase OrfB; Reviewed; Region: PHA02517 407976007005 HTH-like domain; Region: HTH_21; pfam13276 407976007006 Integrase core domain; Region: rve; pfam00665 407976007007 Integrase core domain; Region: rve_3; pfam13683 407976007008 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 407976007009 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 407976007010 catalytic residues [active] 407976007011 catalytic nucleophile [active] 407976007012 Presynaptic Site I dimer interface [polypeptide binding]; other site 407976007013 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 407976007014 Synaptic Flat tetramer interface [polypeptide binding]; other site 407976007015 Synaptic Site I dimer interface [polypeptide binding]; other site 407976007016 DNA binding site [nucleotide binding] 407976007017 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 407976007018 DNA-binding interface [nucleotide binding]; DNA binding site 407976007019 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 407976007020 hypothetical protein; Reviewed; Region: PRK00024 407976007021 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 407976007022 MPN+ (JAMM) motif; other site 407976007023 Zinc-binding site [ion binding]; other site 407976007024 Eukaryotic initiation factor 1 and related proteins; Region: eIF1_SUI1_like; cl00229 407976007025 Helix-turn-helix domain; Region: HTH_36; pfam13730 407976007026 CHC2 zinc finger; Region: zf-CHC2; cl17510 407976007027 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 407976007028 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 407976007029 active site 407976007030 metal binding site [ion binding]; metal-binding site 407976007031 interdomain interaction site; other site 407976007032 D5 N terminal like; Region: D5_N; smart00885 407976007033 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 407976007034 Poxvirus D5 protein-like; Region: Pox_D5; pfam03288 407976007035 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 407976007036 Domain of unknown function DUF87; Region: DUF87; pfam01935 407976007037 HerA helicase [Replication, recombination, and repair]; Region: COG0433 407976007038 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 407976007039 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976007040 active site 407976007041 DNA binding site [nucleotide binding] 407976007042 Int/Topo IB signature motif; other site 407976007043 potential protein location (hypothetical protein Sbal223_2368 [Shewanella baltica OS223]) that overlaps RNA (tRNA-S) 407976007044 Nitrate and nitrite sensing; Region: NIT; pfam08376 407976007045 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976007046 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 407976007047 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976007048 dimer interface [polypeptide binding]; other site 407976007049 putative CheW interface [polypeptide binding]; other site 407976007050 hypothetical protein; Provisional; Region: PRK11111 407976007051 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 407976007052 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 407976007053 putative catalytic cysteine [active] 407976007054 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 407976007055 putative active site [active] 407976007056 metal binding site [ion binding]; metal-binding site 407976007057 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 407976007058 putative active site [active] 407976007059 Zn binding site [ion binding]; other site 407976007060 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976007061 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976007062 Coenzyme A binding pocket [chemical binding]; other site 407976007063 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976007064 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976007065 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 407976007066 Fumarase C-terminus; Region: Fumerase_C; pfam05683 407976007067 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 407976007068 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 407976007069 chorismate binding enzyme; Region: Chorismate_bind; cl10555 407976007070 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 407976007071 putative active site [active] 407976007072 putative CoA binding site [chemical binding]; other site 407976007073 nudix motif; other site 407976007074 metal binding site [ion binding]; metal-binding site 407976007075 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 407976007076 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 407976007077 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 407976007078 putative dimer interface [polypeptide binding]; other site 407976007079 putative anticodon binding site; other site 407976007080 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 407976007081 homodimer interface [polypeptide binding]; other site 407976007082 motif 1; other site 407976007083 motif 2; other site 407976007084 active site 407976007085 motif 3; other site 407976007086 Domain of unknown function (DU1801); Region: DUF1801; pfam08818 407976007087 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 407976007088 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 407976007089 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 407976007090 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 407976007091 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 407976007092 [4Fe-4S] binding site [ion binding]; other site 407976007093 molybdopterin cofactor binding site; other site 407976007094 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 407976007095 molybdopterin cofactor binding site; other site 407976007096 NapD protein; Region: NapD; pfam03927 407976007097 Periplasmic nitrate reductase protein NapE; Region: NapE; cl01848 407976007098 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 407976007099 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 407976007100 ATP binding site [chemical binding]; other site 407976007101 putative Mg++ binding site [ion binding]; other site 407976007102 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 407976007103 nucleotide binding region [chemical binding]; other site 407976007104 ATP-binding site [chemical binding]; other site 407976007105 Helicase associated domain (HA2); Region: HA2; pfam04408 407976007106 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 407976007107 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 407976007108 FOG: CBS domain [General function prediction only]; Region: COG0517 407976007109 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_16; cd04629 407976007110 Predicted membrane protein [Function unknown]; Region: COG4325 407976007111 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 407976007112 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 407976007113 catalytic nucleophile [active] 407976007114 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 407976007115 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976007116 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976007117 Surface antigen; Region: Bac_surface_Ag; pfam01103 407976007118 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 407976007119 Family of unknown function (DUF490); Region: DUF490; pfam04357 407976007120 Family of unknown function (DUF490); Region: DUF490; pfam04357 407976007121 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 407976007122 5S rRNA interface [nucleotide binding]; other site 407976007123 CTC domain interface [polypeptide binding]; other site 407976007124 L16 interface [polypeptide binding]; other site 407976007125 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 407976007126 Bacterial protein of unknown function (DUF882); Region: Peptidase_M15_2; pfam05951 407976007127 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 407976007128 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 407976007129 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 407976007130 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 407976007131 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 407976007132 Ligand binding site; other site 407976007133 DXD motif; other site 407976007134 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 407976007135 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 407976007136 sensor protein QseC; Provisional; Region: PRK10337 407976007137 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 407976007138 dimer interface [polypeptide binding]; other site 407976007139 phosphorylation site [posttranslational modification] 407976007140 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 407976007141 ATP binding site [chemical binding]; other site 407976007142 Mg2+ binding site [ion binding]; other site 407976007143 G-X-G motif; other site 407976007144 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976007145 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 407976007146 active site 407976007147 phosphorylation site [posttranslational modification] 407976007148 intermolecular recognition site; other site 407976007149 dimerization interface [polypeptide binding]; other site 407976007150 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 407976007151 DNA binding site [nucleotide binding] 407976007152 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 407976007153 ApbE family; Region: ApbE; pfam02424 407976007154 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 407976007155 Domain of unknown function (DUF4266); Region: DUF4266; pfam14086 407976007156 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 407976007157 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976007158 catalytic residues [active] 407976007159 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 407976007160 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 407976007161 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 407976007162 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 407976007163 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 407976007164 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 407976007165 putative substrate-binding site; other site 407976007166 nickel binding site [ion binding]; other site 407976007167 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 407976007168 Acylphosphatase; Region: Acylphosphatase; pfam00708 407976007169 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 407976007170 HypF finger; Region: zf-HYPF; pfam07503 407976007171 HypF finger; Region: zf-HYPF; pfam07503 407976007172 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 407976007173 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 407976007174 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 407976007175 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 407976007176 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 407976007177 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 407976007178 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 407976007179 dimerization interface [polypeptide binding]; other site 407976007180 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 407976007181 ATP binding site [chemical binding]; other site 407976007182 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 407976007183 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 407976007184 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 407976007185 putative acyl-acceptor binding pocket; other site 407976007186 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 407976007187 IHF dimer interface [polypeptide binding]; other site 407976007188 IHF - DNA interface [nucleotide binding]; other site 407976007189 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 407976007190 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 407976007191 putative tRNA-binding site [nucleotide binding]; other site 407976007192 B3/4 domain; Region: B3_4; pfam03483 407976007193 tRNA synthetase B5 domain; Region: B5; smart00874 407976007194 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 407976007195 dimer interface [polypeptide binding]; other site 407976007196 motif 1; other site 407976007197 motif 3; other site 407976007198 motif 2; other site 407976007199 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 407976007200 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 407976007201 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 407976007202 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 407976007203 dimer interface [polypeptide binding]; other site 407976007204 motif 1; other site 407976007205 active site 407976007206 motif 2; other site 407976007207 motif 3; other site 407976007208 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976007209 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976007210 dimer interface [polypeptide binding]; other site 407976007211 putative CheW interface [polypeptide binding]; other site 407976007212 hypothetical protein; Provisional; Region: PRK05170 407976007213 Transglycosylase SLT domain; Region: SLT_2; pfam13406 407976007214 murein hydrolase B; Provisional; Region: PRK10760; cl17906 407976007215 YcgL domain; Region: YcgL; pfam05166 407976007216 septum formation inhibitor; Reviewed; Region: minC; PRK04804 407976007217 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 407976007218 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 407976007219 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 407976007220 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 407976007221 Switch I; other site 407976007222 Switch II; other site 407976007223 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 407976007224 ribonuclease D; Provisional; Region: PRK10829 407976007225 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 407976007226 catalytic site [active] 407976007227 putative active site [active] 407976007228 putative substrate binding site [chemical binding]; other site 407976007229 HRDC domain; Region: HRDC; pfam00570 407976007230 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 407976007231 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 407976007232 acyl-activating enzyme (AAE) consensus motif; other site 407976007233 putative AMP binding site [chemical binding]; other site 407976007234 putative active site [active] 407976007235 putative CoA binding site [chemical binding]; other site 407976007236 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 407976007237 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 407976007238 Predicted methyltransferase [General function prediction only]; Region: COG4798 407976007239 Methyltransferase domain; Region: Methyltransf_23; pfam13489 407976007240 Peptidase M50B-like; Region: Peptidase_M50B; pfam13398 407976007241 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 407976007242 Glycoprotease family; Region: Peptidase_M22; pfam00814 407976007243 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; cd00384 407976007244 dimer interface [polypeptide binding]; other site 407976007245 active site 407976007246 Schiff base residues; other site 407976007247 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 407976007248 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 407976007249 methionine sulfoxide reductase A; Provisional; Region: PRK14054 407976007250 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 407976007251 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 407976007252 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 407976007253 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 407976007254 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 407976007255 GTP/Mg2+ binding site [chemical binding]; other site 407976007256 G4 box; other site 407976007257 G5 box; other site 407976007258 G1 box; other site 407976007259 Switch I region; other site 407976007260 G2 box; other site 407976007261 G3 box; other site 407976007262 Switch II region; other site 407976007263 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 407976007264 Low molecular weight phosphatase family; Region: LMWPc; cd00115 407976007265 active site 407976007266 DNA ligase; Provisional; Region: PRK09125 407976007267 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 407976007268 DNA binding site [nucleotide binding] 407976007269 active site 407976007270 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 407976007271 DNA binding site [nucleotide binding] 407976007272 transcriptional regulator HdfR; Provisional; Region: PRK03601 407976007273 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976007274 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 407976007275 dimerization interface [polypeptide binding]; other site 407976007276 hypothetical protein; Provisional; Region: PRK11027 407976007277 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 407976007278 ATP-grasp domain; Region: ATP-grasp_4; cl17255 407976007279 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 407976007280 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 407976007281 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 407976007282 PA/protease or protease-like domain interface [polypeptide binding]; other site 407976007283 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 407976007284 metal binding site [ion binding]; metal-binding site 407976007285 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976007286 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976007287 metal binding site [ion binding]; metal-binding site 407976007288 active site 407976007289 I-site; other site 407976007290 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved...; Region: Sortase_D_4; cd05828 407976007291 active site 407976007292 catalytic site [active] 407976007293 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 407976007294 marine proteobacterial sortase target protein; Region: marine_srt_targ; TIGR03788 407976007295 vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to...; Region: vWA_interalpha_trypsin_inhibitor; cd01461 407976007296 metal ion-dependent adhesion site (MIDAS); other site 407976007297 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976007298 ligand binding site [chemical binding]; other site 407976007299 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 407976007300 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 407976007301 active site 407976007302 phosphorylation site [posttranslational modification] 407976007303 intermolecular recognition site; other site 407976007304 dimerization interface [polypeptide binding]; other site 407976007305 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 407976007306 DNA binding site [nucleotide binding] 407976007307 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 407976007308 DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases; Region: CBM9_like_HisKa; cd09622 407976007309 putative ligand binding site [chemical binding]; other site 407976007310 HAMP domain; Region: HAMP; pfam00672 407976007311 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 407976007312 dimer interface [polypeptide binding]; other site 407976007313 phosphorylation site [posttranslational modification] 407976007314 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 407976007315 ATP binding site [chemical binding]; other site 407976007316 Mg2+ binding site [ion binding]; other site 407976007317 G-X-G motif; other site 407976007318 cystathionine beta-lyase; Provisional; Region: PRK09028 407976007319 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 407976007320 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976007321 catalytic residue [active] 407976007322 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 407976007323 CreA protein; Region: CreA; pfam05981 407976007324 putative chaperone; Provisional; Region: PRK11678 407976007325 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 407976007326 nucleotide binding site [chemical binding]; other site 407976007327 putative NEF/HSP70 interaction site [polypeptide binding]; other site 407976007328 SBD interface [polypeptide binding]; other site 407976007329 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 407976007330 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 407976007331 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 407976007332 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 407976007333 domain interface [polypeptide binding]; other site 407976007334 active site 407976007335 catalytic site [active] 407976007336 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 407976007337 domain interface [polypeptide binding]; other site 407976007338 active site 407976007339 catalytic site [active] 407976007340 exopolyphosphatase; Region: exo_poly_only; TIGR03706 407976007341 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 407976007342 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 407976007343 HSP70 interaction site [polypeptide binding]; other site 407976007344 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 407976007345 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 407976007346 generic binding surface II; other site 407976007347 generic binding surface I; other site 407976007348 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 407976007349 putative catalytic site [active] 407976007350 putative metal binding site [ion binding]; other site 407976007351 putative phosphate binding site [ion binding]; other site 407976007352 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 407976007353 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 407976007354 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 407976007355 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 407976007356 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 407976007357 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976007358 substrate binding pocket [chemical binding]; other site 407976007359 membrane-bound complex binding site; other site 407976007360 hinge residues; other site 407976007361 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 407976007362 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976007363 Coenzyme A binding pocket [chemical binding]; other site 407976007364 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976007365 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976007366 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 407976007367 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 407976007368 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 407976007369 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976007370 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976007371 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 407976007372 putative FMN binding site [chemical binding]; other site 407976007373 DoxX; Region: DoxX; pfam07681 407976007374 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 407976007375 Phosphotransferase enzyme family; Region: APH; pfam01636 407976007376 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 407976007377 substrate binding site [chemical binding]; other site 407976007378 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 407976007379 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 407976007380 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 407976007381 N-terminal plug; other site 407976007382 ligand-binding site [chemical binding]; other site 407976007383 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 407976007384 putative dimer interface [polypeptide binding]; other site 407976007385 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 407976007386 CoenzymeA binding site [chemical binding]; other site 407976007387 subunit interaction site [polypeptide binding]; other site 407976007388 PHB binding site; other site 407976007389 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 407976007390 CoenzymeA binding site [chemical binding]; other site 407976007391 subunit interaction site [polypeptide binding]; other site 407976007392 PHB binding site; other site 407976007393 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 407976007394 nucleotide binding site/active site [active] 407976007395 HIT family signature motif; other site 407976007396 catalytic residue [active] 407976007397 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 407976007398 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 407976007399 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 407976007400 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 407976007401 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 407976007402 DNA binding residues [nucleotide binding] 407976007403 dimerization interface [polypeptide binding]; other site 407976007404 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 407976007405 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 407976007406 Domain of unknown function DUF20; Region: UPF0118; pfam01594 407976007407 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 407976007408 CPxP motif; other site 407976007409 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 407976007410 Peptidase family M48; Region: Peptidase_M48; cl12018 407976007411 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 407976007412 binding surface 407976007413 TPR motif; other site 407976007414 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 407976007415 ArsC family; Region: ArsC; pfam03960 407976007416 catalytic residues [active] 407976007417 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 407976007418 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 407976007419 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 407976007420 Walker A motif; other site 407976007421 ATP binding site [chemical binding]; other site 407976007422 Walker B motif; other site 407976007423 arginine finger; other site 407976007424 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 407976007425 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 407976007426 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 407976007427 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 407976007428 putative GSH binding site [chemical binding]; other site 407976007429 catalytic residues [active] 407976007430 superoxide dismutase; Provisional; Region: PRK10543 407976007431 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 407976007432 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 407976007433 PrkA family serine protein kinase; Provisional; Region: PRK15455 407976007434 AAA ATPase domain; Region: AAA_16; pfam13191 407976007435 Walker A motif; other site 407976007436 ATP binding site [chemical binding]; other site 407976007437 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 407976007438 hypothetical protein; Provisional; Region: PRK05325 407976007439 SpoVR family protein; Provisional; Region: PRK11767 407976007440 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 407976007441 fatty acid metabolism regulator; Provisional; Region: PRK04984 407976007442 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976007443 DNA-binding site [nucleotide binding]; DNA binding site 407976007444 FadR C-terminal domain; Region: FadR_C; pfam07840 407976007445 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 407976007446 disulfide bond formation protein B; Provisional; Region: PRK01749 407976007447 Cache domain; Region: Cache_1; pfam02743 407976007448 PAS fold; Region: PAS_4; pfam08448 407976007449 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976007450 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 407976007451 ATP binding site [chemical binding]; other site 407976007452 Mg2+ binding site [ion binding]; other site 407976007453 G-X-G motif; other site 407976007454 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 407976007455 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 407976007456 YceI-like domain; Region: YceI; pfam04264 407976007457 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 407976007458 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 407976007459 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 407976007460 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 407976007461 Adenosylmethionine decarboxylase; Region: SAM_decarbox; cl03253 407976007462 arginine decarboxylase; Provisional; Region: PRK05354 407976007463 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 407976007464 dimer interface [polypeptide binding]; other site 407976007465 active site 407976007466 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 407976007467 catalytic residues [active] 407976007468 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 407976007469 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 407976007470 S1 domain; Region: S1_2; pfam13509 407976007471 hypothetical protein; Provisional; Region: PRK11239 407976007472 Protein of unknown function, DUF480; Region: DUF480; pfam04337 407976007473 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 407976007474 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976007475 Walker A/P-loop; other site 407976007476 ATP binding site [chemical binding]; other site 407976007477 Q-loop/lid; other site 407976007478 ABC transporter signature motif; other site 407976007479 Walker B; other site 407976007480 D-loop; other site 407976007481 H-loop/switch region; other site 407976007482 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 407976007483 IHF - DNA interface [nucleotide binding]; other site 407976007484 IHF dimer interface [polypeptide binding]; other site 407976007485 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 407976007486 AAA domain; Region: AAA_26; pfam13500 407976007487 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 407976007488 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 407976007489 S-adenosylmethionine binding site [chemical binding]; other site 407976007490 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 407976007491 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 407976007492 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976007493 catalytic residue [active] 407976007494 biotin synthase; Provisional; Region: PRK15108 407976007495 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 407976007496 FeS/SAM binding site; other site 407976007497 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 407976007498 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 407976007499 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 407976007500 inhibitor-cofactor binding pocket; inhibition site 407976007501 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976007502 catalytic residue [active] 407976007503 Cache domain; Region: Cache_2; pfam08269 407976007504 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 407976007505 dimerization interface [polypeptide binding]; other site 407976007506 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976007507 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976007508 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976007509 dimer interface [polypeptide binding]; other site 407976007510 putative CheW interface [polypeptide binding]; other site 407976007511 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 407976007512 Na binding site [ion binding]; other site 407976007513 PAS domain; Region: PAS; smart00091 407976007514 PAS fold; Region: PAS_7; pfam12860 407976007515 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976007516 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 407976007517 dimer interface [polypeptide binding]; other site 407976007518 phosphorylation site [posttranslational modification] 407976007519 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 407976007520 ATP binding site [chemical binding]; other site 407976007521 Mg2+ binding site [ion binding]; other site 407976007522 G-X-G motif; other site 407976007523 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976007524 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 407976007525 active site 407976007526 phosphorylation site [posttranslational modification] 407976007527 intermolecular recognition site; other site 407976007528 dimerization interface [polypeptide binding]; other site 407976007529 acetyl-CoA synthetase; Provisional; Region: PRK00174 407976007530 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 407976007531 active site 407976007532 CoA binding site [chemical binding]; other site 407976007533 acyl-activating enzyme (AAE) consensus motif; other site 407976007534 AMP binding site [chemical binding]; other site 407976007535 acetate binding site [chemical binding]; other site 407976007536 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 407976007537 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 407976007538 ATP binding site [chemical binding]; other site 407976007539 putative Mg++ binding site [ion binding]; other site 407976007540 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 407976007541 nucleotide binding region [chemical binding]; other site 407976007542 ATP-binding site [chemical binding]; other site 407976007543 Double zinc ribbon; Region: DZR; pfam12773 407976007544 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 407976007545 GSH binding site [chemical binding]; other site 407976007546 catalytic residues [active] 407976007547 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 407976007548 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 407976007549 binding surface 407976007550 TPR motif; other site 407976007551 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 407976007552 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976007553 ligand binding site [chemical binding]; other site 407976007554 translocation protein TolB; Provisional; Region: tolB; PRK04792 407976007555 TolB amino-terminal domain; Region: TolB_N; pfam04052 407976007556 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976007557 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976007558 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976007559 TolA protein; Region: tolA_full; TIGR02794 407976007560 TolA C-terminal; Region: TolA; pfam06519 407976007561 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 407976007562 TolR protein; Region: tolR; TIGR02801 407976007563 TolQ protein; Region: tolQ; TIGR02796 407976007564 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 407976007565 active site 407976007566 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 407976007567 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976007568 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 407976007569 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976007570 ligand binding site [chemical binding]; other site 407976007571 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 407976007572 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 407976007573 dimer interface [polypeptide binding]; other site 407976007574 catalytic site [active] 407976007575 putative active site [active] 407976007576 putative substrate binding site [chemical binding]; other site 407976007577 peroxidase; Provisional; Region: PRK15000 407976007578 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 407976007579 dimer interface [polypeptide binding]; other site 407976007580 decamer (pentamer of dimers) interface [polypeptide binding]; other site 407976007581 catalytic triad [active] 407976007582 peroxidatic and resolving cysteines [active] 407976007583 Predicted permease [General function prediction only]; Region: COG2056 407976007584 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 407976007585 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976007586 active site 407976007587 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 407976007588 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 407976007589 dimerization interface [polypeptide binding]; other site 407976007590 putative ATP binding site [chemical binding]; other site 407976007591 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 407976007592 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 407976007593 active site 407976007594 substrate binding site [chemical binding]; other site 407976007595 cosubstrate binding site; other site 407976007596 catalytic site [active] 407976007597 UMP phosphatase; Provisional; Region: PRK10444 407976007598 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 407976007599 active site 407976007600 motif I; other site 407976007601 motif II; other site 407976007602 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 407976007603 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; pfam10137 407976007604 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 407976007605 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 407976007606 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 407976007607 PA/protease or protease-like domain interface [polypeptide binding]; other site 407976007608 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 407976007609 metal binding site [ion binding]; metal-binding site 407976007610 asparagine synthetase B; Provisional; Region: asnB; PRK09431 407976007611 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 407976007612 active site 407976007613 dimer interface [polypeptide binding]; other site 407976007614 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 407976007615 Ligand Binding Site [chemical binding]; other site 407976007616 Molecular Tunnel; other site 407976007617 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 407976007618 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 407976007619 active site 407976007620 nucleophile elbow; other site 407976007621 DKNYY family; Region: DKNYY; pfam13644 407976007622 DKNYY family; Region: DKNYY; pfam13644 407976007623 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976007624 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976007625 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976007626 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 407976007627 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 407976007628 N-terminal plug; other site 407976007629 ligand-binding site [chemical binding]; other site 407976007630 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 407976007631 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 407976007632 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 407976007633 active site 407976007634 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 407976007635 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 407976007636 active site 407976007637 phosphate binding residues; other site 407976007638 catalytic residues [active] 407976007639 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 407976007640 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 407976007641 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 407976007642 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 407976007643 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 407976007644 dimer interface [polypeptide binding]; other site 407976007645 active site 407976007646 acyl carrier protein; Provisional; Region: acpP; PRK00982 407976007647 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 407976007648 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 407976007649 NAD(P) binding site [chemical binding]; other site 407976007650 homotetramer interface [polypeptide binding]; other site 407976007651 homodimer interface [polypeptide binding]; other site 407976007652 active site 407976007653 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 407976007654 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 407976007655 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 407976007656 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 407976007657 dimer interface [polypeptide binding]; other site 407976007658 active site 407976007659 CoA binding pocket [chemical binding]; other site 407976007660 Phage-related protein, tail component [Function unknown]; Region: COG4733 407976007661 Putative phage tail protein; Region: Phage-tail_3; pfam13550 407976007662 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 407976007663 Interdomain contacts; other site 407976007664 Cytokine receptor motif; other site 407976007665 Carbohydrate binding domain; Region: CBM_5_12; pfam02839 407976007666 Domain of unknown function (DUF1983); Region: DUF1983; pfam09327 407976007667 Phage-related protein, tail component [Function unknown]; Region: COG4723 407976007668 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; Region: MPN_NLPC_P60; cd08073 407976007669 MPN+ (JAMM) motif; other site 407976007670 Zinc-binding site [ion binding]; other site 407976007671 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 407976007672 NlpC/P60 family; Region: NLPC_P60; cl17555 407976007673 Phage-related protein [Function unknown]; Region: gp18; COG4672 407976007674 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 407976007675 Phage minor tail protein; Region: Phage_min_tail; pfam05939 407976007676 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 407976007677 phage tail tape measure protein, lambda family; Region: tape_meas_lam_C; TIGR01541 407976007678 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 407976007679 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 407976007680 phage protein, HK97 gp10 family; Region: phge_HK97_gp10; TIGR01725 407976007681 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 407976007682 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 407976007683 oligomerization interface [polypeptide binding]; other site 407976007684 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 407976007685 Phage capsid family; Region: Phage_capsid; pfam05065 407976007686 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 407976007687 oligomer interface [polypeptide binding]; other site 407976007688 active site residues [active] 407976007689 Phage portal protein; Region: Phage_portal; pfam04860 407976007690 Phage-related protein [Function unknown]; Region: COG4695 407976007691 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 407976007692 Phage terminase, small subunit; Region: Terminase_4; pfam05119 407976007693 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 407976007694 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 407976007695 active site 407976007696 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 407976007697 catalytic residue [active] 407976007698 T5orf172 domain; Region: T5orf172; pfam10544 407976007699 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 407976007700 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 407976007701 active site 407976007702 DNA binding site [nucleotide binding] 407976007703 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 407976007704 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 407976007705 Catalytic site [active] 407976007706 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976007707 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976007708 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976007709 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 407976007710 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976007711 active site 407976007712 DNA binding site [nucleotide binding] 407976007713 Int/Topo IB signature motif; other site 407976007714 uncharacterized phage protein; Region: phage_xxxx; TIGR02642 407976007715 Bacteriophage replication protein O; Region: Phage_rep_O; pfam04492 407976007716 DNA-binding transcriptional regulator DicC; Provisional; Region: PRK09744 407976007717 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 407976007718 non-specific DNA binding site [nucleotide binding]; other site 407976007719 Predicted transcriptional regulator [Transcription]; Region: COG2932 407976007720 salt bridge; other site 407976007721 sequence-specific DNA binding site [nucleotide binding]; other site 407976007722 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 407976007723 Catalytic site [active] 407976007724 Superinfection immunity protein; Region: Imm_superinfect; pfam14373 407976007725 DNA polymerase III subunit epsilon; Validated; Region: PRK06195 407976007726 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 407976007727 active site 407976007728 catalytic site [active] 407976007729 substrate binding site [chemical binding]; other site 407976007730 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; cl00038 407976007731 Dimer interface [polypeptide binding]; other site 407976007732 Lipase. 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 process of...; Region: Lipase; cl14883 407976007733 Phage-related protein, tail component [Function unknown]; Region: COG4723 407976007734 Ead/Ea22-like protein; Region: Ead_Ea22; pfam13935 407976007735 DNA N-6-adenine-methyltransferase (Dam); Region: Dam; cl05442 407976007736 Ras GTPase Activating Domain; Region: RasGAP; cl02569 407976007737 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 407976007738 cofactor binding site; other site 407976007739 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 407976007740 DNA binding site [nucleotide binding] 407976007741 substrate interaction site [chemical binding]; other site 407976007742 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 407976007743 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 407976007744 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 407976007745 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976007746 active site 407976007747 Int/Topo IB signature motif; other site 407976007748 putative phosphate acyltransferase; Provisional; Region: PRK05331 407976007749 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 407976007750 hypothetical protein; Provisional; Region: PRK11193 407976007751 Maf-like protein; Region: Maf; pfam02545 407976007752 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 407976007753 active site 407976007754 dimer interface [polypeptide binding]; other site 407976007755 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 407976007756 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 407976007757 motif II; other site 407976007758 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 407976007759 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 407976007760 RNA binding surface [nucleotide binding]; other site 407976007761 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976007762 active site 407976007763 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 407976007764 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 407976007765 homodimer interface [polypeptide binding]; other site 407976007766 oligonucleotide binding site [chemical binding]; other site 407976007767 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 407976007768 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 407976007769 Sulfate transporter family; Region: Sulfate_transp; pfam00916 407976007770 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 407976007771 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 407976007772 DNA-binding site [nucleotide binding]; DNA binding site 407976007773 RNA-binding motif; other site 407976007774 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 407976007775 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 407976007776 S-adenosylmethionine binding site [chemical binding]; other site 407976007777 exonuclease I; Provisional; Region: sbcB; PRK11779 407976007778 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 407976007779 active site 407976007780 catalytic site [active] 407976007781 substrate binding site [chemical binding]; other site 407976007782 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 407976007783 cytidine deaminase; Provisional; Region: PRK09027 407976007784 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 407976007785 active site 407976007786 catalytic motif [active] 407976007787 Zn binding site [ion binding]; other site 407976007788 Cytidine and deoxycytidylate deaminase zinc-binding region; Region: dCMP_cyt_deam_2; pfam08211 407976007789 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 407976007790 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 407976007791 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976007792 Protein of unknown function (DUF445); Region: DUF445; pfam04286 407976007793 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 407976007794 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976007795 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 407976007796 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 407976007797 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 407976007798 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 407976007799 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976007800 Predicted membrane protein [Function unknown]; Region: COG3235 407976007801 Uncharacterized conserved protein [Function unknown]; Region: COG2835 407976007802 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 407976007803 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 407976007804 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 407976007805 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976007806 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 407976007807 Walker A/P-loop; other site 407976007808 ATP binding site [chemical binding]; other site 407976007809 Q-loop/lid; other site 407976007810 ABC transporter signature motif; other site 407976007811 Walker B; other site 407976007812 D-loop; other site 407976007813 H-loop/switch region; other site 407976007814 ComEC family competence protein; Provisional; Region: PRK11539 407976007815 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 407976007816 Competence protein; Region: Competence; pfam03772 407976007817 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 407976007818 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 407976007819 NnrS protein; Region: NnrS; pfam05940 407976007820 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 407976007821 PilZ domain; Region: PilZ; pfam07238 407976007822 ParA-like protein; Provisional; Region: PHA02518 407976007823 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 407976007824 P-loop; other site 407976007825 Magnesium ion binding site [ion binding]; other site 407976007826 Protein of unknown function (DUF2492); Region: DUF2492; pfam10678 407976007827 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 407976007828 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 407976007829 GAF domain; Region: GAF; pfam01590 407976007830 Histidine kinase; Region: His_kinase; pfam06580 407976007831 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 407976007832 ATP binding site [chemical binding]; other site 407976007833 Mg2+ binding site [ion binding]; other site 407976007834 G-X-G motif; other site 407976007835 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 407976007836 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 407976007837 active site 407976007838 phosphorylation site [posttranslational modification] 407976007839 intermolecular recognition site; other site 407976007840 dimerization interface [polypeptide binding]; other site 407976007841 LytTr DNA-binding domain; Region: LytTR; pfam04397 407976007842 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 407976007843 Carbon starvation protein CstA; Region: CstA; pfam02554 407976007844 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 407976007845 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 407976007846 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 407976007847 dimerization interface [polypeptide binding]; other site 407976007848 active site 407976007849 hypothetical protein; Provisional; Region: PRK11020 407976007850 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; PRK11121 407976007851 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 407976007852 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 407976007853 ATP cone domain; Region: ATP-cone; pfam03477 407976007854 Class III ribonucleotide reductase; Region: RNR_III; cd01675 407976007855 effector binding site; other site 407976007856 active site 407976007857 Zn binding site [ion binding]; other site 407976007858 glycine loop; other site 407976007859 Transcriptional regulators [Transcription]; Region: MarR; COG1846 407976007860 MarR family; Region: MarR; pfam01047 407976007861 Prostaglandin dehydrogenases; Region: PGDH; cd05288 407976007862 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 407976007863 NAD(P) binding site [chemical binding]; other site 407976007864 substrate binding site [chemical binding]; other site 407976007865 dimer interface [polypeptide binding]; other site 407976007866 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 407976007867 active site 407976007868 nucleophile elbow; other site 407976007869 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 407976007870 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 407976007871 ATP binding site [chemical binding]; other site 407976007872 Mg++ binding site [ion binding]; other site 407976007873 motif III; other site 407976007874 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 407976007875 nucleotide binding region [chemical binding]; other site 407976007876 ATP-binding site [chemical binding]; other site 407976007877 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 407976007878 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 407976007879 putative peptidase; Provisional; Region: PRK11649 407976007880 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 407976007881 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976007882 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 407976007883 AAA domain; Region: AAA_23; pfam13476 407976007884 Walker A/P-loop; other site 407976007885 ATP binding site [chemical binding]; other site 407976007886 Q-loop/lid; other site 407976007887 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 407976007888 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 407976007889 ABC transporter signature motif; other site 407976007890 Walker B; other site 407976007891 D-loop; other site 407976007892 H-loop/switch region; other site 407976007893 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 407976007894 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 407976007895 active site 407976007896 metal binding site [ion binding]; metal-binding site 407976007897 DNA binding site [nucleotide binding] 407976007898 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 407976007899 hypothetical protein; Provisional; Region: PRK10621 407976007900 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976007901 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 407976007902 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976007903 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 407976007904 dimerization interface [polypeptide binding]; other site 407976007905 substrate binding pocket [chemical binding]; other site 407976007906 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 407976007907 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 407976007908 RNA binding surface [nucleotide binding]; other site 407976007909 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976007910 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976007911 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 407976007912 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 407976007913 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976007914 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976007915 metal binding site [ion binding]; metal-binding site 407976007916 active site 407976007917 I-site; other site 407976007918 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 407976007919 TPR motif; other site 407976007920 binding surface 407976007921 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 407976007922 binding surface 407976007923 TPR motif; other site 407976007924 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 407976007925 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 407976007926 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 407976007927 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 407976007928 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 407976007929 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 407976007930 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 407976007931 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 407976007932 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 407976007933 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976007934 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 407976007935 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 407976007936 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 407976007937 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976007938 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 407976007939 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 407976007940 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 407976007941 trimer interface [polypeptide binding]; other site 407976007942 eyelet of channel; other site 407976007943 DNA polymerase II; Reviewed; Region: PRK05762 407976007944 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 407976007945 active site 407976007946 catalytic site [active] 407976007947 substrate binding site [chemical binding]; other site 407976007948 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 407976007949 active site 407976007950 metal-binding site 407976007951 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 407976007952 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 407976007953 Protein of unknown function (DUF570); Region: DUF570; pfam04489 407976007954 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 407976007955 hypothetical protein; Provisional; Region: PRK10621 407976007956 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976007957 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 407976007958 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 407976007959 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 407976007960 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 407976007961 putative active site [active] 407976007962 Zn binding site [ion binding]; other site 407976007963 Late competence development protein ComFB; Region: ComFB; pfam10719 407976007964 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 407976007965 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 407976007966 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 407976007967 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 407976007968 homodimer interface [polypeptide binding]; other site 407976007969 substrate-cofactor binding pocket; other site 407976007970 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976007971 catalytic residue [active] 407976007972 hypothetical protein; Provisional; Region: PRK05415 407976007973 Domain of unknown function (DUF697); Region: DUF697; pfam05128 407976007974 YcjX-like family, DUF463; Region: DUF463; pfam04317 407976007975 phage shock protein C; Region: phageshock_pspC; TIGR02978 407976007976 PspC domain; Region: PspC; cl00864 407976007977 phage shock protein B; Provisional; Region: pspB; PRK09458 407976007978 phage shock protein A; Region: phageshock_pspA; TIGR02977 407976007979 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 407976007980 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 407976007981 Walker A motif; other site 407976007982 ATP binding site [chemical binding]; other site 407976007983 Walker B motif; other site 407976007984 arginine finger; other site 407976007985 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976007986 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 407976007987 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 407976007988 peptide binding site [polypeptide binding]; other site 407976007989 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 407976007990 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 407976007991 dimer interface [polypeptide binding]; other site 407976007992 conserved gate region; other site 407976007993 putative PBP binding loops; other site 407976007994 ABC-ATPase subunit interface; other site 407976007995 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 407976007996 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 407976007997 dimer interface [polypeptide binding]; other site 407976007998 conserved gate region; other site 407976007999 putative PBP binding loops; other site 407976008000 ABC-ATPase subunit interface; other site 407976008001 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 407976008002 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 407976008003 Walker A/P-loop; other site 407976008004 ATP binding site [chemical binding]; other site 407976008005 Q-loop/lid; other site 407976008006 ABC transporter signature motif; other site 407976008007 Walker B; other site 407976008008 D-loop; other site 407976008009 H-loop/switch region; other site 407976008010 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 407976008011 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 407976008012 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 407976008013 Walker A/P-loop; other site 407976008014 ATP binding site [chemical binding]; other site 407976008015 Q-loop/lid; other site 407976008016 ABC transporter signature motif; other site 407976008017 Walker B; other site 407976008018 D-loop; other site 407976008019 H-loop/switch region; other site 407976008020 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 407976008021 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 407976008022 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 407976008023 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 407976008024 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 407976008025 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 407976008026 periplasmic folding chaperone; Provisional; Region: PRK10788 407976008027 SurA N-terminal domain; Region: SurA_N_3; cl07813 407976008028 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 407976008029 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 407976008030 IHF dimer interface [polypeptide binding]; other site 407976008031 IHF - DNA interface [nucleotide binding]; other site 407976008032 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 407976008033 Found in ATP-dependent protease La (LON); Region: LON; smart00464 407976008034 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 407976008035 Walker A motif; other site 407976008036 ATP binding site [chemical binding]; other site 407976008037 Walker B motif; other site 407976008038 arginine finger; other site 407976008039 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 407976008040 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 407976008041 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 407976008042 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 407976008043 Walker A motif; other site 407976008044 ATP binding site [chemical binding]; other site 407976008045 Walker B motif; other site 407976008046 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 407976008047 Clp protease; Region: CLP_protease; pfam00574 407976008048 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 407976008049 oligomer interface [polypeptide binding]; other site 407976008050 active site residues [active] 407976008051 trigger factor; Provisional; Region: tig; PRK01490 407976008052 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976008053 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 407976008054 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 407976008055 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 407976008056 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 407976008057 homodimer interface [polypeptide binding]; other site 407976008058 NADP binding site [chemical binding]; other site 407976008059 substrate binding site [chemical binding]; other site 407976008060 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 407976008061 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 407976008062 active site 407976008063 HIGH motif; other site 407976008064 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 407976008065 KMSKS motif; other site 407976008066 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 407976008067 tRNA binding surface [nucleotide binding]; other site 407976008068 anticodon binding site; other site 407976008069 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 407976008070 substrate binding site [chemical binding]; other site 407976008071 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 407976008072 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 407976008073 putative active site [active] 407976008074 putative metal binding site [ion binding]; other site 407976008075 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 407976008076 active site 407976008077 dinuclear metal binding site [ion binding]; other site 407976008078 dimerization interface [polypeptide binding]; other site 407976008079 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 407976008080 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 407976008081 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 407976008082 active site 407976008083 HIGH motif; other site 407976008084 nucleotide binding site [chemical binding]; other site 407976008085 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 407976008086 KMSKS motif; other site 407976008087 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 407976008088 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 407976008089 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 407976008090 G1 box; other site 407976008091 GTP/Mg2+ binding site [chemical binding]; other site 407976008092 Switch I region; other site 407976008093 G2 box; other site 407976008094 G3 box; other site 407976008095 Switch II region; other site 407976008096 G4 box; other site 407976008097 G5 box; other site 407976008098 Nucleoside recognition; Region: Gate; pfam07670 407976008099 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 407976008100 Nucleoside recognition; Region: Gate; pfam07670 407976008101 FeoA domain; Region: FeoA; pfam04023 407976008102 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 407976008103 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 407976008104 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 407976008105 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 407976008106 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 407976008107 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 407976008108 heme-binding residues [chemical binding]; other site 407976008109 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 407976008110 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 407976008111 heme-binding residues [chemical binding]; other site 407976008112 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 407976008113 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 407976008114 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 407976008115 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 407976008116 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 407976008117 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 407976008118 putative uracil binding site [chemical binding]; other site 407976008119 putative active site [active] 407976008120 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 407976008121 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 407976008122 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 407976008123 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 407976008124 putative heme binding pocket [chemical binding]; other site 407976008125 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 407976008126 fructuronate transporter; Provisional; Region: PRK10034; cl15264 407976008127 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 407976008128 putative pyridoxal-dependent aspartate 1-decarboxylase; Region: NOD_PanD_pyr; TIGR03799 407976008129 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976008130 catalytic residue [active] 407976008131 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 407976008132 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 407976008133 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 407976008134 trimer interface [polypeptide binding]; other site 407976008135 active site 407976008136 substrate binding site [chemical binding]; other site 407976008137 CoA binding site [chemical binding]; other site 407976008138 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 407976008139 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 407976008140 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976008141 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976008142 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 407976008143 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 407976008144 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976008145 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976008146 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976008147 Predicted transcriptional regulator [Transcription]; Region: COG2378 407976008148 HTH domain; Region: HTH_11; pfam08279 407976008149 WYL domain; Region: WYL; pfam13280 407976008150 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 407976008151 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 407976008152 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976008153 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 407976008154 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 407976008155 active site 407976008156 substrate binding site [chemical binding]; other site 407976008157 metal binding site [ion binding]; metal-binding site 407976008158 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 407976008159 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 407976008160 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 407976008161 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 407976008162 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 407976008163 Zn binding site [ion binding]; other site 407976008164 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 407976008165 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 407976008166 Walker A/P-loop; other site 407976008167 ATP binding site [chemical binding]; other site 407976008168 Q-loop/lid; other site 407976008169 ABC transporter signature motif; other site 407976008170 Walker B; other site 407976008171 D-loop; other site 407976008172 H-loop/switch region; other site 407976008173 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 407976008174 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 407976008175 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 407976008176 putative substrate translocation pore; other site 407976008177 POT family; Region: PTR2; cl17359 407976008178 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 407976008179 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976008180 3-beta hydroxysteroid dehydrogenase/isomerase family; Region: 3Beta_HSD; pfam01073 407976008181 NAD(P) binding site [chemical binding]; other site 407976008182 active site 407976008183 peptide synthase; Provisional; Region: PRK09274 407976008184 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 407976008185 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_1; cd05910 407976008186 acyl-activating enzyme (AAE) consensus motif; other site 407976008187 putative AMP binding site [chemical binding]; other site 407976008188 putative active site [active] 407976008189 putative CoA binding site [chemical binding]; other site 407976008190 haloalkane dehalogenase; Provisional; Region: PRK03592 407976008191 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 407976008192 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 407976008193 dimer interface [polypeptide binding]; other site 407976008194 active site 407976008195 CoA binding pocket [chemical binding]; other site 407976008196 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 407976008197 S-adenosylmethionine binding site [chemical binding]; other site 407976008198 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 407976008199 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 407976008200 active site 407976008201 BCCT family transporter; Region: BCCT; pfam02028 407976008202 Protein of unknown function (DUF502); Region: DUF502; pfam04367 407976008203 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 407976008204 dimer interface [polypeptide binding]; other site 407976008205 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976008206 metal binding site [ion binding]; metal-binding site 407976008207 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 407976008208 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4994 407976008209 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976008210 Coenzyme A binding pocket [chemical binding]; other site 407976008211 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 407976008212 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 407976008213 transcriptional regulator PhoU; Provisional; Region: PRK11115 407976008214 PhoU domain; Region: PhoU; pfam01895 407976008215 PhoU domain; Region: PhoU; pfam01895 407976008216 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 407976008217 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 407976008218 Walker A/P-loop; other site 407976008219 ATP binding site [chemical binding]; other site 407976008220 Q-loop/lid; other site 407976008221 ABC transporter signature motif; other site 407976008222 Walker B; other site 407976008223 D-loop; other site 407976008224 H-loop/switch region; other site 407976008225 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 407976008226 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 407976008227 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 407976008228 dimer interface [polypeptide binding]; other site 407976008229 conserved gate region; other site 407976008230 putative PBP binding loops; other site 407976008231 ABC-ATPase subunit interface; other site 407976008232 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 407976008233 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 407976008234 conserved gate region; other site 407976008235 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 407976008236 ABC-ATPase subunit interface; other site 407976008237 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 407976008238 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 407976008239 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 407976008240 EamA-like transporter family; Region: EamA; pfam00892 407976008241 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 407976008242 EamA-like transporter family; Region: EamA; pfam00892 407976008243 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 407976008244 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 407976008245 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 407976008246 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 407976008247 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 407976008248 Domain of unknown function (DUF4062); Region: DUF4062; pfam13271 407976008249 Beta-lactamase; Region: Beta-lactamase; pfam00144 407976008250 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 407976008251 SseB protein; Region: SseB; cl06279 407976008252 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 407976008253 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 407976008254 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 407976008255 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 407976008256 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 407976008257 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 407976008258 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 407976008259 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 407976008260 Walker A/P-loop; other site 407976008261 ATP binding site [chemical binding]; other site 407976008262 Q-loop/lid; other site 407976008263 ABC transporter signature motif; other site 407976008264 Walker B; other site 407976008265 D-loop; other site 407976008266 H-loop/switch region; other site 407976008267 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976008268 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 407976008269 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976008270 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976008271 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976008272 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976008273 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 407976008274 DNA binding site [nucleotide binding] 407976008275 AAA ATPase domain; Region: AAA_16; pfam13191 407976008276 Domain of unknown function (DUF1888); Region: DUF1888; pfam08985 407976008277 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 407976008278 PAS domain; Region: PAS_9; pfam13426 407976008279 putative active site [active] 407976008280 heme pocket [chemical binding]; other site 407976008281 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976008282 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976008283 metal binding site [ion binding]; metal-binding site 407976008284 active site 407976008285 I-site; other site 407976008286 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 407976008287 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 407976008288 FAD binding domain; Region: FAD_binding_4; pfam01565 407976008289 outer membrane lipoprotein Blc; Provisional; Region: PRK10477 407976008290 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 407976008291 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 407976008292 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976008293 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976008294 ABC transporter; Region: ABC_tran_2; pfam12848 407976008295 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 407976008296 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 407976008297 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 407976008298 metal-binding site [ion binding] 407976008299 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 407976008300 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 407976008301 motif II; other site 407976008302 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 407976008303 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 407976008304 DNA binding residues [nucleotide binding] 407976008305 dimer interface [polypeptide binding]; other site 407976008306 copper binding site [ion binding]; other site 407976008307 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976008308 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976008309 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 407976008310 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976008311 NAD(P) binding site [chemical binding]; other site 407976008312 active site 407976008313 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 407976008314 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 407976008315 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 407976008316 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 407976008317 substrate binding site [chemical binding]; other site 407976008318 oxyanion hole (OAH) forming residues; other site 407976008319 trimer interface [polypeptide binding]; other site 407976008320 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 407976008321 enoyl-CoA hydratase; Provisional; Region: PRK09076 407976008322 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 407976008323 substrate binding site [chemical binding]; other site 407976008324 oxyanion hole (OAH) forming residues; other site 407976008325 trimer interface [polypeptide binding]; other site 407976008326 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 407976008327 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 407976008328 active site 407976008329 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 407976008330 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 407976008331 tetrameric interface [polypeptide binding]; other site 407976008332 NAD binding site [chemical binding]; other site 407976008333 catalytic residues [active] 407976008334 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 407976008335 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 407976008336 dimer interface [polypeptide binding]; other site 407976008337 active site 407976008338 homoserine O-succinyltransferase; Provisional; Region: PRK05368 407976008339 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 407976008340 proposed active site lysine [active] 407976008341 conserved cys residue [active] 407976008342 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 407976008343 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 407976008344 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976008345 NAD(P) binding site [chemical binding]; other site 407976008346 active site 407976008347 outer membrane protein W; Provisional; Region: PRK10959 407976008348 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 407976008349 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 407976008350 maleylacetoacetate isomerase; Region: maiA; TIGR01262 407976008351 C-terminal domain interface [polypeptide binding]; other site 407976008352 GSH binding site (G-site) [chemical binding]; other site 407976008353 putative dimer interface [polypeptide binding]; other site 407976008354 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 407976008355 dimer interface [polypeptide binding]; other site 407976008356 N-terminal domain interface [polypeptide binding]; other site 407976008357 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 407976008358 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 407976008359 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 407976008360 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 407976008361 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 407976008362 putative aromatic amino acid binding site; other site 407976008363 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 407976008364 Walker A motif; other site 407976008365 ATP binding site [chemical binding]; other site 407976008366 Walker B motif; other site 407976008367 arginine finger; other site 407976008368 GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break...; Region: GIY-YIG_Cterm; cl11508 407976008369 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 407976008370 aromatic arch; other site 407976008371 DCoH dimer interaction site [polypeptide binding]; other site 407976008372 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 407976008373 DCoH tetramer interaction site [polypeptide binding]; other site 407976008374 substrate binding site [chemical binding]; other site 407976008375 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 407976008376 cofactor binding site; other site 407976008377 metal binding site [ion binding]; metal-binding site 407976008378 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 407976008379 active site 407976008380 tetramer interface; other site 407976008381 UDP-glucose 4-epimerase; Region: PLN02240 407976008382 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 407976008383 NAD binding site [chemical binding]; other site 407976008384 homodimer interface [polypeptide binding]; other site 407976008385 active site 407976008386 substrate binding site [chemical binding]; other site 407976008387 ferredoxin-type protein; Provisional; Region: PRK10194 407976008388 4Fe-4S binding domain; Region: Fer4; cl02805 407976008389 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 407976008390 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976008391 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976008392 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 407976008393 dimerization interface [polypeptide binding]; other site 407976008394 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 407976008395 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 407976008396 Uncharacterized conserved protein [Function unknown]; Region: COG1434 407976008397 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 407976008398 putative active site [active] 407976008399 fructokinase; Reviewed; Region: PRK09557 407976008400 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 407976008401 nucleotide binding site [chemical binding]; other site 407976008402 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 407976008403 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 407976008404 active site 407976008405 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 407976008406 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 407976008407 NADP binding site [chemical binding]; other site 407976008408 active site 407976008409 putative substrate binding site [chemical binding]; other site 407976008410 putative hydrolase; Validated; Region: PRK09248 407976008411 Polymerase and Histidinol Phosphatase domain of Ycdx like; Region: PHP_HisPPase_Ycdx_like; cd07437 407976008412 active site 407976008413 SWIM zinc finger; Region: SWIM; pfam04434 407976008414 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 407976008415 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 407976008416 ATP binding site [chemical binding]; other site 407976008417 putative Mg++ binding site [ion binding]; other site 407976008418 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 407976008419 nucleotide binding region [chemical binding]; other site 407976008420 ATP-binding site [chemical binding]; other site 407976008421 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 407976008422 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 407976008423 DNA-binding site [nucleotide binding]; DNA binding site 407976008424 RNA-binding motif; other site 407976008425 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 407976008426 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 407976008427 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 407976008428 TrkA-N domain; Region: TrkA_N; pfam02254 407976008429 TrkA-C domain; Region: TrkA_C; pfam02080 407976008430 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976008431 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976008432 metal binding site [ion binding]; metal-binding site 407976008433 active site 407976008434 I-site; other site 407976008435 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 407976008436 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 407976008437 Ligand Binding Site [chemical binding]; other site 407976008438 TilS substrate binding domain; Region: TilS; pfam09179 407976008439 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 407976008440 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 407976008441 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 407976008442 putative active site [active] 407976008443 putative PHP Thumb interface [polypeptide binding]; other site 407976008444 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 407976008445 generic binding surface II; other site 407976008446 generic binding surface I; other site 407976008447 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 407976008448 RNA/DNA hybrid binding site [nucleotide binding]; other site 407976008449 active site 407976008450 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 407976008451 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 407976008452 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 407976008453 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 407976008454 active site 407976008455 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 407976008456 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 407976008457 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 407976008458 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 407976008459 trimer interface [polypeptide binding]; other site 407976008460 active site 407976008461 UDP-GlcNAc binding site [chemical binding]; other site 407976008462 lipid binding site [chemical binding]; lipid-binding site 407976008463 periplasmic chaperone; Provisional; Region: PRK10780 407976008464 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 407976008465 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 407976008466 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976008467 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976008468 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976008469 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976008470 Surface antigen; Region: Bac_surface_Ag; pfam01103 407976008471 zinc metallopeptidase RseP; Provisional; Region: PRK10779 407976008472 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 407976008473 active site 407976008474 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 407976008475 protein binding site [polypeptide binding]; other site 407976008476 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 407976008477 protein binding site [polypeptide binding]; other site 407976008478 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 407976008479 putative substrate binding region [chemical binding]; other site 407976008480 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 407976008481 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 407976008482 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 407976008483 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 407976008484 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 407976008485 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 407976008486 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 407976008487 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 407976008488 catalytic residue [active] 407976008489 putative FPP diphosphate binding site; other site 407976008490 putative FPP binding hydrophobic cleft; other site 407976008491 dimer interface [polypeptide binding]; other site 407976008492 putative IPP diphosphate binding site; other site 407976008493 ribosome recycling factor; Reviewed; Region: frr; PRK00083 407976008494 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 407976008495 hinge region; other site 407976008496 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 407976008497 putative nucleotide binding site [chemical binding]; other site 407976008498 uridine monophosphate binding site [chemical binding]; other site 407976008499 homohexameric interface [polypeptide binding]; other site 407976008500 elongation factor Ts; Provisional; Region: tsf; PRK09377 407976008501 UBA/TS-N domain; Region: UBA; pfam00627 407976008502 Elongation factor TS; Region: EF_TS; pfam00889 407976008503 Elongation factor TS; Region: EF_TS; pfam00889 407976008504 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 407976008505 rRNA interaction site [nucleotide binding]; other site 407976008506 S8 interaction site; other site 407976008507 putative laminin-1 binding site; other site 407976008508 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 407976008509 active site 407976008510 PII uridylyl-transferase; Provisional; Region: PRK05007 407976008511 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 407976008512 metal binding triad; other site 407976008513 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 407976008514 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 407976008515 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 407976008516 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 407976008517 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 407976008518 trimer interface [polypeptide binding]; other site 407976008519 active site 407976008520 substrate binding site [chemical binding]; other site 407976008521 CoA binding site [chemical binding]; other site 407976008522 PAS domain; Region: PAS_9; pfam13426 407976008523 GAF domain; Region: GAF_2; pfam13185 407976008524 GAF domain; Region: GAF; pfam01590 407976008525 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 407976008526 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976008527 Zn2+ binding site [ion binding]; other site 407976008528 Mg2+ binding site [ion binding]; other site 407976008529 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 407976008530 FOG: CBS domain [General function prediction only]; Region: COG0517 407976008531 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 407976008532 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 407976008533 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 407976008534 putative active site [active] 407976008535 putative substrate binding site [chemical binding]; other site 407976008536 putative cosubstrate binding site; other site 407976008537 catalytic site [active] 407976008538 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 407976008539 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 407976008540 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 407976008541 active site turn [active] 407976008542 phosphorylation site [posttranslational modification] 407976008543 flavodoxin; Provisional; Region: PRK08105 407976008544 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976008545 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 407976008546 probable active site [active] 407976008547 tRNA pseudouridine synthase C; Region: DUF446; pfam04287 407976008548 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 407976008549 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 407976008550 Protein of unknown function (DUF962); Region: DUF962; pfam06127 407976008551 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 407976008552 Coenzyme A binding pocket [chemical binding]; other site 407976008553 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 407976008554 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 407976008555 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 407976008556 SecY interacting protein Syd; Provisional; Region: PRK04968 407976008557 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 407976008558 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 407976008559 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 407976008560 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 407976008561 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976008562 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 407976008563 putative substrate binding pocket [chemical binding]; other site 407976008564 putative dimerization interface [polypeptide binding]; other site 407976008565 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 407976008566 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 407976008567 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 407976008568 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 407976008569 Winged helix-turn helix; Region: HTH_29; pfam13551 407976008570 Homeodomain-like domain; Region: HTH_23; pfam13384 407976008571 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 407976008572 3-oxoacyl-acyl carrier protein synthase; Provisional; Region: PTZ00050 407976008573 active site 407976008574 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 407976008575 Acyl transferase domain in polyketide synthase (PKS) enzymes; Region: PKS_AT; smart00827 407976008576 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 407976008577 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 407976008578 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 407976008579 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 407976008580 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 407976008581 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 407976008582 This enzymatic domain is part of bacterial polyketide synthases; Region: PKS_KR; smart00822 407976008583 putative NADP binding site [chemical binding]; other site 407976008584 active site 407976008585 Acyl transferase domain; Region: Acyl_transf_1; cl08282 407976008586 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 407976008587 3-oxoacyl-acyl carrier protein synthase; Provisional; Region: PTZ00050 407976008588 active site 407976008589 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 407976008590 active site 407976008591 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 407976008592 active site 2 [active] 407976008593 dimer interface [polypeptide binding]; other site 407976008594 active site 1 [active] 407976008595 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 407976008596 active site 1 [active] 407976008597 dimer interface [polypeptide binding]; other site 407976008598 active site 2 [active] 407976008599 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding...; Region: NPD_FabD; cd04742 407976008600 FMN binding site [chemical binding]; other site 407976008601 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 407976008602 substrate binding site [chemical binding]; other site 407976008603 putative catalytic residue [active] 407976008604 hypothetical protein; Provisional; Region: PRK12361 407976008605 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 407976008606 active site 407976008607 catalytic residues [active] 407976008608 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 407976008609 Major royal jelly protein; Region: MRJP; pfam03022 407976008610 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 407976008611 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 407976008612 Walker A motif; other site 407976008613 ATP binding site [chemical binding]; other site 407976008614 Walker B motif; other site 407976008615 arginine finger; other site 407976008616 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976008617 BON domain; Region: BON; pfam04972 407976008618 BON domain; Region: BON; pfam04972 407976008619 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976008620 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976008621 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976008622 Protein of unknown function (DUF3224); Region: DUF3224; pfam11528 407976008623 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 407976008624 Putative catalytic NodB homology domain of uncharacterized Mll8295 protein encoded from Rhizobium loti and its bacterial homologs; Region: CE4_Mll8295_like; cd10946 407976008625 NodB motif; other site 407976008626 putative active site [active] 407976008627 putative catalytic site [active] 407976008628 putative Zn binding site [ion binding]; other site 407976008629 chitin-binding domain of Chi A1-like proteins; Region: ChiA1_BD; cd12214 407976008630 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976008631 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 407976008632 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 407976008633 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 407976008634 Helix-turn-helix domain; Region: HTH_18; pfam12833 407976008635 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 407976008636 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 407976008637 putative substrate translocation pore; other site 407976008638 L-fucose transporter; Provisional; Region: PRK10133; cl17665 407976008639 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 407976008640 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 407976008641 nucleotide binding site [chemical binding]; other site 407976008642 Putative carbohydrate binding domain; Region: CHB_HEX; smart01081 407976008643 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 407976008644 Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides; Region: GH20_hexosaminidase; cl02948 407976008645 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 407976008646 active site 407976008647 C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase); Region: E_set_Chitobiase_C; cd02847 407976008648 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 407976008649 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 407976008650 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 407976008651 dimerization interface [polypeptide binding]; other site 407976008652 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976008653 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976008654 dimer interface [polypeptide binding]; other site 407976008655 putative CheW interface [polypeptide binding]; other site 407976008656 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 407976008657 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 407976008658 putative active site [active] 407976008659 Zn binding site [ion binding]; other site 407976008660 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 407976008661 MarR family; Region: MarR; pfam01047 407976008662 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 407976008663 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 407976008664 putative substrate translocation pore; other site 407976008665 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 407976008666 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 407976008667 PhnA protein; Region: PhnA; pfam03831 407976008668 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 407976008669 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 407976008670 N-terminal plug; other site 407976008671 ligand-binding site [chemical binding]; other site 407976008672 TIGR02453 family protein; Region: TIGR02453 407976008673 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976008674 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 407976008675 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 407976008676 Transcriptional regulators [Transcription]; Region: PurR; COG1609 407976008677 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976008678 DNA binding site [nucleotide binding] 407976008679 domain linker motif; other site 407976008680 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 407976008681 putative dimerization interface [polypeptide binding]; other site 407976008682 putative ligand binding site [chemical binding]; other site 407976008683 beta-phosphoglucomutase; Region: bPGM; TIGR01990 407976008684 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 407976008685 motif II; other site 407976008686 Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism]; Region: ATH1; COG1554 407976008687 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 407976008688 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 407976008689 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 407976008690 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 407976008691 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 407976008692 putative substrate translocation pore; other site 407976008693 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976008694 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976008695 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976008696 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 407976008697 putative C-terminal domain interface [polypeptide binding]; other site 407976008698 putative GSH binding site (G-site) [chemical binding]; other site 407976008699 putative dimer interface [polypeptide binding]; other site 407976008700 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 407976008701 putative N-terminal domain interface [polypeptide binding]; other site 407976008702 putative dimer interface [polypeptide binding]; other site 407976008703 putative substrate binding pocket (H-site) [chemical binding]; other site 407976008704 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 407976008705 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 407976008706 C-terminal domain interface [polypeptide binding]; other site 407976008707 GSH binding site (G-site) [chemical binding]; other site 407976008708 dimer interface [polypeptide binding]; other site 407976008709 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 407976008710 N-terminal domain interface [polypeptide binding]; other site 407976008711 putative dimer interface [polypeptide binding]; other site 407976008712 active site 407976008713 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 407976008714 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 407976008715 S-adenosylmethionine binding site [chemical binding]; other site 407976008716 Acetoacetate decarboxylase (ADC); Region: ADC; cl01919 407976008717 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 407976008718 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 407976008719 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 407976008720 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976008721 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976008722 metal binding site [ion binding]; metal-binding site 407976008723 active site 407976008724 I-site; other site 407976008725 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976008726 EamA-like transporter family; Region: EamA; pfam00892 407976008727 YfaZ precursor; Region: YfaZ; pfam07437 407976008728 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 407976008729 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 407976008730 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976008731 Coenzyme A binding pocket [chemical binding]; other site 407976008732 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 407976008733 MgtE intracellular N domain; Region: MgtE_N; smart00924 407976008734 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 407976008735 Divalent cation transporter; Region: MgtE; cl00786 407976008736 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 407976008737 catalytic residues [active] 407976008738 dimer interface [polypeptide binding]; other site 407976008739 putative transposase OrfB; Reviewed; Region: PHA02517 407976008740 Integrase core domain; Region: rve; pfam00665 407976008741 Integrase core domain; Region: rve_3; pfam13683 407976008742 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 407976008743 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 407976008744 active site 407976008745 Zn binding site [ion binding]; other site 407976008746 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 407976008747 PBP superfamily domain; Region: PBP_like_2; cl17296 407976008748 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 407976008749 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 407976008750 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 407976008751 putative active site [active] 407976008752 heme pocket [chemical binding]; other site 407976008753 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 407976008754 dimer interface [polypeptide binding]; other site 407976008755 phosphorylation site [posttranslational modification] 407976008756 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 407976008757 ATP binding site [chemical binding]; other site 407976008758 Mg2+ binding site [ion binding]; other site 407976008759 G-X-G motif; other site 407976008760 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 407976008761 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 407976008762 active site 407976008763 phosphorylation site [posttranslational modification] 407976008764 intermolecular recognition site; other site 407976008765 dimerization interface [polypeptide binding]; other site 407976008766 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 407976008767 DNA binding site [nucleotide binding] 407976008768 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 407976008769 trimer interface [polypeptide binding]; other site 407976008770 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 407976008771 eyelet of channel; other site 407976008772 recombination associated protein; Reviewed; Region: rdgC; PRK00321 407976008773 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 407976008774 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 407976008775 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 407976008776 protein binding site [polypeptide binding]; other site 407976008777 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 407976008778 TPR motif; other site 407976008779 binding surface 407976008780 Tetratricopeptide repeat; Region: TPR_12; pfam13424 407976008781 Tetratricopeptide repeat; Region: TPR_12; pfam13424 407976008782 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976008783 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976008784 metal binding site [ion binding]; metal-binding site 407976008785 active site 407976008786 I-site; other site 407976008787 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 407976008788 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 407976008789 flap endonuclease-like protein; Provisional; Region: PRK09482 407976008790 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 407976008791 active site 407976008792 metal binding site 1 [ion binding]; metal-binding site 407976008793 putative 5' ssDNA interaction site; other site 407976008794 metal binding site 3; metal-binding site 407976008795 metal binding site 2 [ion binding]; metal-binding site 407976008796 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 407976008797 putative DNA binding site [nucleotide binding]; other site 407976008798 putative metal binding site [ion binding]; other site 407976008799 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 407976008800 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976008801 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976008802 isocitrate dehydrogenase; Provisional; Region: PRK08997 407976008803 tartrate dehydrogenase; Region: TTC; TIGR02089 407976008804 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 407976008805 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 407976008806 Protein of unknown function (DUF423); Region: DUF423; pfam04241 407976008807 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 407976008808 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 407976008809 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976008810 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 407976008811 dimerization interface [polypeptide binding]; other site 407976008812 substrate binding pocket [chemical binding]; other site 407976008813 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 407976008814 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 407976008815 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 407976008816 Ligand Binding Site [chemical binding]; other site 407976008817 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 407976008818 active site residue [active] 407976008819 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 407976008820 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 407976008821 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976008822 ligand binding site [chemical binding]; other site 407976008823 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 407976008824 flagellar motor protein PomA; Reviewed; Region: PRK08990 407976008825 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 407976008826 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 407976008827 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 407976008828 substrate binding pocket [chemical binding]; other site 407976008829 chain length determination region; other site 407976008830 substrate-Mg2+ binding site; other site 407976008831 catalytic residues [active] 407976008832 aspartate-rich region 1; other site 407976008833 active site lid residues [active] 407976008834 aspartate-rich region 2; other site 407976008835 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 407976008836 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 407976008837 TPP-binding site; other site 407976008838 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 407976008839 PYR/PP interface [polypeptide binding]; other site 407976008840 dimer interface [polypeptide binding]; other site 407976008841 TPP binding site [chemical binding]; other site 407976008842 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 407976008843 putative transposase OrfB; Reviewed; Region: PHA02517 407976008844 Integrase core domain; Region: rve; pfam00665 407976008845 Integrase core domain; Region: rve_3; pfam13683 407976008846 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 407976008847 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 407976008848 dimer interface [polypeptide binding]; other site 407976008849 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 407976008850 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03378 407976008851 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 407976008852 L-lactate permease; Region: Lactate_perm; cl00701 407976008853 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 407976008854 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 407976008855 FAD binding domain; Region: FAD_binding_4; pfam01565 407976008856 4Fe-4S binding domain; Region: Fer4; pfam00037 407976008857 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 407976008858 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 407976008859 Cysteine-rich domain; Region: CCG; pfam02754 407976008860 Cysteine-rich domain; Region: CCG; pfam02754 407976008861 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 407976008862 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 407976008863 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 407976008864 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 407976008865 This domain is found at the N terminal of the mitochondrial ATPase BSC1. It encodes the import and intramitochondrial sorting for the protein; Region: BCS1_N; smart01024 407976008866 ATPase family associated with various cellular activities (AAA); Region: AAA; pfam00004 407976008867 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976008868 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976008869 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976008870 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 407976008871 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 407976008872 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 407976008873 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976008874 putative substrate translocation pore; other site 407976008875 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 407976008876 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 407976008877 substrate binding pocket [chemical binding]; other site 407976008878 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976008879 membrane-bound complex binding site; other site 407976008880 hinge residues; other site 407976008881 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 407976008882 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 407976008883 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 407976008884 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 407976008885 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 407976008886 ATP binding site [chemical binding]; other site 407976008887 Mg++ binding site [ion binding]; other site 407976008888 motif III; other site 407976008889 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 407976008890 nucleotide binding region [chemical binding]; other site 407976008891 ATP-binding site [chemical binding]; other site 407976008892 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 407976008893 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 407976008894 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 407976008895 putative active site [active] 407976008896 heme pocket [chemical binding]; other site 407976008897 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 407976008898 PAS domain; Region: PAS_9; pfam13426 407976008899 putative active site [active] 407976008900 heme pocket [chemical binding]; other site 407976008901 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976008902 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976008903 metal binding site [ion binding]; metal-binding site 407976008904 active site 407976008905 I-site; other site 407976008906 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 407976008907 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 407976008908 glycogen synthase; Provisional; Region: glgA; PRK00654 407976008909 ADP-binding pocket [chemical binding]; other site 407976008910 homodimer interface [polypeptide binding]; other site 407976008911 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 407976008912 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 407976008913 ligand binding site; other site 407976008914 oligomer interface; other site 407976008915 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 407976008916 dimer interface [polypeptide binding]; other site 407976008917 N-terminal domain interface [polypeptide binding]; other site 407976008918 sulfate 1 binding site; other site 407976008919 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 407976008920 homodimer interface [polypeptide binding]; other site 407976008921 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 407976008922 active site pocket [active] 407976008923 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 407976008924 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 407976008925 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 407976008926 active site 407976008927 catalytic site [active] 407976008928 glycogen branching enzyme; Provisional; Region: PRK05402 407976008929 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 407976008930 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 407976008931 active site 407976008932 catalytic site [active] 407976008933 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 407976008934 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 407976008935 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 407976008936 active site 407976008937 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976008938 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976008939 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976008940 Transcriptional regulators [Transcription]; Region: MarR; COG1846 407976008941 MarR family; Region: MarR; pfam01047 407976008942 MarR family; Region: MarR_2; cl17246 407976008943 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 407976008944 BCCT family transporter; Region: BCCT; cl00569 407976008945 choline dehydrogenase; Validated; Region: PRK02106 407976008946 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 407976008947 betaine aldehyde dehydrogenase; Provisional; Region: PRK13252 407976008948 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 407976008949 NAD(P) binding site [chemical binding]; other site 407976008950 catalytic residues [active] 407976008951 transcriptional regulator BetI; Validated; Region: PRK00767 407976008952 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976008953 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 407976008954 putative alcohol dehydrogenase; Provisional; Region: PRK09860 407976008955 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 407976008956 dimer interface [polypeptide binding]; other site 407976008957 active site 407976008958 metal binding site [ion binding]; metal-binding site 407976008959 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 407976008960 isocitrate lyase; Provisional; Region: PRK15063 407976008961 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 407976008962 tetramer interface [polypeptide binding]; other site 407976008963 active site 407976008964 Mg2+/Mn2+ binding site [ion binding]; other site 407976008965 malate synthase A; Region: malate_syn_A; TIGR01344 407976008966 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 407976008967 active site 407976008968 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976008969 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 407976008970 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 407976008971 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 407976008972 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 407976008973 TrkA-N domain; Region: TrkA_N; pfam02254 407976008974 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976008975 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976008976 metal binding site [ion binding]; metal-binding site 407976008977 active site 407976008978 I-site; other site 407976008979 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cl06673 407976008980 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 407976008981 active site 407976008982 SAM binding site [chemical binding]; other site 407976008983 homodimer interface [polypeptide binding]; other site 407976008984 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 407976008985 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 407976008986 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 407976008987 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 407976008988 putative coenzyme Q binding site [chemical binding]; other site 407976008989 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 407976008990 SmpB-tmRNA interface; other site 407976008991 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 407976008992 Dimer interface [polypeptide binding]; other site 407976008993 BRCT sequence motif; other site 407976008994 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 407976008995 DNA binding site [nucleotide binding] 407976008996 active site 407976008997 Int/Topo IB signature motif; other site 407976008998 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 407976008999 DEAD-like helicases superfamily; Region: DEXDc; smart00487 407976009000 ATP binding site [chemical binding]; other site 407976009001 Mg++ binding site [ion binding]; other site 407976009002 motif III; other site 407976009003 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 407976009004 nucleotide binding region [chemical binding]; other site 407976009005 ATP-binding site [chemical binding]; other site 407976009006 PAS fold; Region: PAS; pfam00989 407976009007 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 407976009008 PAS domain; Region: PAS_9; pfam13426 407976009009 putative active site [active] 407976009010 heme pocket [chemical binding]; other site 407976009011 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976009012 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976009013 metal binding site [ion binding]; metal-binding site 407976009014 active site 407976009015 I-site; other site 407976009016 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 407976009017 AAA domain; Region: AAA_32; pfam13654 407976009018 ATP-dependent protease Lon; Provisional; Region: PRK13765 407976009019 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 407976009020 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 407976009021 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 407976009022 FMN binding site [chemical binding]; other site 407976009023 active site 407976009024 substrate binding site [chemical binding]; other site 407976009025 catalytic residue [active] 407976009026 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976009027 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976009028 Protein of unknown function (DUF2375); Region: DUF2375; pfam09558 407976009029 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976009030 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009031 dimer interface [polypeptide binding]; other site 407976009032 putative CheW interface [polypeptide binding]; other site 407976009033 hypothetical protein; Provisional; Region: PRK12378 407976009034 Retinal pigment epithelial membrane protein; Region: RPE65; pfam03055 407976009035 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 407976009036 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 407976009037 Histidine kinase; Region: HisKA_3; pfam07730 407976009038 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 407976009039 ATP binding site [chemical binding]; other site 407976009040 Mg2+ binding site [ion binding]; other site 407976009041 G-X-G motif; other site 407976009042 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976009043 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 407976009044 active site 407976009045 phosphorylation site [posttranslational modification] 407976009046 intermolecular recognition site; other site 407976009047 dimerization interface [polypeptide binding]; other site 407976009048 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 407976009049 dimerization interface [polypeptide binding]; other site 407976009050 DNA binding residues [nucleotide binding] 407976009051 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 407976009052 30S subunit binding site; other site 407976009053 PAS domain; Region: PAS_9; pfam13426 407976009054 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 407976009055 putative active site [active] 407976009056 heme pocket [chemical binding]; other site 407976009057 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976009058 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009059 dimer interface [polypeptide binding]; other site 407976009060 putative CheW interface [polypeptide binding]; other site 407976009061 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 407976009062 carbohydrate binding site [chemical binding]; other site 407976009063 alpha-1,6-glucosidases, pullulanase-type; Region: pullul_strch; TIGR02103 407976009064 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 407976009065 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 407976009066 Ca binding site [ion binding]; other site 407976009067 active site 407976009068 catalytic site [active] 407976009069 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 407976009070 Early set domain associated with the catalytic domain of pullulanase-like proteins; Region: E_set_pullulanase_like; cd02861 407976009071 Early set domain associated with the catalytic domain of pullulanase-like proteins; Region: E_set_pullulanase_like; cd02861 407976009072 Early set domain associated with the catalytic domain of pullulanase-like proteins; Region: E_set_pullulanase_like; cd02861 407976009073 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976009074 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 407976009075 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 407976009076 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 407976009077 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 407976009078 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 407976009079 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 407976009080 OsmC-like protein; Region: OsmC; cl00767 407976009081 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 407976009082 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 407976009083 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976009084 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 407976009085 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 407976009086 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 407976009087 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 407976009088 protein binding site [polypeptide binding]; other site 407976009089 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 407976009090 Domain interface; other site 407976009091 Peptide binding site; other site 407976009092 Active site tetrad [active] 407976009093 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 407976009094 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976009095 substrate binding pocket [chemical binding]; other site 407976009096 membrane-bound complex binding site; other site 407976009097 hinge residues; other site 407976009098 threonine synthase; Validated; Region: PRK09225 407976009099 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 407976009100 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976009101 catalytic residue [active] 407976009102 homoserine kinase; Provisional; Region: PRK01212 407976009103 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 407976009104 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 407976009105 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 407976009106 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 407976009107 putative catalytic residues [active] 407976009108 putative nucleotide binding site [chemical binding]; other site 407976009109 putative aspartate binding site [chemical binding]; other site 407976009110 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 407976009111 dimer interface [polypeptide binding]; other site 407976009112 putative threonine allosteric regulatory site; other site 407976009113 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 407976009114 putative threonine allosteric regulatory site; other site 407976009115 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 407976009116 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 407976009117 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 407976009118 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976009119 Trp repressor protein; Region: Trp_repressor; pfam01371 407976009120 Cytochrome C' Region: Cytochrom_C_2; pfam01322 407976009121 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 407976009122 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 407976009123 30S subunit binding site; other site 407976009124 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 407976009125 chorismate mutase domain of proteobacterial P-protein, clade 1; Region: CM_P_1; TIGR01797 407976009126 Prephenate dehydratase; Region: PDT; pfam00800 407976009127 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 407976009128 putative L-Phe binding site [chemical binding]; other site 407976009129 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 407976009130 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 407976009131 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 407976009132 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 407976009133 FAD binding pocket [chemical binding]; other site 407976009134 FAD binding motif [chemical binding]; other site 407976009135 phosphate binding motif [ion binding]; other site 407976009136 beta-alpha-beta structure motif; other site 407976009137 NAD binding pocket [chemical binding]; other site 407976009138 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 407976009139 catalytic loop [active] 407976009140 iron binding site [ion binding]; other site 407976009141 hybrid cluster protein; Provisional; Region: PRK05290 407976009142 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 407976009143 ACS interaction site; other site 407976009144 CODH interaction site; other site 407976009145 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 407976009146 hybrid metal cluster; other site 407976009147 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 407976009148 chorismate mutase domain of T-protein; Region: CM_T; TIGR01799 407976009149 prephenate dehydrogenase; Validated; Region: PRK08507 407976009150 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 407976009151 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 407976009152 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 407976009153 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 407976009154 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 407976009155 RimM N-terminal domain; Region: RimM; pfam01782 407976009156 PRC-barrel domain; Region: PRC; pfam05239 407976009157 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 407976009158 signal recognition particle protein; Provisional; Region: PRK10867 407976009159 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 407976009160 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 407976009161 P loop; other site 407976009162 GTP binding site [chemical binding]; other site 407976009163 Signal peptide binding domain; Region: SRP_SPB; pfam02978 407976009164 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 407976009165 Domain of unknown function DUF21; Region: DUF21; pfam01595 407976009166 hypothetical protein; Provisional; Region: PRK11573 407976009167 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 407976009168 Transporter associated domain; Region: CorC_HlyC; smart01091 407976009169 Protein of unknown function (DUF962); Region: DUF962; cl01879 407976009170 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 407976009171 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 407976009172 active site 407976009173 hydrophilic channel; other site 407976009174 dimerization interface [polypeptide binding]; other site 407976009175 catalytic residues [active] 407976009176 active site lid [active] 407976009177 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 407976009178 Recombination protein O N terminal; Region: RecO_N; pfam11967 407976009179 Recombination protein O C terminal; Region: RecO_C; pfam02565 407976009180 GTPase Era; Reviewed; Region: era; PRK00089 407976009181 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 407976009182 G1 box; other site 407976009183 GTP/Mg2+ binding site [chemical binding]; other site 407976009184 Switch I region; other site 407976009185 G2 box; other site 407976009186 Switch II region; other site 407976009187 G3 box; other site 407976009188 G4 box; other site 407976009189 G5 box; other site 407976009190 KH domain; Region: KH_2; pfam07650 407976009191 ribonuclease III; Reviewed; Region: rnc; PRK00102 407976009192 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 407976009193 dimerization interface [polypeptide binding]; other site 407976009194 active site 407976009195 metal binding site [ion binding]; metal-binding site 407976009196 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 407976009197 dsRNA binding site [nucleotide binding]; other site 407976009198 signal peptidase I; Provisional; Region: PRK10861 407976009199 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 407976009200 Catalytic site [active] 407976009201 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 407976009202 GTP-binding protein LepA; Provisional; Region: PRK05433 407976009203 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 407976009204 G1 box; other site 407976009205 putative GEF interaction site [polypeptide binding]; other site 407976009206 GTP/Mg2+ binding site [chemical binding]; other site 407976009207 Switch I region; other site 407976009208 G2 box; other site 407976009209 G3 box; other site 407976009210 Switch II region; other site 407976009211 G4 box; other site 407976009212 G5 box; other site 407976009213 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 407976009214 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 407976009215 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 407976009216 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 407976009217 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 407976009218 anti-sigma E factor; Provisional; Region: rseB; PRK09455 407976009219 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 407976009220 anti-RNA polymerase sigma factor SigE; Provisional; Region: PRK10863 407976009221 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 407976009222 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 407976009223 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976009224 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 407976009225 DNA binding residues [nucleotide binding] 407976009226 L-aspartate oxidase; Provisional; Region: PRK09077 407976009227 L-aspartate oxidase; Provisional; Region: PRK06175 407976009228 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 407976009229 Uncharacterized conserved protein [Function unknown]; Region: COG2938 407976009230 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 407976009231 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976009232 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 407976009233 dimerization interface [polypeptide binding]; other site 407976009234 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09561 407976009235 thymidylate synthase; Reviewed; Region: thyA; PRK01827 407976009236 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 407976009237 dimerization interface [polypeptide binding]; other site 407976009238 active site 407976009239 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 407976009240 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976009241 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 407976009242 GAF domain; Region: GAF; pfam01590 407976009243 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 407976009244 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 407976009245 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 407976009246 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 407976009247 putative active site [active] 407976009248 Ap4A binding site [chemical binding]; other site 407976009249 nudix motif; other site 407976009250 putative metal binding site [ion binding]; other site 407976009251 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 407976009252 putative DNA-binding cleft [nucleotide binding]; other site 407976009253 putative DNA clevage site; other site 407976009254 molecular lever; other site 407976009255 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 407976009256 cyclase homology domain; Region: CHD; cd07302 407976009257 nucleotidyl binding site; other site 407976009258 metal binding site [ion binding]; metal-binding site 407976009259 dimer interface [polypeptide binding]; other site 407976009260 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976009261 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976009262 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 407976009263 dimerization interface [polypeptide binding]; other site 407976009264 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 407976009265 putative binding surface; other site 407976009266 active site 407976009267 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 407976009268 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 407976009269 FeS/SAM binding site; other site 407976009270 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 407976009271 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 407976009272 active site 407976009273 dimer interface [polypeptide binding]; other site 407976009274 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 407976009275 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 407976009276 active site 407976009277 FMN binding site [chemical binding]; other site 407976009278 substrate binding site [chemical binding]; other site 407976009279 3Fe-4S cluster binding site [ion binding]; other site 407976009280 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 407976009281 domain interface; other site 407976009282 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 407976009283 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 407976009284 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976009285 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 407976009286 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 407976009287 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 407976009288 Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]; Region: CbiB; COG1270 407976009289 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 407976009290 hypothetical protein; Provisional; Region: PRK10578 407976009291 UPF0126 domain; Region: UPF0126; pfam03458 407976009292 UPF0126 domain; Region: UPF0126; pfam03458 407976009293 SnoaL-like domain; Region: SnoaL_2; pfam12680 407976009294 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 407976009295 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 407976009296 active site 407976009297 HIGH motif; other site 407976009298 dimer interface [polypeptide binding]; other site 407976009299 KMSKS motif; other site 407976009300 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 407976009301 RNA binding surface [nucleotide binding]; other site 407976009302 putative peptidase; Provisional; Region: PRK11649 407976009303 Opacity-associated protein A N-terminal motif; Region: OapA_N; pfam08525 407976009304 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 407976009305 Peptidase family M23; Region: Peptidase_M23; pfam01551 407976009306 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 407976009307 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 407976009308 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 407976009309 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 407976009310 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 407976009311 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 407976009312 Cl- selectivity filter; other site 407976009313 Cl- binding residues [ion binding]; other site 407976009314 pore gating glutamate residue; other site 407976009315 dimer interface [polypeptide binding]; other site 407976009316 aspartate carbamoyltransferase; Provisional; Region: PRK08192 407976009317 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 407976009318 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 407976009319 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 407976009320 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 407976009321 inhibitor-cofactor binding pocket; inhibition site 407976009322 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976009323 catalytic residue [active] 407976009324 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 407976009325 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 407976009326 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 407976009327 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 407976009328 Walker A motif; other site 407976009329 ATP binding site [chemical binding]; other site 407976009330 Walker B motif; other site 407976009331 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 407976009332 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 407976009333 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 407976009334 active site 407976009335 NTP binding site [chemical binding]; other site 407976009336 metal binding triad [ion binding]; metal-binding site 407976009337 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 407976009338 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976009339 Zn2+ binding site [ion binding]; other site 407976009340 Mg2+ binding site [ion binding]; other site 407976009341 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 407976009342 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 407976009343 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 407976009344 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 407976009345 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 407976009346 catalytic center binding site [active] 407976009347 ATP binding site [chemical binding]; other site 407976009348 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 407976009349 homooctamer interface [polypeptide binding]; other site 407976009350 active site 407976009351 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 407976009352 UGMP family protein; Validated; Region: PRK09604 407976009353 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 407976009354 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 407976009355 Yqey-like protein; Region: YqeY; pfam09424 407976009356 DNA primase; Validated; Region: dnaG; PRK05667 407976009357 CHC2 zinc finger; Region: zf-CHC2; pfam01807 407976009358 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 407976009359 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 407976009360 active site 407976009361 metal binding site [ion binding]; metal-binding site 407976009362 interdomain interaction site; other site 407976009363 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 407976009364 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 407976009365 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 407976009366 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 407976009367 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 407976009368 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 407976009369 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976009370 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 407976009371 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 407976009372 DNA binding residues [nucleotide binding] 407976009373 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 407976009374 dimerization interface [polypeptide binding]; other site 407976009375 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976009376 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009377 dimer interface [polypeptide binding]; other site 407976009378 putative CheW interface [polypeptide binding]; other site 407976009379 fructokinase; Reviewed; Region: PRK09557 407976009380 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 407976009381 nucleotide binding site [chemical binding]; other site 407976009382 Acetokinase family; Region: Acetate_kinase; cl17229 407976009383 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 407976009384 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 407976009385 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 407976009386 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 407976009387 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 407976009388 putative substrate translocation pore; other site 407976009389 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 407976009390 beta-galactosidase; Region: BGL; TIGR03356 407976009391 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 407976009392 putative symporter YagG; Provisional; Region: PRK09669 407976009393 Transcriptional regulators [Transcription]; Region: PurR; COG1609 407976009394 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976009395 DNA binding site [nucleotide binding] 407976009396 domain linker motif; other site 407976009397 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 407976009398 dimerization interface (closed form) [polypeptide binding]; other site 407976009399 ligand binding site [chemical binding]; other site 407976009400 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 407976009401 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 407976009402 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 407976009403 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 407976009404 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 407976009405 SapC; Region: SapC; pfam07277 407976009406 Cupin-like domain; Region: Cupin_8; pfam13621 407976009407 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 407976009408 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 407976009409 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 407976009410 putative substrate translocation pore; other site 407976009411 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 407976009412 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 407976009413 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976009414 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976009415 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976009416 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 407976009417 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 407976009418 inhibitor-cofactor binding pocket; inhibition site 407976009419 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976009420 catalytic residue [active] 407976009421 succinate-semialdehyde dehydrogenase I; Provisional; Region: gabD; PRK11241 407976009422 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 407976009423 tetramerization interface [polypeptide binding]; other site 407976009424 NAD(P) binding site [chemical binding]; other site 407976009425 catalytic residues [active] 407976009426 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 407976009427 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 407976009428 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 407976009429 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 407976009430 dimer interface [polypeptide binding]; other site 407976009431 conserved gate region; other site 407976009432 putative PBP binding loops; other site 407976009433 ABC-ATPase subunit interface; other site 407976009434 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 407976009435 dimer interface [polypeptide binding]; other site 407976009436 conserved gate region; other site 407976009437 putative PBP binding loops; other site 407976009438 ABC-ATPase subunit interface; other site 407976009439 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 407976009440 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976009441 Walker A/P-loop; other site 407976009442 ATP binding site [chemical binding]; other site 407976009443 Q-loop/lid; other site 407976009444 ABC transporter signature motif; other site 407976009445 Walker B; other site 407976009446 D-loop; other site 407976009447 H-loop/switch region; other site 407976009448 TOBE domain; Region: TOBE_2; pfam08402 407976009449 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 407976009450 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 407976009451 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 407976009452 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 407976009453 Peptidase C26; Region: Peptidase_C26; pfam07722 407976009454 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 407976009455 catalytic triad [active] 407976009456 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 407976009457 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 407976009458 non-specific DNA binding site [nucleotide binding]; other site 407976009459 salt bridge; other site 407976009460 sequence-specific DNA binding site [nucleotide binding]; other site 407976009461 Cupin domain; Region: Cupin_2; pfam07883 407976009462 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 407976009463 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 407976009464 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 407976009465 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 407976009466 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 407976009467 active site residue [active] 407976009468 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 407976009469 active site residue [active] 407976009470 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 407976009471 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 407976009472 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 407976009473 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 407976009474 NAD(P) binding site [chemical binding]; other site 407976009475 catalytic residues [active] 407976009476 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 407976009477 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 407976009478 inhibitor-cofactor binding pocket; inhibition site 407976009479 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976009480 catalytic residue [active] 407976009481 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 407976009482 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 407976009483 tetrameric interface [polypeptide binding]; other site 407976009484 NAD binding site [chemical binding]; other site 407976009485 catalytic residues [active] 407976009486 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 407976009487 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 407976009488 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 407976009489 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 407976009490 putative substrate translocation pore; other site 407976009491 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 407976009492 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 407976009493 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 407976009494 active site 407976009495 dimer interface [polypeptide binding]; other site 407976009496 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 407976009497 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 407976009498 dimer interface [polypeptide binding]; other site 407976009499 active site 407976009500 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 407976009501 dimer interface [polypeptide binding]; other site 407976009502 active site 407976009503 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 407976009504 Putative carbohydrate binding domain; Region: CHB_HEX; smart01081 407976009505 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 407976009506 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a...; Region: GH20_Sm-chitobiase-like; cd06569 407976009507 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 407976009508 active site 407976009509 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 407976009510 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 407976009511 dimerization interface [polypeptide binding]; other site 407976009512 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976009513 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009514 dimer interface [polypeptide binding]; other site 407976009515 putative CheW interface [polypeptide binding]; other site 407976009516 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976009517 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 407976009518 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 407976009519 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 407976009520 SapC; Region: SapC; pfam07277 407976009521 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976009522 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976009523 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976009524 Transcriptional regulators [Transcription]; Region: PurR; COG1609 407976009525 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976009526 DNA binding site [nucleotide binding] 407976009527 domain linker motif; other site 407976009528 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 407976009529 putative ligand binding site [chemical binding]; other site 407976009530 putative dimerization interface [polypeptide binding]; other site 407976009531 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 407976009532 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 407976009533 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 407976009534 Nitrogen regulatory protein P-II; Region: P-II; smart00938 407976009535 Type II transport protein GspH; Region: GspH; pfam12019 407976009536 Type II transport protein GspH; Region: GspH; pfam12019 407976009537 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 407976009538 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 407976009539 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 407976009540 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 407976009541 PilX N-terminal; Region: PilX_N; pfam14341 407976009542 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 407976009543 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 407976009544 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 407976009545 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 407976009546 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 407976009547 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 407976009548 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976009549 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 407976009550 lipoprotein signal peptidase; Provisional; Region: PRK14787 407976009551 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 407976009552 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 407976009553 HIGH motif; other site 407976009554 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 407976009555 active site 407976009556 KMSKS motif; other site 407976009557 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 407976009558 tRNA binding surface [nucleotide binding]; other site 407976009559 anticodon binding site; other site 407976009560 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 407976009561 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 407976009562 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 407976009563 active site 407976009564 Riboflavin kinase; Region: Flavokinase; smart00904 407976009565 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 407976009566 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 407976009567 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 407976009568 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 407976009569 dimerization interface [polypeptide binding]; other site 407976009570 putative DNA binding site [nucleotide binding]; other site 407976009571 putative Zn2+ binding site [ion binding]; other site 407976009572 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 407976009573 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 407976009574 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 407976009575 PA/protease or protease-like domain interface [polypeptide binding]; other site 407976009576 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 407976009577 Peptidase family M28; Region: Peptidase_M28; pfam04389 407976009578 metal binding site [ion binding]; metal-binding site 407976009579 hypothetical protein; Validated; Region: PRK02101 407976009580 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 407976009581 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 407976009582 putative phosphoketolase; Provisional; Region: PRK05261 407976009583 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 407976009584 TPP-binding site; other site 407976009585 XFP C-terminal domain; Region: XFP_C; pfam09363 407976009586 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 407976009587 outer membrane protein A; Reviewed; Region: PRK10808 407976009588 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976009589 ligand binding site [chemical binding]; other site 407976009590 transaldolase-like protein; Provisional; Region: PTZ00411 407976009591 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 407976009592 active site 407976009593 dimer interface [polypeptide binding]; other site 407976009594 catalytic residue [active] 407976009595 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 407976009596 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 407976009597 active site 407976009598 dimer interface [polypeptide binding]; other site 407976009599 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 407976009600 dimer interface [polypeptide binding]; other site 407976009601 active site 407976009602 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 407976009603 putative transposase OrfB; Reviewed; Region: PHA02517 407976009604 Integrase core domain; Region: rve; pfam00665 407976009605 Integrase core domain; Region: rve_3; pfam13683 407976009606 Hemerythrin-like domain; Region: Hr-like; cd12108 407976009607 Fe binding site [ion binding]; other site 407976009608 RNA polymerase sigma factor; Provisional; Region: PRK12513 407976009609 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976009610 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 407976009611 DNA binding residues [nucleotide binding] 407976009612 von Willebrand factor; Region: vWF_A; pfam12450 407976009613 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 407976009614 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 407976009615 metal ion-dependent adhesion site (MIDAS); other site 407976009616 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 407976009617 putative transporter; Provisional; Region: PRK11660 407976009618 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 407976009619 Sulfate transporter family; Region: Sulfate_transp; pfam00916 407976009620 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 407976009621 AIR carboxylase; Region: AIRC; pfam00731 407976009622 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 407976009623 ATP-grasp domain; Region: ATP-grasp; pfam02222 407976009624 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976009625 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976009626 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976009627 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976009628 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 407976009629 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976009630 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976009631 metal binding site [ion binding]; metal-binding site 407976009632 active site 407976009633 I-site; other site 407976009634 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 407976009635 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976009636 catalytic residue [active] 407976009637 glutamate--cysteine ligase; Provisional; Region: PRK02107 407976009638 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976009639 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976009640 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976009641 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 407976009642 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 407976009643 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 407976009644 Predicted membrane protein [Function unknown]; Region: COG1238 407976009645 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976009646 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 407976009647 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 407976009648 oxaloacetate decarboxylase; Provisional; Region: PRK14040 407976009649 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 407976009650 active site 407976009651 catalytic residues [active] 407976009652 metal binding site [ion binding]; metal-binding site 407976009653 homodimer binding site [polypeptide binding]; other site 407976009654 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 407976009655 carboxyltransferase (CT) interaction site; other site 407976009656 biotinylation site [posttranslational modification]; other site 407976009657 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 407976009658 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 407976009659 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 407976009660 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 407976009661 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 407976009662 Clp amino terminal domain; Region: Clp_N; pfam02861 407976009663 Clp amino terminal domain; Region: Clp_N; pfam02861 407976009664 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 407976009665 Walker A motif; other site 407976009666 ATP binding site [chemical binding]; other site 407976009667 Walker B motif; other site 407976009668 arginine finger; other site 407976009669 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 407976009670 Walker A motif; other site 407976009671 ATP binding site [chemical binding]; other site 407976009672 Walker B motif; other site 407976009673 arginine finger; other site 407976009674 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 407976009675 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 407976009676 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 407976009677 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 407976009678 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 407976009679 RNA binding surface [nucleotide binding]; other site 407976009680 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976009681 active site 407976009682 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 407976009683 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 407976009684 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976009685 HAMP domain; Region: HAMP; pfam00672 407976009686 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009687 dimer interface [polypeptide binding]; other site 407976009688 putative CheW interface [polypeptide binding]; other site 407976009689 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 407976009690 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 407976009691 heme-binding site [chemical binding]; other site 407976009692 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 407976009693 FAD binding pocket [chemical binding]; other site 407976009694 FAD binding motif [chemical binding]; other site 407976009695 phosphate binding motif [ion binding]; other site 407976009696 beta-alpha-beta structure motif; other site 407976009697 NAD binding pocket [chemical binding]; other site 407976009698 Heme binding pocket [chemical binding]; other site 407976009699 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 407976009700 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 407976009701 RNA binding surface [nucleotide binding]; other site 407976009702 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 407976009703 active site 407976009704 uracil binding [chemical binding]; other site 407976009705 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 407976009706 TPR motif; other site 407976009707 TPR repeat; Region: TPR_11; pfam13414 407976009708 binding surface 407976009709 Predicted transcriptional regulator [Transcription]; Region: COG2345 407976009710 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 407976009711 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 407976009712 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976009713 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 407976009714 active site 407976009715 metal binding site [ion binding]; metal-binding site 407976009716 Domain of unknown function (DUF1971); Region: DUF1971; pfam09313 407976009717 YcxB-like protein; Region: YcxB; pfam14317 407976009718 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 407976009719 MltA-interacting protein MipA; Region: MipA; cl01504 407976009720 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 407976009721 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 407976009722 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 407976009723 active site 407976009724 phosphorylation site [posttranslational modification] 407976009725 intermolecular recognition site; other site 407976009726 dimerization interface [polypeptide binding]; other site 407976009727 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 407976009728 DNA binding site [nucleotide binding] 407976009729 sensor protein RstB; Provisional; Region: PRK10604 407976009730 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 407976009731 dimer interface [polypeptide binding]; other site 407976009732 phosphorylation site [posttranslational modification] 407976009733 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 407976009734 ATP binding site [chemical binding]; other site 407976009735 Mg2+ binding site [ion binding]; other site 407976009736 G-X-G motif; other site 407976009737 Predicted Fe-S protein [General function prediction only]; Region: COG3313 407976009738 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 407976009739 cysteine synthase B; Region: cysM; TIGR01138 407976009740 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 407976009741 dimer interface [polypeptide binding]; other site 407976009742 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976009743 catalytic residue [active] 407976009744 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CysP; COG4150 407976009745 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 407976009746 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 407976009747 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 407976009748 dimer interface [polypeptide binding]; other site 407976009749 conserved gate region; other site 407976009750 putative PBP binding loops; other site 407976009751 ABC-ATPase subunit interface; other site 407976009752 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 407976009753 dimer interface [polypeptide binding]; other site 407976009754 conserved gate region; other site 407976009755 putative PBP binding loops; other site 407976009756 ABC-ATPase subunit interface; other site 407976009757 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 407976009758 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 407976009759 Walker A/P-loop; other site 407976009760 ATP binding site [chemical binding]; other site 407976009761 Q-loop/lid; other site 407976009762 ABC transporter signature motif; other site 407976009763 Walker B; other site 407976009764 D-loop; other site 407976009765 H-loop/switch region; other site 407976009766 TOBE-like domain; Region: TOBE_3; pfam12857 407976009767 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 407976009768 Ycf46; Provisional; Region: ycf46; CHL00195 407976009769 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 407976009770 Walker A motif; other site 407976009771 ATP binding site [chemical binding]; other site 407976009772 Walker B motif; other site 407976009773 arginine finger; other site 407976009774 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 407976009775 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976009776 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976009777 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 407976009778 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 407976009779 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976009780 ATP-grasp domain; Region: ATP-grasp; pfam02222 407976009781 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976009782 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976009783 active site 407976009784 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 407976009785 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 407976009786 glycerate dehydrogenase; Provisional; Region: PRK06487 407976009787 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 407976009788 putative ligand binding site [chemical binding]; other site 407976009789 putative NAD binding site [chemical binding]; other site 407976009790 catalytic site [active] 407976009791 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 407976009792 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 407976009793 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 407976009794 putative metal binding site [ion binding]; other site 407976009795 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 407976009796 HSP70 interaction site [polypeptide binding]; other site 407976009797 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 407976009798 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 407976009799 Substrate binding site; other site 407976009800 metal-binding site 407976009801 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 407976009802 Phosphotransferase enzyme family; Region: APH; pfam01636 407976009803 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 407976009804 OstA-like protein; Region: OstA; cl00844 407976009805 Organic solvent tolerance protein; Region: OstA_C; pfam04453 407976009806 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 407976009807 SurA N-terminal domain; Region: SurA_N; pfam09312 407976009808 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 407976009809 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 407976009810 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 407976009811 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 407976009812 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 407976009813 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 407976009814 S-adenosylmethionine binding site [chemical binding]; other site 407976009815 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 407976009816 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 407976009817 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 407976009818 active site 407976009819 metal binding site [ion binding]; metal-binding site 407976009820 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 407976009821 dimerization interface [polypeptide binding]; other site 407976009822 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976009823 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009824 dimer interface [polypeptide binding]; other site 407976009825 putative CheW interface [polypeptide binding]; other site 407976009826 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 407976009827 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 407976009828 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 407976009829 NADP+ binding site [chemical binding]; other site 407976009830 folate binding site [chemical binding]; other site 407976009831 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 407976009832 Uncharacterized conserved protein [Function unknown]; Region: COG2966 407976009833 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 407976009834 GTPase CgtA; Reviewed; Region: obgE; PRK12298 407976009835 GTP1/OBG; Region: GTP1_OBG; pfam01018 407976009836 Obg GTPase; Region: Obg; cd01898 407976009837 G1 box; other site 407976009838 GTP/Mg2+ binding site [chemical binding]; other site 407976009839 Switch I region; other site 407976009840 G2 box; other site 407976009841 G3 box; other site 407976009842 Switch II region; other site 407976009843 G4 box; other site 407976009844 G5 box; other site 407976009845 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 407976009846 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 407976009847 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 407976009848 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 407976009849 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 407976009850 substrate binding pocket [chemical binding]; other site 407976009851 chain length determination region; other site 407976009852 substrate-Mg2+ binding site; other site 407976009853 catalytic residues [active] 407976009854 aspartate-rich region 1; other site 407976009855 active site lid residues [active] 407976009856 aspartate-rich region 2; other site 407976009857 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 407976009858 ligand binding site [chemical binding]; other site 407976009859 active site 407976009860 UGI interface [polypeptide binding]; other site 407976009861 catalytic site [active] 407976009862 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 407976009863 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 407976009864 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 407976009865 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 407976009866 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 407976009867 DsbD alpha interface [polypeptide binding]; other site 407976009868 catalytic residues [active] 407976009869 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976009870 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 407976009871 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 407976009872 PAS domain S-box; Region: sensory_box; TIGR00229 407976009873 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 407976009874 putative active site [active] 407976009875 heme pocket [chemical binding]; other site 407976009876 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 407976009877 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 407976009878 Walker A motif; other site 407976009879 ATP binding site [chemical binding]; other site 407976009880 Walker B motif; other site 407976009881 arginine finger; other site 407976009882 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976009883 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 407976009884 4Fe-4S binding domain; Region: Fer4_5; pfam12801 407976009885 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 407976009886 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 407976009887 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 407976009888 acyl-activating enzyme (AAE) consensus motif; other site 407976009889 putative AMP binding site [chemical binding]; other site 407976009890 putative active site [active] 407976009891 putative CoA binding site [chemical binding]; other site 407976009892 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 407976009893 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976009894 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976009895 Walker A/P-loop; other site 407976009896 ATP binding site [chemical binding]; other site 407976009897 Q-loop/lid; other site 407976009898 ABC transporter signature motif; other site 407976009899 Walker B; other site 407976009900 D-loop; other site 407976009901 H-loop/switch region; other site 407976009902 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 407976009903 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 407976009904 Haem utilisation ChuX/HutX; Region: ChuX_HutX; pfam06228 407976009905 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 407976009906 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 407976009907 N-terminal plug; other site 407976009908 ligand-binding site [chemical binding]; other site 407976009909 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 407976009910 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 407976009911 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 407976009912 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 407976009913 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 407976009914 putative hemin binding site; other site 407976009915 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 407976009916 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 407976009917 ABC-ATPase subunit interface; other site 407976009918 dimer interface [polypeptide binding]; other site 407976009919 putative PBP binding regions; other site 407976009920 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 407976009921 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 407976009922 Walker A/P-loop; other site 407976009923 ATP binding site [chemical binding]; other site 407976009924 Q-loop/lid; other site 407976009925 ABC transporter signature motif; other site 407976009926 Walker B; other site 407976009927 D-loop; other site 407976009928 H-loop/switch region; other site 407976009929 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 407976009930 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 407976009931 interface (dimer of trimers) [polypeptide binding]; other site 407976009932 Substrate-binding/catalytic site; other site 407976009933 Zn-binding sites [ion binding]; other site 407976009934 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 407976009935 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 407976009936 metal binding site [ion binding]; metal-binding site 407976009937 dimer interface [polypeptide binding]; other site 407976009938 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 407976009939 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976009940 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 407976009941 dimerization interface [polypeptide binding]; other site 407976009942 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009943 dimer interface [polypeptide binding]; other site 407976009944 putative CheW interface [polypeptide binding]; other site 407976009945 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976009946 EamA-like transporter family; Region: EamA; pfam00892 407976009947 EamA-like transporter family; Region: EamA; pfam00892 407976009948 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976009949 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976009950 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 407976009951 putative effector binding pocket; other site 407976009952 dimerization interface [polypeptide binding]; other site 407976009953 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 407976009954 active site 407976009955 DNA polymerase IV; Validated; Region: PRK02406 407976009956 DNA binding site [nucleotide binding] 407976009957 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 407976009958 dimerization interface [polypeptide binding]; other site 407976009959 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976009960 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976009961 dimer interface [polypeptide binding]; other site 407976009962 putative CheW interface [polypeptide binding]; other site 407976009963 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 407976009964 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 407976009965 heme binding site [chemical binding]; other site 407976009966 ferroxidase pore; other site 407976009967 ferroxidase diiron center [ion binding]; other site 407976009968 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 407976009969 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 407976009970 heme binding site [chemical binding]; other site 407976009971 ferroxidase pore; other site 407976009972 ferroxidase diiron center [ion binding]; other site 407976009973 Protein of unknown function (DUF539); Region: DUF539; cl01129 407976009974 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 407976009975 ApbE family; Region: ApbE; pfam02424 407976009976 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 407976009977 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 407976009978 FAD binding pocket [chemical binding]; other site 407976009979 FAD binding motif [chemical binding]; other site 407976009980 phosphate binding motif [ion binding]; other site 407976009981 beta-alpha-beta structure motif; other site 407976009982 NAD binding pocket [chemical binding]; other site 407976009983 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 407976009984 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 407976009985 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 407976009986 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 407976009987 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 407976009988 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 407976009989 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 407976009990 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976009991 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 407976009992 S-ribosylhomocysteinase; Provisional; Region: PRK02260 407976009993 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 407976009994 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 407976009995 BolA-like protein; Region: BolA; cl00386 407976009996 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 407976009997 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 407976009998 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 407976009999 S-adenosylmethionine binding site [chemical binding]; other site 407976010000 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 407976010001 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 407976010002 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 407976010003 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 407976010004 homodimer interface [polypeptide binding]; other site 407976010005 substrate-cofactor binding pocket; other site 407976010006 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976010007 catalytic residue [active] 407976010008 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 407976010009 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976010010 DNA-binding site [nucleotide binding]; DNA binding site 407976010011 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 407976010012 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976010013 homodimer interface [polypeptide binding]; other site 407976010014 catalytic residue [active] 407976010015 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 407976010016 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 407976010017 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 407976010018 Protein of unknown function (DUF2474); Region: DUF2474; pfam10617 407976010019 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 407976010020 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 407976010021 Helix-turn-helix domain; Region: HTH_18; pfam12833 407976010022 EamA-like transporter family; Region: EamA; pfam00892 407976010023 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 407976010024 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 407976010025 dimerization interface [polypeptide binding]; other site 407976010026 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976010027 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010028 dimer interface [polypeptide binding]; other site 407976010029 putative CheW interface [polypeptide binding]; other site 407976010030 ApbE family; Region: ApbE; pfam02424 407976010031 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 407976010032 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 407976010033 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 407976010034 RNA binding surface [nucleotide binding]; other site 407976010035 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 407976010036 probable active site [active] 407976010037 Peptidase S46; Region: Peptidase_S46; pfam10459 407976010038 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]; Region: COG3591 407976010039 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 407976010040 aromatic amino acid transport protein; Region: araaP; TIGR00837 407976010041 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 407976010042 Chitin binding domain; Region: Chitin_bind_3; pfam03067 407976010043 Predicted membrane protein [Function unknown]; Region: COG2119 407976010044 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 407976010045 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 407976010046 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 407976010047 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 407976010048 tetramer interface [polypeptide binding]; other site 407976010049 heme binding pocket [chemical binding]; other site 407976010050 NADPH binding site [chemical binding]; other site 407976010051 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976010052 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976010053 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976010054 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 407976010055 CoenzymeA binding site [chemical binding]; other site 407976010056 subunit interaction site [polypeptide binding]; other site 407976010057 PHB binding site; other site 407976010058 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 407976010059 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 407976010060 generic binding surface I; other site 407976010061 generic binding surface II; other site 407976010062 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 407976010063 putative catalytic site [active] 407976010064 putative metal binding site [ion binding]; other site 407976010065 putative phosphate binding site [ion binding]; other site 407976010066 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 407976010067 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 407976010068 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976010069 FOG: WD40 repeat [General function prediction only]; Region: COG2319 407976010070 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 407976010071 structural tetrad; other site 407976010072 SlyX; Region: SlyX; pfam04102 407976010073 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 407976010074 active site 407976010075 catalytic residues [active] 407976010076 metal binding site [ion binding]; metal-binding site 407976010077 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 407976010078 uncharacterized proteobacterial lipoprotein; Region: lp_; TIGR02722 407976010079 aminopeptidase N, Streptomyces lividans type; Region: pepN_strep_liv; TIGR02412 407976010080 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_3; cd09602 407976010081 Zn binding site [ion binding]; other site 407976010082 Cache domain; Region: Cache_1; pfam02743 407976010083 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 407976010084 dimerization interface [polypeptide binding]; other site 407976010085 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976010086 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010087 dimer interface [polypeptide binding]; other site 407976010088 putative CheW interface [polypeptide binding]; other site 407976010089 PAS domain S-box; Region: sensory_box; TIGR00229 407976010090 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 407976010091 putative active site [active] 407976010092 heme pocket [chemical binding]; other site 407976010093 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976010094 GAF domain; Region: GAF; pfam01590 407976010095 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976010096 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976010097 metal binding site [ion binding]; metal-binding site 407976010098 active site 407976010099 I-site; other site 407976010100 Protein of unknown function DUF72; Region: DUF72; cl00777 407976010101 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 407976010102 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 407976010103 tetramer interface [polypeptide binding]; other site 407976010104 active site 407976010105 Mg2+/Mn2+ binding site [ion binding]; other site 407976010106 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 407976010107 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 407976010108 Cupin domain; Region: Cupin_2; cl17218 407976010109 Helix-turn-helix domain; Region: HTH_18; pfam12833 407976010110 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976010111 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 407976010112 catalytic triad [active] 407976010113 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 407976010114 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 407976010115 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 407976010116 CoenzymeA binding site [chemical binding]; other site 407976010117 subunit interaction site [polypeptide binding]; other site 407976010118 PHB binding site; other site 407976010119 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 407976010120 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 407976010121 dimer interface [polypeptide binding]; other site 407976010122 active site 407976010123 heme binding site [chemical binding]; other site 407976010124 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 407976010125 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 407976010126 Carbon starvation protein CstA; Region: CstA; pfam02554 407976010127 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 407976010128 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 407976010129 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 407976010130 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 407976010131 dimer interface [polypeptide binding]; other site 407976010132 putative anticodon binding site; other site 407976010133 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 407976010134 motif 1; other site 407976010135 active site 407976010136 motif 2; other site 407976010137 motif 3; other site 407976010138 peptide chain release factor 2; Validated; Region: prfB; PRK00578 407976010139 This domain is found in peptide chain release factors; Region: PCRF; smart00937 407976010140 RF-1 domain; Region: RF-1; pfam00472 407976010141 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 407976010142 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 407976010143 catalytic loop [active] 407976010144 iron binding site [ion binding]; other site 407976010145 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976010146 4Fe-4S binding domain; Region: Fer4_6; pfam12837 407976010147 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 407976010148 4Fe-4S binding domain; Region: Fer4; pfam00037 407976010149 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 407976010150 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 407976010151 [4Fe-4S] binding site [ion binding]; other site 407976010152 molybdopterin cofactor binding site; other site 407976010153 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 407976010154 molybdopterin cofactor binding site; other site 407976010155 Cache domain; Region: Cache_2; pfam08269 407976010156 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976010157 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 407976010158 dimerization interface [polypeptide binding]; other site 407976010159 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010160 dimer interface [polypeptide binding]; other site 407976010161 putative CheW interface [polypeptide binding]; other site 407976010162 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 407976010163 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 407976010164 Chromate transporter; Region: Chromate_transp; pfam02417 407976010165 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 407976010166 FAD dependent oxidoreductase; Region: DAO; pfam01266 407976010167 Transcriptional regulators [Transcription]; Region: MarR; COG1846 407976010168 MarR family; Region: MarR; pfam01047 407976010169 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 407976010170 Thiol-disulfide isomerase and thioredoxins [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: TrxA; COG0526 407976010171 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 407976010172 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 407976010173 S-adenosylmethionine binding site [chemical binding]; other site 407976010174 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 407976010175 heme-binding residues [chemical binding]; other site 407976010176 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 407976010177 L-aspartate oxidase; Provisional; Region: PRK06175 407976010178 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 407976010179 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 407976010180 putative ligand binding site [chemical binding]; other site 407976010181 putative NAD binding site [chemical binding]; other site 407976010182 catalytic site [active] 407976010183 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 407976010184 Domain of unknown function (DU1801); Region: DUF1801; cl17490 407976010185 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976010186 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 407976010187 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 407976010188 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 407976010189 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 407976010190 Mechanosensitive ion channel; Region: MS_channel; pfam00924 407976010191 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 407976010192 multifunctional aminopeptidase A; Provisional; Region: PRK00913 407976010193 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 407976010194 interface (dimer of trimers) [polypeptide binding]; other site 407976010195 Substrate-binding/catalytic site; other site 407976010196 Zn-binding sites [ion binding]; other site 407976010197 peroxiredoxin; Region: AhpC; TIGR03137 407976010198 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 407976010199 dimer interface [polypeptide binding]; other site 407976010200 decamer (pentamer of dimers) interface [polypeptide binding]; other site 407976010201 catalytic triad [active] 407976010202 peroxidatic and resolving cysteines [active] 407976010203 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 407976010204 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 407976010205 catalytic residue [active] 407976010206 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 407976010207 catalytic residues [active] 407976010208 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976010209 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 407976010210 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976010211 Coenzyme A binding pocket [chemical binding]; other site 407976010212 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 407976010213 DHH family; Region: DHH; pfam01368 407976010214 DHHA1 domain; Region: DHHA1; pfam02272 407976010215 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 407976010216 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 407976010217 dimerization domain [polypeptide binding]; other site 407976010218 dimer interface [polypeptide binding]; other site 407976010219 catalytic residues [active] 407976010220 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 407976010221 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 407976010222 active site 407976010223 Int/Topo IB signature motif; other site 407976010224 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 407976010225 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 407976010226 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 407976010227 S-adenosylmethionine binding site [chemical binding]; other site 407976010228 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 407976010229 DEAD-like helicases superfamily; Region: DEXDc; smart00487 407976010230 ATP binding site [chemical binding]; other site 407976010231 Mg++ binding site [ion binding]; other site 407976010232 motif III; other site 407976010233 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 407976010234 nucleotide binding region [chemical binding]; other site 407976010235 ATP-binding site [chemical binding]; other site 407976010236 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976010237 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976010238 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 407976010239 Protein export membrane protein; Region: SecD_SecF; cl14618 407976010240 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 407976010241 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 407976010242 FeS/SAM binding site; other site 407976010243 PAS domain; Region: PAS_9; pfam13426 407976010244 PAS domain; Region: PAS_9; pfam13426 407976010245 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976010246 I-site; other site 407976010247 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 407976010248 DNA binding site [nucleotide binding] 407976010249 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 407976010250 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 407976010251 Protein of unknown function, DUF481; Region: DUF481; pfam04338 407976010252 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 407976010253 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 407976010254 intersubunit interface [polypeptide binding]; other site 407976010255 active site 407976010256 zinc binding site [ion binding]; other site 407976010257 Na+ binding site [ion binding]; other site 407976010258 Phosphoglycerate kinase; Region: PGK; pfam00162 407976010259 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 407976010260 substrate binding site [chemical binding]; other site 407976010261 hinge regions; other site 407976010262 ADP binding site [chemical binding]; other site 407976010263 catalytic site [active] 407976010264 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 407976010265 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 407976010266 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 407976010267 transketolase; Reviewed; Region: PRK12753 407976010268 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 407976010269 TPP-binding site [chemical binding]; other site 407976010270 dimer interface [polypeptide binding]; other site 407976010271 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 407976010272 PYR/PP interface [polypeptide binding]; other site 407976010273 dimer interface [polypeptide binding]; other site 407976010274 TPP binding site [chemical binding]; other site 407976010275 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 407976010276 S-adenosylmethionine synthetase; Validated; Region: PRK05250 407976010277 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 407976010278 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 407976010279 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 407976010280 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 407976010281 active site 407976010282 catalytic residues [active] 407976010283 DNA binding site [nucleotide binding] 407976010284 Int/Topo IB signature motif; other site 407976010285 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976010286 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 407976010287 non-specific DNA binding site [nucleotide binding]; other site 407976010288 salt bridge; other site 407976010289 sequence-specific DNA binding site [nucleotide binding]; other site 407976010290 Domain of unknown function (DUF955); Region: DUF955; cl01076 407976010291 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 407976010292 HsdM N-terminal domain; Region: HsdM_N; pfam12161 407976010293 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 407976010294 S-adenosylmethionine binding site [chemical binding]; other site 407976010295 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976010296 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 407976010297 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976010298 Fic family protein [Function unknown]; Region: COG3177 407976010299 Fic/DOC family; Region: Fic; pfam02661 407976010300 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 407976010301 non-specific DNA interactions [nucleotide binding]; other site 407976010302 DNA binding site [nucleotide binding] 407976010303 sequence specific DNA binding site [nucleotide binding]; other site 407976010304 putative cAMP binding site [chemical binding]; other site 407976010305 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 407976010306 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 407976010307 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 407976010308 ATP binding site [chemical binding]; other site 407976010309 putative Mg++ binding site [ion binding]; other site 407976010310 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976010311 Coenzyme A binding pocket [chemical binding]; other site 407976010312 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976010313 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976010314 metal binding site [ion binding]; metal-binding site 407976010315 active site 407976010316 I-site; other site 407976010317 META domain; Region: META; pfam03724 407976010318 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 407976010319 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976010320 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976010321 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976010322 Coenzyme A binding pocket [chemical binding]; other site 407976010323 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 407976010324 serine transporter; Region: stp; TIGR00814 407976010325 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976010326 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976010327 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976010328 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 407976010329 MarR family; Region: MarR; pfam01047 407976010330 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 407976010331 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976010332 Coenzyme A binding pocket [chemical binding]; other site 407976010333 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 407976010334 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976010335 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 407976010336 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 407976010337 catalytic loop [active] 407976010338 iron binding site [ion binding]; other site 407976010339 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 407976010340 FAD binding pocket [chemical binding]; other site 407976010341 FAD binding motif [chemical binding]; other site 407976010342 phosphate binding motif [ion binding]; other site 407976010343 beta-alpha-beta structure motif; other site 407976010344 NAD binding pocket [chemical binding]; other site 407976010345 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 407976010346 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 407976010347 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 407976010348 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 407976010349 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 407976010350 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 407976010351 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 407976010352 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 407976010353 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 407976010354 active site 407976010355 catalytic tetrad [active] 407976010356 MltA-interacting protein MipA; Region: MipA; cl01504 407976010357 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976010358 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 407976010359 dimerization interface [polypeptide binding]; other site 407976010360 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 407976010361 dimer interface [polypeptide binding]; other site 407976010362 phosphorylation site [posttranslational modification] 407976010363 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 407976010364 ATP binding site [chemical binding]; other site 407976010365 Mg2+ binding site [ion binding]; other site 407976010366 G-X-G motif; other site 407976010367 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976010368 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 407976010369 active site 407976010370 phosphorylation site [posttranslational modification] 407976010371 intermolecular recognition site; other site 407976010372 dimerization interface [polypeptide binding]; other site 407976010373 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 407976010374 DNA binding site [nucleotide binding] 407976010375 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 407976010376 MltA-interacting protein MipA; Region: MipA; cl01504 407976010377 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 407976010378 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976010379 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 407976010380 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 407976010381 dimerization interface [polypeptide binding]; other site 407976010382 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976010383 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010384 dimer interface [polypeptide binding]; other site 407976010385 putative CheW interface [polypeptide binding]; other site 407976010386 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 407976010387 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 407976010388 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 407976010389 catalytic residue [active] 407976010390 Fe-S metabolism associated domain; Region: SufE; cl00951 407976010391 Membrane dipeptidase (Peptidase family M19); Region: Peptidase_M19; pfam01244 407976010392 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 407976010393 active site 407976010394 Predicted ATPase [General function prediction only]; Region: COG4637 407976010395 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976010396 Walker A/P-loop; other site 407976010397 ATP binding site [chemical binding]; other site 407976010398 Cupin domain; Region: Cupin_2; pfam07883 407976010399 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976010400 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 407976010401 Pleckstrin homology (PH)-like domains in bacteria (PHb); Region: PH-like_bacteria; cd13225 407976010402 pentamer interface [polypeptide binding]; other site 407976010403 dodecaamer interface [polypeptide binding]; other site 407976010404 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 407976010405 Peptidase family U32; Region: Peptidase_U32; pfam01136 407976010406 Collagenase; Region: DUF3656; pfam12392 407976010407 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 407976010408 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 407976010409 active site 407976010410 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 407976010411 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 407976010412 putative DNA binding site [nucleotide binding]; other site 407976010413 putative Zn2+ binding site [ion binding]; other site 407976010414 AsnC family; Region: AsnC_trans_reg; pfam01037 407976010415 Peptidase S8 family domain in Vpr-like proteins; Region: Peptidases_S8_subtilisin_Vpr-like; cd07474 407976010416 putative active site [active] 407976010417 catalytic triad [active] 407976010418 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 407976010419 PA/protease or protease-like domain interface [polypeptide binding]; other site 407976010420 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 407976010421 catalytic residues [active] 407976010422 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 407976010423 putative transposase OrfB; Reviewed; Region: PHA02517 407976010424 Integrase core domain; Region: rve; pfam00665 407976010425 Integrase core domain; Region: rve_3; pfam13683 407976010426 inner membrane transport permease; Provisional; Region: PRK15066 407976010427 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 407976010428 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 407976010429 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 407976010430 Walker A/P-loop; other site 407976010431 ATP binding site [chemical binding]; other site 407976010432 Q-loop/lid; other site 407976010433 ABC transporter signature motif; other site 407976010434 Walker B; other site 407976010435 D-loop; other site 407976010436 H-loop/switch region; other site 407976010437 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976010438 active site 407976010439 aromatic acid decarboxylase; Validated; Region: PRK05920 407976010440 Flavoprotein; Region: Flavoprotein; pfam02441 407976010441 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 407976010442 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 407976010443 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 407976010444 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 407976010445 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 407976010446 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 407976010447 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 407976010448 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 407976010449 hypothetical protein; Provisional; Region: PRK11627 407976010450 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 407976010451 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 407976010452 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 407976010453 substrate binding site [chemical binding]; other site 407976010454 AmpG-like permease; Region: 2A0125; TIGR00901 407976010455 muropeptide transporter; Reviewed; Region: ampG; PRK11902 407976010456 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 407976010457 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 407976010458 Predicted integral membrane protein [Function unknown]; Region: COG5652 407976010459 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 407976010460 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 407976010461 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 407976010462 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 407976010463 Nitrogen regulatory protein P-II; Region: P-II; smart00938 407976010464 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 407976010465 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 407976010466 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 407976010467 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 407976010468 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 407976010469 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 407976010470 Protein of unknown function (DUF819); Region: DUF819; cl02317 407976010471 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 407976010472 Tetratricopeptide repeat; Region: TPR_9; pfam13371 407976010473 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 407976010474 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976010475 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976010476 Coenzyme A binding pocket [chemical binding]; other site 407976010477 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 407976010478 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 407976010479 peptide chain release factor 1; Validated; Region: prfA; PRK00591 407976010480 This domain is found in peptide chain release factors; Region: PCRF; smart00937 407976010481 RF-1 domain; Region: RF-1; pfam00472 407976010482 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 407976010483 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 407976010484 tRNA; other site 407976010485 putative tRNA binding site [nucleotide binding]; other site 407976010486 putative NADP binding site [chemical binding]; other site 407976010487 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 407976010488 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 407976010489 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 407976010490 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 407976010491 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 407976010492 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 407976010493 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 407976010494 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976010495 active site 407976010496 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976010497 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 407976010498 dimerization interface [polypeptide binding]; other site 407976010499 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010500 dimer interface [polypeptide binding]; other site 407976010501 putative CheW interface [polypeptide binding]; other site 407976010502 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 407976010503 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976010504 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 407976010505 DNA binding residues [nucleotide binding] 407976010506 Uncharacterized conserved protein [Function unknown]; Region: COG3595 407976010507 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 407976010508 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 407976010509 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 407976010510 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 407976010511 RNA binding surface [nucleotide binding]; other site 407976010512 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 407976010513 active site 407976010514 uracil binding [chemical binding]; other site 407976010515 maltose O-acetyltransferase; Provisional; Region: PRK10092 407976010516 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 407976010517 active site 407976010518 substrate binding site [chemical binding]; other site 407976010519 trimer interface [polypeptide binding]; other site 407976010520 CoA binding site [chemical binding]; other site 407976010521 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 407976010522 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 407976010523 active site 407976010524 Zn binding site [ion binding]; other site 407976010525 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 407976010526 synthetase active site [active] 407976010527 NTP binding site [chemical binding]; other site 407976010528 metal binding site [ion binding]; metal-binding site 407976010529 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 407976010530 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976010531 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 407976010532 putative C-terminal domain interface [polypeptide binding]; other site 407976010533 putative GSH binding site (G-site) [chemical binding]; other site 407976010534 putative dimer interface [polypeptide binding]; other site 407976010535 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 407976010536 dimer interface [polypeptide binding]; other site 407976010537 N-terminal domain interface [polypeptide binding]; other site 407976010538 substrate binding pocket (H-site) [chemical binding]; other site 407976010539 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 407976010540 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 407976010541 N-terminal plug; other site 407976010542 ligand-binding site [chemical binding]; other site 407976010543 Bacterial PH domain; Region: DUF304; pfam03703 407976010544 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 407976010545 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 407976010546 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 407976010547 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 407976010548 malate dehydrogenase; Provisional; Region: PRK13529 407976010549 Malic enzyme, N-terminal domain; Region: malic; pfam00390 407976010550 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 407976010551 NAD(P) binding site [chemical binding]; other site 407976010552 Protein of unknown function (DUF3069); Region: DUF3069; pfam11269 407976010553 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 407976010554 active site 407976010555 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 407976010556 Tetratricopeptide repeat; Region: TPR_12; pfam13424 407976010557 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976010558 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976010559 metal binding site [ion binding]; metal-binding site 407976010560 active site 407976010561 I-site; other site 407976010562 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976010563 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 407976010564 substrate binding pocket [chemical binding]; other site 407976010565 membrane-bound complex binding site; other site 407976010566 hinge residues; other site 407976010567 epoxyqueuosine reductase; Region: TIGR00276 407976010568 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 407976010569 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 407976010570 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 407976010571 THF binding site; other site 407976010572 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 407976010573 substrate binding site [chemical binding]; other site 407976010574 THF binding site; other site 407976010575 zinc-binding site [ion binding]; other site 407976010576 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976010577 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976010578 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 407976010579 putative dimerization interface [polypeptide binding]; other site 407976010580 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 407976010581 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 407976010582 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 407976010583 N-terminal plug; other site 407976010584 ligand-binding site [chemical binding]; other site 407976010585 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 407976010586 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 407976010587 active site 407976010588 tetramer interface [polypeptide binding]; other site 407976010589 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 407976010590 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 407976010591 substrate binding site [chemical binding]; other site 407976010592 dimer interface [polypeptide binding]; other site 407976010593 ATP binding site [chemical binding]; other site 407976010594 azurin; Region: azurin; TIGR02695 407976010595 Protein of unknown function (DUF3103); Region: DUF3103; pfam11301 407976010596 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 407976010597 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins; Region: GDPD_EcGlpQ_like_1; cd08560 407976010598 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 407976010599 putative active site [active] 407976010600 catalytic site [active] 407976010601 putative metal binding site [ion binding]; other site 407976010602 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 407976010603 active site 407976010604 Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]; Region: PhoD; COG3540 407976010605 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 407976010606 putative active site [active] 407976010607 putative metal binding site [ion binding]; other site 407976010608 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 407976010609 FOG: CBS domain [General function prediction only]; Region: COG0517 407976010610 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 407976010611 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 407976010612 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 407976010613 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 407976010614 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 407976010615 substrate binding pocket [chemical binding]; other site 407976010616 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 407976010617 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976010618 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976010619 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976010620 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 407976010621 metal ion-dependent adhesion site (MIDAS); other site 407976010622 Domain of unknown function (DUF1973); Region: DUF1973; pfam09315 407976010623 VCBS repeat; Region: VCBS_repeat; TIGR01965 407976010624 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 407976010625 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976010626 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976010627 metal binding site [ion binding]; metal-binding site 407976010628 active site 407976010629 I-site; other site 407976010630 Mannan-binding protein; Region: MVL; pfam12151 407976010631 YcaO domain protein; Region: TIGR03549 407976010632 OsmC-like protein; Region: OsmC; pfam02566 407976010633 YcaO-like family; Region: YcaO; pfam02624 407976010634 Cache domain; Region: Cache_2; pfam08269 407976010635 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 407976010636 dimerization interface [polypeptide binding]; other site 407976010637 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976010638 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010639 dimer interface [polypeptide binding]; other site 407976010640 putative CheW interface [polypeptide binding]; other site 407976010641 Ribosome recycling factor; Region: RRF_GI; pfam12614 407976010642 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 407976010643 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976010644 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976010645 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976010646 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 407976010647 Uncharacterized conserved protein [Function unknown]; Region: COG4925 407976010648 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 407976010649 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 407976010650 putative NAD(P) binding site [chemical binding]; other site 407976010651 putative substrate binding site [chemical binding]; other site 407976010652 catalytic Zn binding site [ion binding]; other site 407976010653 structural Zn binding site [ion binding]; other site 407976010654 dimer interface [polypeptide binding]; other site 407976010655 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 407976010656 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 407976010657 putative substrate translocation pore; other site 407976010658 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976010659 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976010660 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 407976010661 putative effector binding pocket; other site 407976010662 putative dimerization interface [polypeptide binding]; other site 407976010663 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976010664 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976010665 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976010666 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976010667 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 407976010668 active site 407976010669 dimer interface [polypeptide binding]; other site 407976010670 motif 1; other site 407976010671 motif 2; other site 407976010672 motif 3; other site 407976010673 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 407976010674 anticodon binding site; other site 407976010675 glycine dehydrogenase; Provisional; Region: PRK05367 407976010676 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 407976010677 tetramer interface [polypeptide binding]; other site 407976010678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976010679 catalytic residue [active] 407976010680 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 407976010681 tetramer interface [polypeptide binding]; other site 407976010682 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976010683 catalytic residue [active] 407976010684 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 407976010685 lipoyl attachment site [posttranslational modification]; other site 407976010686 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 407976010687 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 407976010688 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 407976010689 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 407976010690 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK05732 407976010691 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 407976010692 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 407976010693 Cell division protein ZapA; Region: ZapA; pfam05164 407976010694 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 407976010695 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 407976010696 dihydromonapterin reductase; Provisional; Region: PRK06483 407976010697 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976010698 NAD(P) binding site [chemical binding]; other site 407976010699 active site 407976010700 Protein of unknown function, DUF393; Region: DUF393; pfam04134 407976010701 malate dehydrogenase; Provisional; Region: PRK05086 407976010702 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 407976010703 NAD binding site [chemical binding]; other site 407976010704 dimerization interface [polypeptide binding]; other site 407976010705 Substrate binding site [chemical binding]; other site 407976010706 arginine repressor; Provisional; Region: PRK05066 407976010707 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 407976010708 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 407976010709 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976010710 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976010711 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 407976010712 putative effector binding pocket; other site 407976010713 dimerization interface [polypeptide binding]; other site 407976010714 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 407976010715 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 407976010716 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 407976010717 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 407976010718 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 407976010719 Walker A/P-loop; other site 407976010720 ATP binding site [chemical binding]; other site 407976010721 Q-loop/lid; other site 407976010722 ABC transporter signature motif; other site 407976010723 Walker B; other site 407976010724 D-loop; other site 407976010725 H-loop/switch region; other site 407976010726 TOBE domain; Region: TOBE_2; pfam08402 407976010727 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 407976010728 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 407976010729 dimer interface [polypeptide binding]; other site 407976010730 conserved gate region; other site 407976010731 putative PBP binding loops; other site 407976010732 ABC-ATPase subunit interface; other site 407976010733 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 407976010734 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 407976010735 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 407976010736 putative C-terminal domain interface [polypeptide binding]; other site 407976010737 putative GSH binding site (G-site) [chemical binding]; other site 407976010738 putative dimer interface [polypeptide binding]; other site 407976010739 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 407976010740 dimer interface [polypeptide binding]; other site 407976010741 N-terminal domain interface [polypeptide binding]; other site 407976010742 substrate binding pocket (H-site) [chemical binding]; other site 407976010743 ferredoxin-NADP reductase; Provisional; Region: PRK10926 407976010744 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 407976010745 FAD binding pocket [chemical binding]; other site 407976010746 FAD binding motif [chemical binding]; other site 407976010747 phosphate binding motif [ion binding]; other site 407976010748 beta-alpha-beta structure motif; other site 407976010749 NAD binding pocket [chemical binding]; other site 407976010750 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 407976010751 catalytic core [active] 407976010752 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 407976010753 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 407976010754 active site 407976010755 FMN binding site [chemical binding]; other site 407976010756 substrate binding site [chemical binding]; other site 407976010757 3Fe-4S cluster binding site [ion binding]; other site 407976010758 Src Homology 3 domain superfamily; Region: SH3; cl17036 407976010759 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976010760 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 407976010761 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976010762 Walker A/P-loop; other site 407976010763 ATP binding site [chemical binding]; other site 407976010764 Q-loop/lid; other site 407976010765 ABC transporter signature motif; other site 407976010766 Walker B; other site 407976010767 D-loop; other site 407976010768 H-loop/switch region; other site 407976010769 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 407976010770 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 407976010771 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 407976010772 binding surface 407976010773 TPR motif; other site 407976010774 Tetratricopeptide repeat; Region: TPR_12; pfam13424 407976010775 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 407976010776 binding surface 407976010777 TPR motif; other site 407976010778 TPR repeat; Region: TPR_11; pfam13414 407976010779 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 407976010780 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 407976010781 Nitrogen regulatory protein P-II; Region: P-II; smart00938 407976010782 Isochorismatase family; Region: Isochorismatase; pfam00857 407976010783 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 407976010784 catalytic triad [active] 407976010785 dimer interface [polypeptide binding]; other site 407976010786 conserved cis-peptide bond; other site 407976010787 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 407976010788 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 407976010789 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 407976010790 HAMP domain; Region: HAMP; pfam00672 407976010791 Histidine kinase; Region: HisKA_3; pfam07730 407976010792 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 407976010793 ATP binding site [chemical binding]; other site 407976010794 Mg2+ binding site [ion binding]; other site 407976010795 G-X-G motif; other site 407976010796 transcriptional regulator NarL; Provisional; Region: PRK10651 407976010797 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 407976010798 active site 407976010799 phosphorylation site [posttranslational modification] 407976010800 intermolecular recognition site; other site 407976010801 dimerization interface [polypeptide binding]; other site 407976010802 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 407976010803 DNA binding residues [nucleotide binding] 407976010804 dimerization interface [polypeptide binding]; other site 407976010805 Uncharacterized protein family (UPF0231); Region: UPF0231; pfam06062 407976010806 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 407976010807 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 407976010808 Cl binding site [ion binding]; other site 407976010809 oligomer interface [polypeptide binding]; other site 407976010810 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 407976010811 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 407976010812 active site 407976010813 Zn binding site [ion binding]; other site 407976010814 aspartate kinase III; Validated; Region: PRK09084 407976010815 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 407976010816 nucleotide binding site [chemical binding]; other site 407976010817 substrate binding site [chemical binding]; other site 407976010818 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 407976010819 dimer interface [polypeptide binding]; other site 407976010820 allosteric regulatory binding pocket; other site 407976010821 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 407976010822 dimer interface [polypeptide binding]; other site 407976010823 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 407976010824 two-component response regulator; Provisional; Region: PRK11173 407976010825 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 407976010826 active site 407976010827 phosphorylation site [posttranslational modification] 407976010828 intermolecular recognition site; other site 407976010829 dimerization interface [polypeptide binding]; other site 407976010830 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 407976010831 DNA binding site [nucleotide binding] 407976010832 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 407976010833 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976010834 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976010835 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 407976010836 AMP binding site [chemical binding]; other site 407976010837 metal binding site [ion binding]; metal-binding site 407976010838 active site 407976010839 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976010840 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976010841 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976010842 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 407976010843 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 407976010844 putative active site [active] 407976010845 putative NTP binding site [chemical binding]; other site 407976010846 putative nucleic acid binding site [nucleotide binding]; other site 407976010847 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976010848 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976010849 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976010850 hypothetical protein; Provisional; Region: PRK05208 407976010851 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 407976010852 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 407976010853 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 407976010854 active site 407976010855 metal binding site [ion binding]; metal-binding site 407976010856 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 407976010857 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 407976010858 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 407976010859 active site 407976010860 phosphorylation site [posttranslational modification] 407976010861 intermolecular recognition site; other site 407976010862 dimerization interface [polypeptide binding]; other site 407976010863 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 407976010864 DNA binding residues [nucleotide binding] 407976010865 dimerization interface [polypeptide binding]; other site 407976010866 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 407976010867 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 407976010868 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 407976010869 dimer interface [polypeptide binding]; other site 407976010870 phosphorylation site [posttranslational modification] 407976010871 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 407976010872 ATP binding site [chemical binding]; other site 407976010873 Mg2+ binding site [ion binding]; other site 407976010874 G-X-G motif; other site 407976010875 tetrathionate reductase subunit B; Provisional; Region: PRK14993 407976010876 4Fe-4S binding domain; Region: Fer4; pfam00037 407976010877 tetrathionate reductase subunit C; Provisional; Region: PRK14992 407976010878 tetrathionate reductase subunit A; Provisional; Region: PRK14991 407976010879 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 407976010880 molybdopterin cofactor binding site; other site 407976010881 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 407976010882 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 407976010883 putative molybdopterin cofactor binding site; other site 407976010884 PAS domain; Region: PAS_9; pfam13426 407976010885 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 407976010886 putative active site [active] 407976010887 heme pocket [chemical binding]; other site 407976010888 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 407976010889 PAS domain; Region: PAS_9; pfam13426 407976010890 putative active site [active] 407976010891 heme pocket [chemical binding]; other site 407976010892 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976010893 dimer interface [polypeptide binding]; other site 407976010894 putative CheW interface [polypeptide binding]; other site 407976010895 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 407976010896 phage shock protein C; Region: phageshock_pspC; TIGR02978 407976010897 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 407976010898 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 407976010899 Transglycosylase; Region: Transgly; pfam00912 407976010900 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 407976010901 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 407976010902 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 407976010903 ATP binding site [chemical binding]; other site 407976010904 putative Mg++ binding site [ion binding]; other site 407976010905 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 407976010906 nucleotide binding region [chemical binding]; other site 407976010907 ATP-binding site [chemical binding]; other site 407976010908 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 407976010909 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 407976010910 GAF domain; Region: GAF; cl17456 407976010911 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976010912 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976010913 metal binding site [ion binding]; metal-binding site 407976010914 active site 407976010915 I-site; other site 407976010916 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 407976010917 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 407976010918 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 407976010919 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 407976010920 Sel1-like repeats; Region: SEL1; smart00671 407976010921 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 407976010922 TPR motif; other site 407976010923 binding surface 407976010924 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 407976010925 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 407976010926 ligand binding site [chemical binding]; other site 407976010927 flexible hinge region; other site 407976010928 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 407976010929 putative switch regulator; other site 407976010930 non-specific DNA interactions [nucleotide binding]; other site 407976010931 DNA binding site [nucleotide binding] 407976010932 sequence specific DNA binding site [nucleotide binding]; other site 407976010933 putative cAMP binding site [chemical binding]; other site 407976010934 Predicted membrane protein [Function unknown]; Region: COG3212 407976010935 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976010936 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 407976010937 active site 407976010938 phosphorylation site [posttranslational modification] 407976010939 intermolecular recognition site; other site 407976010940 dimerization interface [polypeptide binding]; other site 407976010941 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 407976010942 DNA binding site [nucleotide binding] 407976010943 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976010944 HAMP domain; Region: HAMP; pfam00672 407976010945 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 407976010946 dimer interface [polypeptide binding]; other site 407976010947 phosphorylation site [posttranslational modification] 407976010948 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 407976010949 ATP binding site [chemical binding]; other site 407976010950 Mg2+ binding site [ion binding]; other site 407976010951 G-X-G motif; other site 407976010952 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 407976010953 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 407976010954 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 407976010955 NAD(P) binding site [chemical binding]; other site 407976010956 catalytic residues [active] 407976010957 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 407976010958 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 407976010959 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 407976010960 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 407976010961 inhibitor-cofactor binding pocket; inhibition site 407976010962 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976010963 catalytic residue [active] 407976010964 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 407976010965 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 407976010966 HDOD domain; Region: HDOD; pfam08668 407976010967 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976010968 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976010969 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 407976010970 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 407976010971 glutamine binding [chemical binding]; other site 407976010972 catalytic triad [active] 407976010973 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 407976010974 stringent starvation protein A; Provisional; Region: sspA; PRK09481 407976010975 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 407976010976 C-terminal domain interface [polypeptide binding]; other site 407976010977 putative GSH binding site (G-site) [chemical binding]; other site 407976010978 dimer interface [polypeptide binding]; other site 407976010979 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 407976010980 dimer interface [polypeptide binding]; other site 407976010981 N-terminal domain interface [polypeptide binding]; other site 407976010982 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 407976010983 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 407976010984 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 407976010985 Qi binding site; other site 407976010986 intrachain domain interface; other site 407976010987 interchain domain interface [polypeptide binding]; other site 407976010988 heme bH binding site [chemical binding]; other site 407976010989 heme bL binding site [chemical binding]; other site 407976010990 Qo binding site; other site 407976010991 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 407976010992 interchain domain interface [polypeptide binding]; other site 407976010993 intrachain domain interface; other site 407976010994 Qi binding site; other site 407976010995 Qo binding site; other site 407976010996 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 407976010997 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 407976010998 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 407976010999 [2Fe-2S] cluster binding site [ion binding]; other site 407976011000 FtsH protease regulator HflC; Provisional; Region: PRK11029 407976011001 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 407976011002 FtsH protease regulator HflK; Provisional; Region: PRK10930 407976011003 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 407976011004 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 407976011005 GTPase HflX; Provisional; Region: PRK11058 407976011006 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 407976011007 HflX GTPase family; Region: HflX; cd01878 407976011008 G1 box; other site 407976011009 GTP/Mg2+ binding site [chemical binding]; other site 407976011010 Switch I region; other site 407976011011 G2 box; other site 407976011012 G3 box; other site 407976011013 Switch II region; other site 407976011014 G4 box; other site 407976011015 G5 box; other site 407976011016 bacterial Hfq-like; Region: Hfq; cd01716 407976011017 hexamer interface [polypeptide binding]; other site 407976011018 Sm1 motif; other site 407976011019 RNA binding site [nucleotide binding]; other site 407976011020 Sm2 motif; other site 407976011021 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 407976011022 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cd02019 407976011023 active site 407976011024 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 407976011025 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 407976011026 ATP binding site [chemical binding]; other site 407976011027 Mg2+ binding site [ion binding]; other site 407976011028 G-X-G motif; other site 407976011029 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 407976011030 ATP binding site [chemical binding]; other site 407976011031 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 407976011032 AMIN domain; Region: AMIN; pfam11741 407976011033 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 407976011034 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 407976011035 active site 407976011036 metal binding site [ion binding]; metal-binding site 407976011037 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 407976011038 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 407976011039 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 407976011040 putative carbohydrate kinase; Provisional; Region: PRK10565 407976011041 Uncharacterized conserved protein [Function unknown]; Region: COG0062 407976011042 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 407976011043 putative substrate binding site [chemical binding]; other site 407976011044 putative ATP binding site [chemical binding]; other site 407976011045 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 407976011046 catalytic site [active] 407976011047 putative active site [active] 407976011048 putative substrate binding site [chemical binding]; other site 407976011049 dimer interface [polypeptide binding]; other site 407976011050 GTPase RsgA; Reviewed; Region: PRK12288 407976011051 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 407976011052 RNA binding site [nucleotide binding]; other site 407976011053 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 407976011054 GTPase/Zn-binding domain interface [polypeptide binding]; other site 407976011055 GTP/Mg2+ binding site [chemical binding]; other site 407976011056 G4 box; other site 407976011057 G5 box; other site 407976011058 G1 box; other site 407976011059 Switch I region; other site 407976011060 G2 box; other site 407976011061 G3 box; other site 407976011062 Switch II region; other site 407976011063 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 407976011064 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976011065 EamA-like transporter family; Region: EamA; pfam00892 407976011066 EamA-like transporter family; Region: EamA; pfam00892 407976011067 putative mechanosensitive channel protein; Provisional; Region: PRK10929 407976011068 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 407976011069 Mechanosensitive ion channel; Region: MS_channel; pfam00924 407976011070 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 407976011071 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 407976011072 active site 407976011073 catalytic site [active] 407976011074 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 407976011075 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 407976011076 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 407976011077 NAD binding site [chemical binding]; other site 407976011078 ligand binding site [chemical binding]; other site 407976011079 catalytic site [active] 407976011080 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 407976011081 PAS fold; Region: PAS_3; pfam08447 407976011082 putative active site [active] 407976011083 heme pocket [chemical binding]; other site 407976011084 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 407976011085 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976011086 dimer interface [polypeptide binding]; other site 407976011087 putative CheW interface [polypeptide binding]; other site 407976011088 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 407976011089 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 407976011090 Protein kinase domain; Region: Pkinase; pfam00069 407976011091 Catalytic domain of Protein Kinases; Region: PKc; cd00180 407976011092 active site 407976011093 ATP binding site [chemical binding]; other site 407976011094 substrate binding site [chemical binding]; other site 407976011095 activation loop (A-loop); other site 407976011096 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 407976011097 active site 407976011098 Cache domain; Region: Cache_1; pfam02743 407976011099 PAS fold; Region: PAS_4; pfam08448 407976011100 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 407976011101 putative active site [active] 407976011102 heme pocket [chemical binding]; other site 407976011103 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 407976011104 PAS fold; Region: PAS_3; pfam08447 407976011105 putative active site [active] 407976011106 heme pocket [chemical binding]; other site 407976011107 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 407976011108 dimer interface [polypeptide binding]; other site 407976011109 phosphorylation site [posttranslational modification] 407976011110 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 407976011111 ATP binding site [chemical binding]; other site 407976011112 Mg2+ binding site [ion binding]; other site 407976011113 G-X-G motif; other site 407976011114 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 407976011115 Response regulator receiver domain; Region: Response_reg; pfam00072 407976011116 active site 407976011117 phosphorylation site [posttranslational modification] 407976011118 intermolecular recognition site; other site 407976011119 dimerization interface [polypeptide binding]; other site 407976011120 Response regulator receiver domain; Region: Response_reg; pfam00072 407976011121 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 407976011122 active site 407976011123 phosphorylation site [posttranslational modification] 407976011124 intermolecular recognition site; other site 407976011125 dimerization interface [polypeptide binding]; other site 407976011126 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 407976011127 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 407976011128 putative active site [active] 407976011129 PhoH-like protein; Region: PhoH; pfam02562 407976011130 ATP-dependent helicase HepA; Validated; Region: PRK04914 407976011131 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 407976011132 ATP binding site [chemical binding]; other site 407976011133 putative Mg++ binding site [ion binding]; other site 407976011134 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 407976011135 nucleotide binding region [chemical binding]; other site 407976011136 ATP-binding site [chemical binding]; other site 407976011137 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 407976011138 enoyl-CoA hydratase; Provisional; Region: PRK07509 407976011139 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 407976011140 substrate binding site [chemical binding]; other site 407976011141 oxyanion hole (OAH) forming residues; other site 407976011142 trimer interface [polypeptide binding]; other site 407976011143 Response regulator receiver domain; Region: Response_reg; pfam00072 407976011144 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 407976011145 active site 407976011146 phosphorylation site [posttranslational modification] 407976011147 intermolecular recognition site; other site 407976011148 dimerization interface [polypeptide binding]; other site 407976011149 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 407976011150 PAS domain; Region: PAS_9; pfam13426 407976011151 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011152 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011153 metal binding site [ion binding]; metal-binding site 407976011154 active site 407976011155 I-site; other site 407976011156 RNase E inhibitor protein; Provisional; Region: PRK11191 407976011157 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 407976011158 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 407976011159 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 407976011160 putative acyl-acceptor binding pocket; other site 407976011161 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 407976011162 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 407976011163 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 407976011164 putative ligand binding site [chemical binding]; other site 407976011165 Mechanosensitive ion channel; Region: MS_channel; pfam00924 407976011166 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 407976011167 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 407976011168 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 407976011169 Potassium binding sites [ion binding]; other site 407976011170 Cesium cation binding sites [ion binding]; other site 407976011171 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 407976011172 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 407976011173 active site 407976011174 catalytic tetrad [active] 407976011175 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 407976011176 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 407976011177 active site 2 [active] 407976011178 active site 1 [active] 407976011179 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 407976011180 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 407976011181 S-adenosylmethionine binding site [chemical binding]; other site 407976011182 TraB family; Region: TraB; pfam01963 407976011183 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 407976011184 FOG: CBS domain [General function prediction only]; Region: COG0517 407976011185 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 407976011186 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011187 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011188 metal binding site [ion binding]; metal-binding site 407976011189 active site 407976011190 I-site; other site 407976011191 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 407976011192 Protein of unknown function (DUF4240); Region: DUF4240; pfam14024 407976011193 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976011194 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 407976011195 active site 407976011196 phosphorylation site [posttranslational modification] 407976011197 intermolecular recognition site; other site 407976011198 dimerization interface [polypeptide binding]; other site 407976011199 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 407976011200 Response regulator receiver domain; Region: Response_reg; pfam00072 407976011201 active site 407976011202 phosphorylation site [posttranslational modification] 407976011203 intermolecular recognition site; other site 407976011204 dimerization interface [polypeptide binding]; other site 407976011205 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 407976011206 IHF dimer interface [polypeptide binding]; other site 407976011207 IHF - DNA interface [nucleotide binding]; other site 407976011208 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 407976011209 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 407976011210 ATP-grasp domain; Region: ATP-grasp_4; cl17255 407976011211 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976011212 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 407976011213 active site 407976011214 phosphorylation site [posttranslational modification] 407976011215 intermolecular recognition site; other site 407976011216 dimerization interface [polypeptide binding]; other site 407976011217 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011218 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011219 metal binding site [ion binding]; metal-binding site 407976011220 active site 407976011221 I-site; other site 407976011222 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 407976011223 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 407976011224 active site 407976011225 phosphorylation site [posttranslational modification] 407976011226 intermolecular recognition site; other site 407976011227 CHASE domain; Region: CHASE; pfam03924 407976011228 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 407976011229 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 407976011230 putative active site [active] 407976011231 heme pocket [chemical binding]; other site 407976011232 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 407976011233 dimer interface [polypeptide binding]; other site 407976011234 phosphorylation site [posttranslational modification] 407976011235 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 407976011236 ATP binding site [chemical binding]; other site 407976011237 Mg2+ binding site [ion binding]; other site 407976011238 G-X-G motif; other site 407976011239 conserved hypothetical protein; Region: QEGLA; TIGR02421 407976011240 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 407976011241 amino acid carrier protein; Region: agcS; TIGR00835 407976011242 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 407976011243 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 407976011244 Beta-Casp domain; Region: Beta-Casp; smart01027 407976011245 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 407976011246 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 407976011247 Major Facilitator Superfamily; Region: MFS_1; pfam07690 407976011248 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 407976011249 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 407976011250 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 407976011251 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 407976011252 catalytic residues [active] 407976011253 Predicted permeases [General function prediction only]; Region: COG0701 407976011254 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 407976011255 dimerization interface [polypeptide binding]; other site 407976011256 putative DNA binding site [nucleotide binding]; other site 407976011257 putative Zn2+ binding site [ion binding]; other site 407976011258 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 407976011259 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 407976011260 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976011261 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 407976011262 dimerization interface [polypeptide binding]; other site 407976011263 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 407976011264 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 407976011265 conserved cys residue [active] 407976011266 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976011267 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976011268 Isochorismatase family; Region: Isochorismatase; pfam00857 407976011269 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 407976011270 catalytic triad [active] 407976011271 conserved cis-peptide bond; other site 407976011272 Uncharacterized conserved protein [Function unknown]; Region: COG1359 407976011273 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976011274 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976011275 Coenzyme A binding pocket [chemical binding]; other site 407976011276 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 407976011277 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 407976011278 putative substrate translocation pore; other site 407976011279 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 407976011280 putative substrate translocation pore; other site 407976011281 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 407976011282 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976011283 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976011284 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976011285 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976011286 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 407976011287 putative effector binding pocket; other site 407976011288 dimerization interface [polypeptide binding]; other site 407976011289 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 407976011290 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 407976011291 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 407976011292 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 407976011293 Protein export membrane protein; Region: SecD_SecF; cl14618 407976011294 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976011295 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976011296 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976011297 Outer membrane efflux protein; Region: OEP; pfam02321 407976011298 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 407976011299 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 407976011300 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 407976011301 hypothetical protein; Provisional; Region: PRK09256 407976011302 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 407976011303 Dehydroquinase class II; Region: DHquinase_II; pfam01220 407976011304 active site 407976011305 trimer interface [polypeptide binding]; other site 407976011306 dimer interface [polypeptide binding]; other site 407976011307 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 407976011308 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 407976011309 carboxyltransferase (CT) interaction site; other site 407976011310 biotinylation site [posttranslational modification]; other site 407976011311 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 407976011312 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976011313 NAD(P) binding site [chemical binding]; other site 407976011314 active site 407976011315 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 407976011316 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 407976011317 putative substrate translocation pore; other site 407976011318 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 407976011319 FMN reductase; Validated; Region: fre; PRK08051 407976011320 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 407976011321 FAD binding pocket [chemical binding]; other site 407976011322 FAD binding motif [chemical binding]; other site 407976011323 phosphate binding motif [ion binding]; other site 407976011324 beta-alpha-beta structure motif; other site 407976011325 NAD binding pocket [chemical binding]; other site 407976011326 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976011327 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976011328 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976011329 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 407976011330 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 407976011331 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 407976011332 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 407976011333 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 407976011334 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 407976011335 active site 407976011336 Zn binding site [ion binding]; other site 407976011337 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 407976011338 Pathogenicity locus; Region: Cdd1; pfam11731 407976011339 Domain of unknown function DUF20; Region: UPF0118; pfam01594 407976011340 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 407976011341 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 407976011342 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976011343 catalytic residues [active] 407976011344 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 407976011345 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976011346 catalytic residues [active] 407976011347 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 407976011348 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 407976011349 FMN binding site [chemical binding]; other site 407976011350 substrate binding site [chemical binding]; other site 407976011351 putative catalytic residue [active] 407976011352 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 407976011353 putative dimer interface [polypeptide binding]; other site 407976011354 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976011355 TMAO reductase system periplasmic protein TorT; Provisional; Region: PRK10936 407976011356 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 407976011357 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 407976011358 UbiA prenyltransferase family; Region: UbiA; pfam01040 407976011359 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 407976011360 Part of AAA domain; Region: AAA_19; pfam13245 407976011361 Family description; Region: UvrD_C_2; pfam13538 407976011362 Methyltransferase domain; Region: Methyltransf_31; pfam13847 407976011363 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 407976011364 S-adenosylmethionine binding site [chemical binding]; other site 407976011365 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_21; cd04680 407976011366 nudix motif; other site 407976011367 Predicted metalloprotease [General function prediction only]; Region: COG2321 407976011368 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 407976011369 Poxvirus P35 protein; Region: Pox_P35; pfam03213 407976011370 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 407976011371 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 407976011372 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 407976011373 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 407976011374 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 407976011375 DctM-like transporters; Region: DctM; pfam06808 407976011376 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 407976011377 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 407976011378 putative active site [active] 407976011379 PAS fold; Region: PAS_3; pfam08447 407976011380 heme pocket [chemical binding]; other site 407976011381 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011382 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011383 metal binding site [ion binding]; metal-binding site 407976011384 active site 407976011385 I-site; other site 407976011386 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 407976011387 thioredoxin 2; Provisional; Region: PRK10996 407976011388 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 407976011389 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 407976011390 catalytic residues [active] 407976011391 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 407976011392 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 407976011393 transmembrane helices; other site 407976011394 putative MFS family transporter protein; Provisional; Region: PRK03633 407976011395 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 407976011396 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 407976011397 RNA binding surface [nucleotide binding]; other site 407976011398 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 407976011399 active site 407976011400 uracil binding [chemical binding]; other site 407976011401 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 407976011402 SPFH domain / Band 7 family; Region: Band_7; pfam01145 407976011403 Predicted permease; Region: DUF318; cl17795 407976011404 Predicted permease; Region: DUF318; cl17795 407976011405 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 407976011406 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 407976011407 DNA binding residues [nucleotide binding] 407976011408 dimer interface [polypeptide binding]; other site 407976011409 metal binding site [ion binding]; metal-binding site 407976011410 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 407976011411 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 407976011412 purine monophosphate binding site [chemical binding]; other site 407976011413 dimer interface [polypeptide binding]; other site 407976011414 putative catalytic residues [active] 407976011415 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 407976011416 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 407976011417 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 407976011418 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 407976011419 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 407976011420 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 407976011421 Peptidase M60-like family; Region: M60-like; pfam13402 407976011422 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs; Region: 11beta-HSD1_like_SDR_c; cd05332 407976011423 short chain dehydrogenase; Provisional; Region: PRK06181 407976011424 NADP binding site [chemical binding]; other site 407976011425 homodimer interface [polypeptide binding]; other site 407976011426 substrate binding site [chemical binding]; other site 407976011427 active site 407976011428 PAS fold; Region: PAS_4; pfam08448 407976011429 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 407976011430 putative active site [active] 407976011431 heme pocket [chemical binding]; other site 407976011432 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011433 metal binding site [ion binding]; metal-binding site 407976011434 active site 407976011435 I-site; other site 407976011436 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 407976011437 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 407976011438 substrate binding site [chemical binding]; other site 407976011439 active site 407976011440 anti-RNA polymerase sigma 70 factor; Provisional; Region: PRK11718 407976011441 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 407976011442 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 407976011443 substrate binding site [chemical binding]; other site 407976011444 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 407976011445 substrate binding site [chemical binding]; other site 407976011446 ligand binding site [chemical binding]; other site 407976011447 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 407976011448 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 407976011449 motif II; other site 407976011450 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 407976011451 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 407976011452 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 407976011453 active site 407976011454 Zn binding site [ion binding]; other site 407976011455 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 407976011456 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 407976011457 active site 407976011458 nucleophile elbow; other site 407976011459 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 407976011460 Surface antigen; Region: Bac_surface_Ag; pfam01103 407976011461 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 407976011462 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 407976011463 heme pocket [chemical binding]; other site 407976011464 putative active site [active] 407976011465 PAS fold; Region: PAS_3; pfam08447 407976011466 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 407976011467 PAS domain; Region: PAS_9; pfam13426 407976011468 putative active site [active] 407976011469 heme pocket [chemical binding]; other site 407976011470 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011471 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011472 metal binding site [ion binding]; metal-binding site 407976011473 active site 407976011474 I-site; other site 407976011475 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 407976011476 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 407976011477 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 407976011478 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 407976011479 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 407976011480 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 407976011481 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 407976011482 E3 interaction surface; other site 407976011483 lipoyl attachment site [posttranslational modification]; other site 407976011484 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 407976011485 E3 interaction surface; other site 407976011486 lipoyl attachment site [posttranslational modification]; other site 407976011487 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 407976011488 E3 interaction surface; other site 407976011489 lipoyl attachment site [posttranslational modification]; other site 407976011490 e3 binding domain; Region: E3_binding; pfam02817 407976011491 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 407976011492 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 407976011493 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 407976011494 dimer interface [polypeptide binding]; other site 407976011495 TPP-binding site [chemical binding]; other site 407976011496 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 407976011497 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976011498 DNA-binding site [nucleotide binding]; DNA binding site 407976011499 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 407976011500 regulatory protein AmpE; Provisional; Region: PRK10987 407976011501 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 407976011502 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 407976011503 amidase catalytic site [active] 407976011504 Zn binding residues [ion binding]; other site 407976011505 substrate binding site [chemical binding]; other site 407976011506 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 407976011507 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 407976011508 dimerization interface [polypeptide binding]; other site 407976011509 active site 407976011510 Domain of unknown function (DUF1835); Region: DUF1835; pfam08874 407976011511 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976011512 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976011513 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976011514 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 407976011515 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 407976011516 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 407976011517 Walker A motif; other site 407976011518 ATP binding site [chemical binding]; other site 407976011519 Walker B motif; other site 407976011520 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 407976011521 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 407976011522 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 407976011523 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 407976011524 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 407976011525 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 407976011526 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 407976011527 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 407976011528 CoA-binding site [chemical binding]; other site 407976011529 ATP-binding [chemical binding]; other site 407976011530 hypothetical protein; Provisional; Region: PRK05287 407976011531 Domain of unknown function (DUF329); Region: DUF329; pfam03884 407976011532 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 407976011533 active site 407976011534 8-oxo-dGMP binding site [chemical binding]; other site 407976011535 nudix motif; other site 407976011536 metal binding site [ion binding]; metal-binding site 407976011537 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976011538 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 407976011539 catalytic residues [active] 407976011540 exopolyphosphatase; Region: exo_poly_only; TIGR03706 407976011541 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 407976011542 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 407976011543 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 407976011544 ATP binding site [chemical binding]; other site 407976011545 Mg++ binding site [ion binding]; other site 407976011546 motif III; other site 407976011547 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 407976011548 nucleotide binding region [chemical binding]; other site 407976011549 ATP-binding site [chemical binding]; other site 407976011550 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 407976011551 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976011552 catalytic residues [active] 407976011553 transcription termination factor Rho; Provisional; Region: rho; PRK09376 407976011554 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 407976011555 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 407976011556 RNA binding site [nucleotide binding]; other site 407976011557 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 407976011558 multimer interface [polypeptide binding]; other site 407976011559 Walker A motif; other site 407976011560 ATP binding site [chemical binding]; other site 407976011561 Walker B motif; other site 407976011562 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976011563 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976011564 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 407976011565 putative effector binding pocket; other site 407976011566 dimerization interface [polypeptide binding]; other site 407976011567 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 407976011568 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 407976011569 putative NAD(P) binding site [chemical binding]; other site 407976011570 dimer interface [polypeptide binding]; other site 407976011571 Uncharacterized conserved protein [Function unknown]; Region: COG1359 407976011572 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 407976011573 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 407976011574 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 407976011575 L-aspartate oxidase; Provisional; Region: PRK06175 407976011576 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 407976011577 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 407976011578 Iron-sulfur protein interface; other site 407976011579 proximal heme binding site [chemical binding]; other site 407976011580 distal heme binding site [chemical binding]; other site 407976011581 dimer interface [polypeptide binding]; other site 407976011582 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13554 407976011583 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 407976011584 Iron-sulfur protein interface; other site 407976011585 proximal heme binding site [chemical binding]; other site 407976011586 distal heme binding site [chemical binding]; other site 407976011587 dimer interface [polypeptide binding]; other site 407976011588 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 407976011589 DNA methylase; Region: N6_N4_Mtase; cl17433 407976011590 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 407976011591 S-adenosylmethionine binding site [chemical binding]; other site 407976011592 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 407976011593 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 407976011594 FMN binding site [chemical binding]; other site 407976011595 active site 407976011596 catalytic residues [active] 407976011597 substrate binding site [chemical binding]; other site 407976011598 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 407976011599 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 407976011600 Part of AAA domain; Region: AAA_19; pfam13245 407976011601 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 407976011602 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 407976011603 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 407976011604 Hemerythrin-like domain; Region: Hr-like; cd12108 407976011605 Divergent AAA domain; Region: AAA_4; pfam04326 407976011606 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 407976011607 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 407976011608 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 407976011609 motif II; other site 407976011610 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 407976011611 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 407976011612 active site 407976011613 Int/Topo IB signature motif; other site 407976011614 Protein of unknown function, DUF484; Region: DUF484; cl17449 407976011615 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 407976011616 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 407976011617 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 407976011618 diaminopimelate decarboxylase; Region: lysA; TIGR01048 407976011619 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 407976011620 active site 407976011621 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 407976011622 substrate binding site [chemical binding]; other site 407976011623 catalytic residues [active] 407976011624 dimer interface [polypeptide binding]; other site 407976011625 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; pfam13627 407976011626 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate...; Region: Frataxin; cd00503 407976011627 putative iron binding site [ion binding]; other site 407976011628 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 407976011629 adenylate cyclase; Provisional; Region: cyaA; PRK09450 407976011630 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 407976011631 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 407976011632 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 407976011633 domain interfaces; other site 407976011634 active site 407976011635 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 407976011636 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 407976011637 active site 407976011638 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 407976011639 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 407976011640 HemY protein N-terminus; Region: HemY_N; pfam07219 407976011641 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 407976011642 binding surface 407976011643 TPR motif; other site 407976011644 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 407976011645 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011646 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011647 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011648 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011649 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011650 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011651 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011652 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011653 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011654 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011655 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011656 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011657 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011658 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 407976011659 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 407976011660 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 407976011661 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 407976011662 metal ion-dependent adhesion site (MIDAS); other site 407976011663 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 407976011664 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 407976011665 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 407976011666 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 407976011667 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 407976011668 Walker A/P-loop; other site 407976011669 ATP binding site [chemical binding]; other site 407976011670 Q-loop/lid; other site 407976011671 ABC transporter signature motif; other site 407976011672 Walker B; other site 407976011673 D-loop; other site 407976011674 H-loop/switch region; other site 407976011675 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 407976011676 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976011677 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976011678 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 407976011679 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 407976011680 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 407976011681 ligand binding site [chemical binding]; other site 407976011682 Predicted transglutaminase-like cysteine proteinase [General function prediction only]; Region: COG3672 407976011683 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 407976011684 dimerization interface [polypeptide binding]; other site 407976011685 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011686 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011687 metal binding site [ion binding]; metal-binding site 407976011688 active site 407976011689 I-site; other site 407976011690 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 407976011691 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976011692 GAF domain; Region: GAF; pfam01590 407976011693 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976011694 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 407976011695 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011696 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011697 metal binding site [ion binding]; metal-binding site 407976011698 active site 407976011699 I-site; other site 407976011700 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 407976011701 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 407976011702 Part of AAA domain; Region: AAA_19; pfam13245 407976011703 Family description; Region: UvrD_C_2; pfam13538 407976011704 Membrane fusogenic activity; Region: BMFP; pfam04380 407976011705 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 407976011706 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 407976011707 inner membrane protein; Provisional; Region: PRK11715 407976011708 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 407976011709 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 407976011710 active site 407976011711 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 407976011712 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 407976011713 substrate binding pocket [chemical binding]; other site 407976011714 membrane-bound complex binding site; other site 407976011715 hinge residues; other site 407976011716 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 407976011717 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 407976011718 putative DNA binding site [nucleotide binding]; other site 407976011719 putative Zn2+ binding site [ion binding]; other site 407976011720 AsnC family; Region: AsnC_trans_reg; pfam01037 407976011721 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 407976011722 Na2 binding site [ion binding]; other site 407976011723 putative substrate binding site 1 [chemical binding]; other site 407976011724 Na binding site 1 [ion binding]; other site 407976011725 putative substrate binding site 2 [chemical binding]; other site 407976011726 Tim44-like domain; Region: Tim44; pfam04280 407976011727 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 407976011728 homodimer interface [polypeptide binding]; other site 407976011729 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976011730 catalytic residue [active] 407976011731 threonine dehydratase; Reviewed; Region: PRK09224 407976011732 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 407976011733 tetramer interface [polypeptide binding]; other site 407976011734 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976011735 catalytic residue [active] 407976011736 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 407976011737 putative Ile/Val binding site [chemical binding]; other site 407976011738 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 407976011739 putative Ile/Val binding site [chemical binding]; other site 407976011740 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 407976011741 acetolactate synthase 2 regulatory subunit; Provisional; Region: ilvM; PRK11152 407976011742 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 407976011743 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 407976011744 PYR/PP interface [polypeptide binding]; other site 407976011745 dimer interface [polypeptide binding]; other site 407976011746 TPP binding site [chemical binding]; other site 407976011747 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 407976011748 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 407976011749 TPP-binding site [chemical binding]; other site 407976011750 dimer interface [polypeptide binding]; other site 407976011751 ketol-acid reductoisomerase; Validated; Region: PRK05225 407976011752 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 407976011753 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 407976011754 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 407976011755 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976011756 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 407976011757 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 407976011758 putative dimerization interface [polypeptide binding]; other site 407976011759 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 407976011760 Domain of unknown function DUF21; Region: DUF21; pfam01595 407976011761 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 407976011762 Transporter associated domain; Region: CorC_HlyC; smart01091 407976011763 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 407976011764 GAF domain; Region: GAF; pfam01590 407976011765 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011766 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011767 metal binding site [ion binding]; metal-binding site 407976011768 active site 407976011769 I-site; other site 407976011770 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 407976011771 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 407976011772 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 407976011773 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 407976011774 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 407976011775 Walker A motif; other site 407976011776 ATP binding site [chemical binding]; other site 407976011777 Walker B motif; other site 407976011778 arginine finger; other site 407976011779 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 407976011780 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 407976011781 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 407976011782 putative acyl-acceptor binding pocket; other site 407976011783 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 407976011784 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 407976011785 putative acyl-acceptor binding pocket; other site 407976011786 Uncharacterized conserved protein [Function unknown]; Region: COG1683 407976011787 Transcriptional regulators [Transcription]; Region: GntR; COG1802 407976011788 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 407976011789 DNA-binding site [nucleotide binding]; DNA binding site 407976011790 FCD domain; Region: FCD; pfam07729 407976011791 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 407976011792 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 407976011793 tetramer interface [polypeptide binding]; other site 407976011794 active site 407976011795 Mg2+/Mn2+ binding site [ion binding]; other site 407976011796 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 407976011797 dimer interface [polypeptide binding]; other site 407976011798 Citrate synthase; Region: Citrate_synt; pfam00285 407976011799 active site 407976011800 citrylCoA binding site [chemical binding]; other site 407976011801 oxalacetate/citrate binding site [chemical binding]; other site 407976011802 coenzyme A binding site [chemical binding]; other site 407976011803 catalytic triad [active] 407976011804 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 407976011805 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 407976011806 substrate binding site [chemical binding]; other site 407976011807 ligand binding site [chemical binding]; other site 407976011808 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 407976011809 substrate binding site [chemical binding]; other site 407976011810 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 407976011811 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 407976011812 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 407976011813 tetramer interface [polypeptide binding]; other site 407976011814 active site 407976011815 Mg2+/Mn2+ binding site [ion binding]; other site 407976011816 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 407976011817 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 407976011818 PAS fold; Region: PAS_3; pfam08447 407976011819 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 407976011820 PAS domain; Region: PAS_9; pfam13426 407976011821 putative active site [active] 407976011822 heme pocket [chemical binding]; other site 407976011823 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011824 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011825 metal binding site [ion binding]; metal-binding site 407976011826 active site 407976011827 I-site; other site 407976011828 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 407976011829 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 407976011830 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 407976011831 homodimer interface [polypeptide binding]; other site 407976011832 substrate-cofactor binding pocket; other site 407976011833 catalytic residue [active] 407976011834 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; pfam07073 407976011835 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 407976011836 homotrimer interaction site [polypeptide binding]; other site 407976011837 putative active site [active] 407976011838 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 407976011839 Protein of unknown function (DUF904); Region: DUF904; cl11531 407976011840 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 407976011841 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 407976011842 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 407976011843 catalytic residues [active] 407976011844 hinge region; other site 407976011845 alpha helical domain; other site 407976011846 serine/threonine protein kinase; Provisional; Region: PRK11768 407976011847 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 407976011848 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 407976011849 Uncharacterized conserved protein [Function unknown]; Region: COG0397 407976011850 hypothetical protein; Validated; Region: PRK00029 407976011851 DsrE/DsrF-like family; Region: DrsE; cl00672 407976011852 Nitrous oxide-stimulated promoter; Region: YgbA_NO; pfam11756 407976011853 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 407976011854 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976011855 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976011856 metal binding site [ion binding]; metal-binding site 407976011857 active site 407976011858 I-site; other site 407976011859 Acyltransferase family; Region: Acyl_transf_3; pfam01757 407976011860 Uncharacterized conserved protein [Function unknown]; Region: COG3339 407976011861 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 407976011862 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 407976011863 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 407976011864 substrate binding site [chemical binding]; other site 407976011865 ornithine decarboxylase; Provisional; Region: PRK13578 407976011866 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 407976011867 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 407976011868 homodimer interface [polypeptide binding]; other site 407976011869 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976011870 catalytic residue [active] 407976011871 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 407976011872 putrescine transporter; Provisional; Region: potE; PRK10655 407976011873 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 407976011874 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 407976011875 trimer interface [polypeptide binding]; other site 407976011876 eyelet of channel; other site 407976011877 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 407976011878 Shikimate kinase; Region: SKI; pfam01202 407976011879 ATP-binding site [chemical binding]; other site 407976011880 Gluconate-6-phosphate binding site [chemical binding]; other site 407976011881 low affinity gluconate transporter; Provisional; Region: PRK10472 407976011882 GntP family permease; Region: GntP_permease; pfam02447 407976011883 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 407976011884 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 407976011885 DNA binding site [nucleotide binding] 407976011886 domain linker motif; other site 407976011887 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 407976011888 putative ligand binding site [chemical binding]; other site 407976011889 putative dimerization interface [polypeptide binding]; other site 407976011890 hypothetical protein; Provisional; Region: PRK01254 407976011891 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 407976011892 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 407976011893 MAPEG family; Region: MAPEG; cl09190 407976011894 Uncharacterized conserved protein [Function unknown]; Region: COG2966 407976011895 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 407976011896 Uncharacterized conserved protein [Function unknown]; Region: COG3610 407976011897 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 407976011898 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 407976011899 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 407976011900 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 407976011901 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 407976011902 putative SAM binding site [chemical binding]; other site 407976011903 putative homodimer interface [polypeptide binding]; other site 407976011904 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 407976011905 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 407976011906 putative ligand binding site [chemical binding]; other site 407976011907 hypothetical protein; Reviewed; Region: PRK12497 407976011908 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 407976011909 dimer interface [polypeptide binding]; other site 407976011910 active site 407976011911 outer membrane lipoprotein; Provisional; Region: PRK11023 407976011912 BON domain; Region: BON; pfam04972 407976011913 BON domain; Region: BON; pfam04972 407976011914 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 407976011915 EamA-like transporter family; Region: EamA; pfam00892 407976011916 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 407976011917 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976011918 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 407976011919 dimerization interface [polypeptide binding]; other site 407976011920 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 407976011921 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 407976011922 active site 407976011923 HIGH motif; other site 407976011924 dimer interface [polypeptide binding]; other site 407976011925 KMSKS motif; other site 407976011926 phosphoglycolate phosphatase; Provisional; Region: PRK13222 407976011927 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cl17915 407976011928 motif I; other site 407976011929 active site 407976011930 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 407976011931 motif II; other site 407976011932 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 407976011933 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 407976011934 substrate binding site [chemical binding]; other site 407976011935 hexamer interface [polypeptide binding]; other site 407976011936 metal binding site [ion binding]; metal-binding site 407976011937 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 407976011938 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 407976011939 AAA ATPase domain; Region: AAA_16; pfam13191 407976011940 AAA domain; Region: AAA_22; pfam13401 407976011941 Walker A motif; other site 407976011942 ATP binding site [chemical binding]; other site 407976011943 Walker B motif; other site 407976011944 Sporulation related domain; Region: SPOR; pfam05036 407976011945 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 407976011946 active site 407976011947 dimer interface [polypeptide binding]; other site 407976011948 metal binding site [ion binding]; metal-binding site 407976011949 shikimate kinase; Reviewed; Region: aroK; PRK00131 407976011950 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 407976011951 ADP binding site [chemical binding]; other site 407976011952 magnesium binding site [ion binding]; other site 407976011953 putative shikimate binding site; other site 407976011954 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 407976011955 Secretin and TonB N terminus short domain; Region: STN; smart00965 407976011956 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 407976011957 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 407976011958 Pilus assembly protein, PilP; Region: PilP; pfam04351 407976011959 Pilus assembly protein, PilO; Region: PilO; pfam04350 407976011960 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 407976011961 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 407976011962 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 407976011963 Competence protein A; Region: Competence_A; pfam11104 407976011964 nucleotide binding site [chemical binding]; other site 407976011965 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 407976011966 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 407976011967 Transglycosylase; Region: Transgly; pfam00912 407976011968 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 407976011969 argininosuccinate lyase; Provisional; Region: PRK04833 407976011970 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 407976011971 active sites [active] 407976011972 tetramer interface [polypeptide binding]; other site 407976011973 argininosuccinate synthase; Provisional; Region: PRK13820 407976011974 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 407976011975 ANP binding site [chemical binding]; other site 407976011976 Substrate Binding Site II [chemical binding]; other site 407976011977 Substrate Binding Site I [chemical binding]; other site 407976011978 ornithine carbamoyltransferase; Provisional; Region: PRK14805 407976011979 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 407976011980 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 407976011981 acetylglutamate kinase; Provisional; Region: PRK00942 407976011982 nucleotide binding site [chemical binding]; other site 407976011983 substrate binding site [chemical binding]; other site 407976011984 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 407976011985 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 407976011986 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 407976011987 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 407976011988 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 407976011989 competence damage-inducible protein A; Provisional; Region: PRK00549 407976011990 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 407976011991 putative MPT binding site; other site 407976011992 Competence-damaged protein; Region: CinA; pfam02464 407976011993 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 407976011994 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976011995 catalytic residues [active] 407976011996 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 407976011997 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 407976011998 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 407976011999 catalytic residues [active] 407976012000 central insert; other site 407976012001 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 407976012002 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 407976012003 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 407976012004 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 407976012005 TPR motif; other site 407976012006 binding surface 407976012007 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 407976012008 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 407976012009 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976012010 Walker A/P-loop; other site 407976012011 ATP binding site [chemical binding]; other site 407976012012 Q-loop/lid; other site 407976012013 ABC transporter signature motif; other site 407976012014 Walker B; other site 407976012015 D-loop; other site 407976012016 H-loop/switch region; other site 407976012017 CcmB protein; Region: CcmB; pfam03379 407976012018 heme exporter protein CcmC; Region: ccmC; TIGR01191 407976012019 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 407976012020 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13165 407976012021 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 407976012022 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 407976012023 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 407976012024 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 407976012025 alphaNTD homodimer interface [polypeptide binding]; other site 407976012026 alphaNTD - beta interaction site [polypeptide binding]; other site 407976012027 alphaNTD - beta' interaction site [polypeptide binding]; other site 407976012028 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 407976012029 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 407976012030 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 407976012031 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 407976012032 RNA binding surface [nucleotide binding]; other site 407976012033 30S ribosomal protein S11; Validated; Region: PRK05309 407976012034 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 407976012035 30S ribosomal protein S13; Region: bact_S13; TIGR03631 407976012036 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 407976012037 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 407976012038 SecY translocase; Region: SecY; pfam00344 407976012039 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 407976012040 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 407976012041 23S rRNA binding site [nucleotide binding]; other site 407976012042 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 407976012043 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 407976012044 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 407976012045 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 407976012046 23S rRNA interface [nucleotide binding]; other site 407976012047 L21e interface [polypeptide binding]; other site 407976012048 5S rRNA interface [nucleotide binding]; other site 407976012049 L27 interface [polypeptide binding]; other site 407976012050 L5 interface [polypeptide binding]; other site 407976012051 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 407976012052 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 407976012053 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 407976012054 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 407976012055 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 407976012056 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 407976012057 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 407976012058 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 407976012059 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 407976012060 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 407976012061 RNA binding site [nucleotide binding]; other site 407976012062 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 407976012063 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 407976012064 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 407976012065 23S rRNA interface [nucleotide binding]; other site 407976012066 putative translocon interaction site; other site 407976012067 signal recognition particle (SRP54) interaction site; other site 407976012068 L23 interface [polypeptide binding]; other site 407976012069 trigger factor interaction site; other site 407976012070 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 407976012071 23S rRNA interface [nucleotide binding]; other site 407976012072 5S rRNA interface [nucleotide binding]; other site 407976012073 putative antibiotic binding site [chemical binding]; other site 407976012074 L25 interface [polypeptide binding]; other site 407976012075 L27 interface [polypeptide binding]; other site 407976012076 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 407976012077 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 407976012078 G-X-X-G motif; other site 407976012079 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 407976012080 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 407976012081 putative translocon binding site; other site 407976012082 protein-rRNA interface [nucleotide binding]; other site 407976012083 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 407976012084 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 407976012085 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 407976012086 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 407976012087 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 407976012088 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 407976012089 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 407976012090 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 407976012091 elongation factor Tu; Reviewed; Region: PRK00049 407976012092 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 407976012093 G1 box; other site 407976012094 GEF interaction site [polypeptide binding]; other site 407976012095 GTP/Mg2+ binding site [chemical binding]; other site 407976012096 Switch I region; other site 407976012097 G2 box; other site 407976012098 G3 box; other site 407976012099 Switch II region; other site 407976012100 G4 box; other site 407976012101 G5 box; other site 407976012102 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 407976012103 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 407976012104 Antibiotic Binding Site [chemical binding]; other site 407976012105 elongation factor G; Reviewed; Region: PRK00007 407976012106 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 407976012107 G1 box; other site 407976012108 putative GEF interaction site [polypeptide binding]; other site 407976012109 GTP/Mg2+ binding site [chemical binding]; other site 407976012110 Switch I region; other site 407976012111 G2 box; other site 407976012112 G3 box; other site 407976012113 Switch II region; other site 407976012114 G4 box; other site 407976012115 G5 box; other site 407976012116 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 407976012117 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 407976012118 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 407976012119 30S ribosomal protein S7; Validated; Region: PRK05302 407976012120 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 407976012121 S17 interaction site [polypeptide binding]; other site 407976012122 S8 interaction site; other site 407976012123 16S rRNA interaction site [nucleotide binding]; other site 407976012124 streptomycin interaction site [chemical binding]; other site 407976012125 23S rRNA interaction site [nucleotide binding]; other site 407976012126 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 407976012127 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 407976012128 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 407976012129 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 407976012130 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 407976012131 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 407976012132 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 407976012133 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 407976012134 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 407976012135 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 407976012136 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 407976012137 DNA binding site [nucleotide binding] 407976012138 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 407976012139 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 407976012140 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 407976012141 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 407976012142 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 407976012143 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 407976012144 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 407976012145 RPB3 interaction site [polypeptide binding]; other site 407976012146 RPB1 interaction site [polypeptide binding]; other site 407976012147 RPB11 interaction site [polypeptide binding]; other site 407976012148 RPB10 interaction site [polypeptide binding]; other site 407976012149 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 407976012150 core dimer interface [polypeptide binding]; other site 407976012151 peripheral dimer interface [polypeptide binding]; other site 407976012152 L10 interface [polypeptide binding]; other site 407976012153 L11 interface [polypeptide binding]; other site 407976012154 putative EF-Tu interaction site [polypeptide binding]; other site 407976012155 putative EF-G interaction site [polypeptide binding]; other site 407976012156 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 407976012157 23S rRNA interface [nucleotide binding]; other site 407976012158 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 407976012159 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 407976012160 mRNA/rRNA interface [nucleotide binding]; other site 407976012161 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 407976012162 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 407976012163 23S rRNA interface [nucleotide binding]; other site 407976012164 L7/L12 interface [polypeptide binding]; other site 407976012165 putative thiostrepton binding site; other site 407976012166 L25 interface [polypeptide binding]; other site 407976012167 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 407976012168 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 407976012169 putative homodimer interface [polypeptide binding]; other site 407976012170 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 407976012171 heterodimer interface [polypeptide binding]; other site 407976012172 homodimer interface [polypeptide binding]; other site 407976012173 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 407976012174 elongation factor Tu; Reviewed; Region: PRK00049 407976012175 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 407976012176 G1 box; other site 407976012177 GEF interaction site [polypeptide binding]; other site 407976012178 GTP/Mg2+ binding site [chemical binding]; other site 407976012179 Switch I region; other site 407976012180 G2 box; other site 407976012181 G3 box; other site 407976012182 Switch II region; other site 407976012183 G4 box; other site 407976012184 G5 box; other site 407976012185 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 407976012186 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 407976012187 Antibiotic Binding Site [chemical binding]; other site 407976012188 pantothenate kinase; Provisional; Region: PRK05439 407976012189 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point...; Region: PanK; cd02025 407976012190 ATP-binding site [chemical binding]; other site 407976012191 CoA-binding site [chemical binding]; other site 407976012192 Mg2+-binding site [ion binding]; other site 407976012193 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 407976012194 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 407976012195 dimerization interface [polypeptide binding]; other site 407976012196 putative Zn2+ binding site [ion binding]; other site 407976012197 putative DNA binding site [nucleotide binding]; other site 407976012198 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 407976012199 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 407976012200 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 407976012201 FAD binding domain; Region: FAD_binding_4; pfam01565 407976012202 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 407976012203 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 407976012204 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 407976012205 glutamate racemase; Provisional; Region: PRK00865 407976012206 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 407976012207 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 407976012208 S-adenosylmethionine binding site [chemical binding]; other site 407976012209 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 407976012210 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012211 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 407976012212 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 407976012213 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976012214 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 407976012215 Fatty acid desaturase; Region: FA_desaturase; pfam00487 407976012216 Di-iron ligands [ion binding]; other site 407976012217 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 407976012218 selenophosphate synthetase; Provisional; Region: PRK00943 407976012219 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 407976012220 dimerization interface [polypeptide binding]; other site 407976012221 putative ATP binding site [chemical binding]; other site 407976012222 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 407976012223 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 407976012224 active site residue [active] 407976012225 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 407976012226 putative substrate translocation pore; other site 407976012227 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 407976012228 putative acyl-acceptor binding pocket; other site 407976012229 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976012230 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976012231 WHG domain; Region: WHG; pfam13305 407976012232 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 407976012233 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976012234 Coenzyme A binding pocket [chemical binding]; other site 407976012235 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 407976012236 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 407976012237 active site 407976012238 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976012239 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012240 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976012241 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 407976012242 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976012243 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 407976012244 DNA binding residues [nucleotide binding] 407976012245 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 407976012246 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 407976012247 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 407976012248 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976012249 Walker A/P-loop; other site 407976012250 ATP binding site [chemical binding]; other site 407976012251 Q-loop/lid; other site 407976012252 ABC transporter signature motif; other site 407976012253 Walker B; other site 407976012254 D-loop; other site 407976012255 H-loop/switch region; other site 407976012256 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 407976012257 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 407976012258 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 407976012259 P loop; other site 407976012260 GTP binding site [chemical binding]; other site 407976012261 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 407976012262 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 407976012263 S-adenosylmethionine binding site [chemical binding]; other site 407976012264 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 407976012265 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 407976012266 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 407976012267 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 407976012268 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 407976012269 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976012270 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 407976012271 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 407976012272 B1 nucleotide binding pocket [chemical binding]; other site 407976012273 B2 nucleotide binding pocket [chemical binding]; other site 407976012274 CAS motifs; other site 407976012275 active site 407976012276 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976012277 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012278 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976012279 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 407976012280 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 407976012281 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 407976012282 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 407976012283 aromatic amino acid transport protein; Region: araaP; TIGR00837 407976012284 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 407976012285 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 407976012286 putative acyl-acceptor binding pocket; other site 407976012287 LexA repressor; Validated; Region: PRK00215 407976012288 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 407976012289 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 407976012290 Catalytic site [active] 407976012291 Cell division inhibitor SulA; Region: SulA; cl01880 407976012292 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 407976012293 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00038 407976012294 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 407976012295 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 407976012296 Cytochrome c; Region: Cytochrom_C; pfam00034 407976012297 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 407976012298 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 407976012299 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 407976012300 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 407976012301 Subunit I/III interface [polypeptide binding]; other site 407976012302 D-pathway; other site 407976012303 Subunit I/VIIc interface [polypeptide binding]; other site 407976012304 Subunit I/IV interface [polypeptide binding]; other site 407976012305 Subunit I/II interface [polypeptide binding]; other site 407976012306 Low-spin heme (heme a) binding site [chemical binding]; other site 407976012307 Subunit I/VIIa interface [polypeptide binding]; other site 407976012308 Subunit I/VIa interface [polypeptide binding]; other site 407976012309 Dimer interface; other site 407976012310 Putative water exit pathway; other site 407976012311 Binuclear center (heme a3/CuB) [ion binding]; other site 407976012312 K-pathway; other site 407976012313 Subunit I/Vb interface [polypeptide binding]; other site 407976012314 Putative proton exit pathway; other site 407976012315 Subunit I/VIb interface; other site 407976012316 Subunit I/VIc interface [polypeptide binding]; other site 407976012317 Electron transfer pathway; other site 407976012318 Subunit I/VIIIb interface [polypeptide binding]; other site 407976012319 Subunit I/VIIb interface [polypeptide binding]; other site 407976012320 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 407976012321 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 407976012322 Subunit III/VIIa interface [polypeptide binding]; other site 407976012323 Phospholipid binding site [chemical binding]; other site 407976012324 Subunit I/III interface [polypeptide binding]; other site 407976012325 Subunit III/VIb interface [polypeptide binding]; other site 407976012326 Subunit III/VIa interface; other site 407976012327 Subunit III/Vb interface [polypeptide binding]; other site 407976012328 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 407976012329 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 407976012330 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 407976012331 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 407976012332 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 407976012333 UbiA prenyltransferase family; Region: UbiA; pfam01040 407976012334 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 407976012335 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 407976012336 Cu(I) binding site [ion binding]; other site 407976012337 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 407976012338 putative active site [active] 407976012339 putative metal binding site [ion binding]; other site 407976012340 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 407976012341 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 407976012342 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 407976012343 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 407976012344 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 407976012345 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 407976012346 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 407976012347 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 407976012348 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 407976012349 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 407976012350 Sulfatase; Region: Sulfatase; pfam00884 407976012351 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 407976012352 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 407976012353 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 407976012354 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 407976012355 RNA binding site [nucleotide binding]; other site 407976012356 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 407976012357 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 407976012358 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 407976012359 Response regulator receiver domain; Region: Response_reg; pfam00072 407976012360 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 407976012361 active site 407976012362 phosphorylation site [posttranslational modification] 407976012363 intermolecular recognition site; other site 407976012364 dimerization interface [polypeptide binding]; other site 407976012365 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976012366 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976012367 metal binding site [ion binding]; metal-binding site 407976012368 active site 407976012369 I-site; other site 407976012370 CHASE domain; Region: CHASE; pfam03924 407976012371 PAS domain S-box; Region: sensory_box; TIGR00229 407976012372 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 407976012373 putative active site [active] 407976012374 heme pocket [chemical binding]; other site 407976012375 PAS domain; Region: PAS_9; pfam13426 407976012376 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 407976012377 putative active site [active] 407976012378 heme pocket [chemical binding]; other site 407976012379 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 407976012380 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 407976012381 putative active site [active] 407976012382 heme pocket [chemical binding]; other site 407976012383 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 407976012384 putative active site [active] 407976012385 heme pocket [chemical binding]; other site 407976012386 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976012387 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 407976012388 dimer interface [polypeptide binding]; other site 407976012389 phosphorylation site [posttranslational modification] 407976012390 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 407976012391 ATP binding site [chemical binding]; other site 407976012392 Mg2+ binding site [ion binding]; other site 407976012393 G-X-G motif; other site 407976012394 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976012395 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 407976012396 active site 407976012397 phosphorylation site [posttranslational modification] 407976012398 intermolecular recognition site; other site 407976012399 dimerization interface [polypeptide binding]; other site 407976012400 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 407976012401 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 407976012402 active site 407976012403 phosphorylation site [posttranslational modification] 407976012404 intermolecular recognition site; other site 407976012405 dimerization interface [polypeptide binding]; other site 407976012406 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 407976012407 osmolarity response regulator; Provisional; Region: ompR; PRK09468 407976012408 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 407976012409 active site 407976012410 phosphorylation site [posttranslational modification] 407976012411 intermolecular recognition site; other site 407976012412 dimerization interface [polypeptide binding]; other site 407976012413 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 407976012414 DNA binding site [nucleotide binding] 407976012415 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 407976012416 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 407976012417 dimerization interface [polypeptide binding]; other site 407976012418 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 407976012419 dimer interface [polypeptide binding]; other site 407976012420 phosphorylation site [posttranslational modification] 407976012421 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 407976012422 ATP binding site [chemical binding]; other site 407976012423 Mg2+ binding site [ion binding]; other site 407976012424 G-X-G motif; other site 407976012425 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 407976012426 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 407976012427 dimerization interface [polypeptide binding]; other site 407976012428 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 407976012429 dimer interface [polypeptide binding]; other site 407976012430 putative CheW interface [polypeptide binding]; other site 407976012431 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 407976012432 catalytic triad [active] 407976012433 dimer interface [polypeptide binding]; other site 407976012434 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 407976012435 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 407976012436 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 407976012437 active site 407976012438 phosphorylation site [posttranslational modification] 407976012439 intermolecular recognition site; other site 407976012440 dimerization interface [polypeptide binding]; other site 407976012441 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 407976012442 DNA binding site [nucleotide binding] 407976012443 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 407976012444 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 407976012445 ATP binding site [chemical binding]; other site 407976012446 Mg2+ binding site [ion binding]; other site 407976012447 G-X-G motif; other site 407976012448 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 407976012449 MASE1; Region: MASE1; cl17823 407976012450 CHASE domain; Region: CHASE; pfam03924 407976012451 PAS domain S-box; Region: sensory_box; TIGR00229 407976012452 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 407976012453 putative active site [active] 407976012454 heme pocket [chemical binding]; other site 407976012455 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 407976012456 PAS domain; Region: PAS_9; pfam13426 407976012457 putative active site [active] 407976012458 heme pocket [chemical binding]; other site 407976012459 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 407976012460 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976012461 metal binding site [ion binding]; metal-binding site 407976012462 active site 407976012463 I-site; other site 407976012464 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 407976012465 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 407976012466 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 407976012467 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 407976012468 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 407976012469 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 407976012470 D-pathway; other site 407976012471 Putative ubiquinol binding site [chemical binding]; other site 407976012472 Low-spin heme (heme b) binding site [chemical binding]; other site 407976012473 Putative water exit pathway; other site 407976012474 Binuclear center (heme o3/CuB) [ion binding]; other site 407976012475 K-pathway; other site 407976012476 Putative proton exit pathway; other site 407976012477 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 407976012478 Subunit I/III interface [polypeptide binding]; other site 407976012479 Subunit III/IV interface [polypeptide binding]; other site 407976012480 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 407976012481 protoheme IX farnesyltransferase; Provisional; Region: PRK13362 407976012482 UbiA prenyltransferase family; Region: UbiA; pfam01040 407976012483 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 407976012484 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 407976012485 catalytic residues [active] 407976012486 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 407976012487 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 407976012488 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 407976012489 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 407976012490 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 407976012491 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 407976012492 DsbD alpha interface [polypeptide binding]; other site 407976012493 catalytic residues [active] 407976012494 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 407976012495 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 407976012496 NAD(P) binding site [chemical binding]; other site 407976012497 active site 407976012498 Transcriptional regulator [Transcription]; Region: LysR; COG0583 407976012499 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 407976012500 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_6; cd08475 407976012501 putative effector binding pocket; other site 407976012502 putative dimerization interface [polypeptide binding]; other site 407976012503 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 407976012504 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 407976012505 trimer interface [polypeptide binding]; other site 407976012506 active site 407976012507 substrate binding site [chemical binding]; other site 407976012508 CoA binding site [chemical binding]; other site 407976012509 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 407976012510 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 407976012511 substrate binding pocket [chemical binding]; other site 407976012512 membrane-bound complex binding site; other site 407976012513 hinge residues; other site 407976012514 RNA polymerase sigma factor; Provisional; Region: PRK12528 407976012515 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 407976012516 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 407976012517 DNA binding residues [nucleotide binding] 407976012518 fec operon regulator FecR; Reviewed; Region: PRK09774 407976012519 FecR protein; Region: FecR; pfam04773 407976012520 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 407976012521 Secretin and TonB N terminus short domain; Region: STN; smart00965 407976012522 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 407976012523 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 407976012524 N-terminal plug; other site 407976012525 ligand-binding site [chemical binding]; other site 407976012526 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 407976012527 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 407976012528 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 407976012529 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 407976012530 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 407976012531 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 407976012532 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 407976012533 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 407976012534 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 407976012535 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 407976012536 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976012537 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012538 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976012539 Protein of unknown function (DUF2384); Region: DUF2384; cl17718 407976012540 Fic family protein [Function unknown]; Region: COG3177 407976012541 Fic/DOC family; Region: Fic; pfam02661 407976012542 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 407976012543 putative DNA binding site [nucleotide binding]; other site 407976012544 putative Zn2+ binding site [ion binding]; other site 407976012545 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976012546 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 407976012547 non-specific DNA binding site [nucleotide binding]; other site 407976012548 salt bridge; other site 407976012549 sequence-specific DNA binding site [nucleotide binding]; other site 407976012550 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976012551 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012552 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976012553 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976012554 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 407976012555 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 407976012556 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012557 CRISPR/Cas system-associated RAMP superfamily protein Csy3; Region: Csy3_I-F; cd09737 407976012558 CRISPR/Cas system-associated RAMP superfamily protein Csy2; Region: Csy2_I-F; cl12127 407976012559 TniQ; Region: TniQ; pfam06527 407976012560 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 407976012561 HsdM N-terminal domain; Region: HsdM_N; pfam12161 407976012562 Methyltransferase domain; Region: Methyltransf_26; pfam13659 407976012563 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 407976012564 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976012565 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976012566 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 407976012567 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 407976012568 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 407976012569 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 407976012570 ATP binding site [chemical binding]; other site 407976012571 putative Mg++ binding site [ion binding]; other site 407976012572 Transposase; Region: HTH_Tnp_1; pfam01527 407976012573 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 407976012574 putative transposase OrfB; Reviewed; Region: PHA02517 407976012575 HTH-like domain; Region: HTH_21; pfam13276 407976012576 Integrase core domain; Region: rve; pfam00665 407976012577 Integrase core domain; Region: rve_2; pfam13333 407976012578 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; pfam09907 407976012579 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 407976012580 Domain of unknown function (DUF955); Region: DUF955; pfam06114 407976012581 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976012582 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 407976012583 non-specific DNA binding site [nucleotide binding]; other site 407976012584 salt bridge; other site 407976012585 sequence-specific DNA binding site [nucleotide binding]; other site 407976012586 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 407976012587 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 407976012588 ATP binding site [chemical binding]; other site 407976012589 putative Mg++ binding site [ion binding]; other site 407976012590 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; cl17351 407976012591 AAA domain; Region: AAA_22; pfam13401 407976012592 Bacterial TniB protein; Region: TniB; pfam05621 407976012593 Integrase core domain; Region: rve; pfam00665 407976012594 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 407976012595 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 407976012596 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 407976012597 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 407976012598 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976012599 metal binding site [ion binding]; metal-binding site 407976012600 active site 407976012601 I-site; other site 407976012602 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 407976012603 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 407976012604 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 407976012605 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 407976012606 N-acetyl-D-glucosamine binding site [chemical binding]; other site 407976012607 catalytic residue [active] 407976012608 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 407976012609 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 407976012610 AbgT putative transporter family; Region: ABG_transport; pfam03806 407976012611 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 407976012612 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 407976012613 Protein export membrane protein; Region: SecD_SecF; cl14618 407976012614 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 407976012615 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976012616 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976012617 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 407976012618 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 407976012619 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 407976012620 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 407976012621 C-terminal domain interface [polypeptide binding]; other site 407976012622 GSH binding site (G-site) [chemical binding]; other site 407976012623 dimer interface [polypeptide binding]; other site 407976012624 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 407976012625 N-terminal domain interface [polypeptide binding]; other site 407976012626 dimer interface [polypeptide binding]; other site 407976012627 substrate binding pocket (H-site) [chemical binding]; other site 407976012628 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 407976012629 active site 407976012630 oligopeptidase A; Provisional; Region: PRK10911 407976012631 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 407976012632 active site 407976012633 Zn binding site [ion binding]; other site 407976012634 glutathione reductase; Validated; Region: PRK06116 407976012635 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 407976012636 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 407976012637 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 407976012638 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 407976012639 active site 407976012640 catalytic residues [active] 407976012641 DNA binding site [nucleotide binding] 407976012642 Int/Topo IB signature motif; other site 407976012643 TIR domain; Region: TIR_2; pfam13676 407976012644 TIR domain; Region: TIR_2; pfam13676 407976012645 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 407976012646 TIR domain; Region: TIR_2; pfam13676 407976012647 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 407976012648 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 407976012649 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 407976012650 HlyD family secretion protein; Region: HlyD_3; pfam13437 407976012651 Fusaric acid resistance protein family; Region: FUSC; pfam04632 407976012652 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 407976012653 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 407976012654 Na binding site [ion binding]; other site 407976012655 gamma-glutamyl kinase; Provisional; Region: PRK13402 407976012656 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 407976012657 nucleotide binding site [chemical binding]; other site 407976012658 homotetrameric interface [polypeptide binding]; other site 407976012659 putative phosphate binding site [ion binding]; other site 407976012660 putative allosteric binding site; other site 407976012661 PUA domain; Region: PUA; cl00607 407976012662 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 407976012663 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 407976012664 putative catalytic cysteine [active] 407976012665 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 407976012666 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 407976012667 non-specific DNA binding site [nucleotide binding]; other site 407976012668 salt bridge; other site 407976012669 sequence-specific DNA binding site [nucleotide binding]; other site 407976012670 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 407976012671 malate synthase; Provisional; Region: PRK08951 407976012672 Predicted membrane protein [Function unknown]; Region: COG2855 407976012673 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 407976012674 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 407976012675 DNA binding residues [nucleotide binding] 407976012676 dimerization interface [polypeptide binding]; other site 407976012677 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 407976012678 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 407976012679 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 407976012680 Paraquat-inducible protein A; Region: PqiA; pfam04403 407976012681 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 407976012682 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 407976012683 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 407976012684 Zn2+ binding site [ion binding]; other site 407976012685 Mg2+ binding site [ion binding]; other site 407976012686 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 407976012687 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 407976012688 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 407976012689 Walker A/P-loop; other site 407976012690 ATP binding site [chemical binding]; other site 407976012691 Q-loop/lid; other site 407976012692 ABC transporter signature motif; other site 407976012693 Walker B; other site 407976012694 D-loop; other site 407976012695 H-loop/switch region; other site 407976012696 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976012697 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 407976012698 Walker A/P-loop; other site 407976012699 ATP binding site [chemical binding]; other site 407976012700 Q-loop/lid; other site 407976012701 ABC transporter signature motif; other site 407976012702 Walker B; other site 407976012703 D-loop; other site 407976012704 H-loop/switch region; other site 407976012705 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 407976012706 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 407976012707 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 407976012708 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 407976012709 chorismate binding enzyme; Region: Chorismate_bind; cl10555 407976012710 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 407976012711 hypothetical protein; Provisional; Region: PRK11212 407976012712 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 407976012713 Coenzyme A binding pocket [chemical binding]; other site 407976012714 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 407976012715 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 407976012716 dimer interface [polypeptide binding]; other site 407976012717 phosphorylation site [posttranslational modification] 407976012718 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 407976012719 ATP binding site [chemical binding]; other site 407976012720 G-X-G motif; other site 407976012721 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 407976012722 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 407976012723 active site 407976012724 phosphorylation site [posttranslational modification] 407976012725 intermolecular recognition site; other site 407976012726 dimerization interface [polypeptide binding]; other site 407976012727 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 407976012728 Walker A motif; other site 407976012729 ATP binding site [chemical binding]; other site 407976012730 Walker B motif; other site 407976012731 arginine finger; other site 407976012732 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 407976012733 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 407976012734 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 407976012735 dimerization interface [polypeptide binding]; other site 407976012736 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 407976012737 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 407976012738 dimer interface [polypeptide binding]; other site 407976012739 conserved gate region; other site 407976012740 putative PBP binding loops; other site 407976012741 ABC-ATPase subunit interface; other site 407976012742 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 407976012743 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976012744 Walker A/P-loop; other site 407976012745 ATP binding site [chemical binding]; other site 407976012746 Q-loop/lid; other site 407976012747 ABC transporter signature motif; other site 407976012748 Walker B; other site 407976012749 D-loop; other site 407976012750 H-loop/switch region; other site 407976012751 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 407976012752 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 407976012753 GTP binding site; other site 407976012754 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 407976012755 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 407976012756 Walker A motif; other site 407976012757 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 407976012758 dimer interface [polypeptide binding]; other site 407976012759 putative functional site; other site 407976012760 putative MPT binding site; other site 407976012761 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 407976012762 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 407976012763 FeS/SAM binding site; other site 407976012764 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 407976012765 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 407976012766 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 407976012767 DNA binding site [nucleotide binding] 407976012768 catalytic residue [active] 407976012769 H2TH interface [polypeptide binding]; other site 407976012770 putative catalytic residues [active] 407976012771 turnover-facilitating residue; other site 407976012772 intercalation triad [nucleotide binding]; other site 407976012773 8OG recognition residue [nucleotide binding]; other site 407976012774 putative reading head residues; other site 407976012775 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 407976012776 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 407976012777 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 407976012778 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 407976012779 Uncharacterized conserved protein [Function unknown]; Region: COG0398 407976012780 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 407976012781 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 407976012782 Ligand binding site; other site 407976012783 Putative Catalytic site; other site 407976012784 DXD motif; other site 407976012785 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 407976012786 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 407976012787 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 407976012788 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 407976012789 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 407976012790 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 407976012791 putative NAD(P) binding site [chemical binding]; other site 407976012792 active site 407976012793 putative substrate binding site [chemical binding]; other site 407976012794 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 407976012795 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 407976012796 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 407976012797 active site 407976012798 (T/H)XGH motif; other site 407976012799 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 407976012800 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 407976012801 putative ADP-binding pocket [chemical binding]; other site 407976012802 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 407976012803 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 407976012804 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 407976012805 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 407976012806 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 407976012807 putative ADP-binding pocket [chemical binding]; other site 407976012808 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 407976012809 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 407976012810 putative active site [active] 407976012811 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 407976012812 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 407976012813 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 407976012814 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 407976012815 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 407976012816 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 407976012817 Bacterial transcriptional repressor; Region: TetR; pfam13972 407976012818 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 407976012819 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 407976012820 substrate-cofactor binding pocket; other site 407976012821 pyridoxal 5'-phosphate binding site [chemical binding]; other site 407976012822 catalytic residue [active] 407976012823 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 407976012824 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 407976012825 NAD(P) binding site [chemical binding]; other site 407976012826 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 407976012827 active site residue [active] 407976012828 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 407976012829 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 407976012830 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 407976012831 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 407976012832 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 407976012833 conserved cys residue [active] 407976012834 DNA polymerase I; Provisional; Region: PRK05755 407976012835 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 407976012836 active site 407976012837 metal binding site 1 [ion binding]; metal-binding site 407976012838 putative 5' ssDNA interaction site; other site 407976012839 metal binding site 3; metal-binding site 407976012840 metal binding site 2 [ion binding]; metal-binding site 407976012841 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 407976012842 putative DNA binding site [nucleotide binding]; other site 407976012843 putative metal binding site [ion binding]; other site 407976012844 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 407976012845 active site 407976012846 catalytic site [active] 407976012847 substrate binding site [chemical binding]; other site 407976012848 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 407976012849 active site 407976012850 DNA binding site [nucleotide binding] 407976012851 catalytic site [active] 407976012852 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 407976012853 G1 box; other site 407976012854 GTP/Mg2+ binding site [chemical binding]; other site 407976012855 Switch I region; other site 407976012856 G2 box; other site 407976012857 G3 box; other site 407976012858 Switch II region; other site 407976012859 G4 box; other site 407976012860 G5 box; other site 407976012861 Cytochrome c553 [Energy production and conversion]; Region: COG2863 407976012862 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 407976012863 Cytochrome c; Region: Cytochrom_C; cl11414 407976012864 Methyltransferase domain; Region: Methyltransf_12; pfam08242 407976012865 Methyltransferase domain; Region: Methyltransf_23; pfam13489 407976012866 Der GTPase activator (YihI); Region: YihI; pfam04220 407976012867 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 407976012868 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 407976012869 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 407976012870 FeS/SAM binding site; other site 407976012871 HemN C-terminal domain; Region: HemN_C; pfam06969 407976012872 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 407976012873 adenosine deaminase; Provisional; Region: PRK09358 407976012874 active site 407976012875 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 407976012876 lysophospholipase L2; Provisional; Region: PRK10749 407976012877 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 407976012878 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 407976012879 PAS fold; Region: PAS_3; pfam08447 407976012880 putative active site [active] 407976012881 heme pocket [chemical binding]; other site 407976012882 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 407976012883 metal binding site [ion binding]; metal-binding site 407976012884 active site 407976012885 I-site; other site 407976012886 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 407976012887 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 407976012888 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 407976012889 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 407976012890 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 407976012891 substrate binding site [chemical binding]; other site 407976012892 oxyanion hole (OAH) forming residues; other site 407976012893 trimer interface [polypeptide binding]; other site 407976012894 Predicted membrane protein [Function unknown]; Region: COG3205 407976012895 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 407976012896 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 407976012897 glutaminase active site [active] 407976012898 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 407976012899 dimer interface [polypeptide binding]; other site 407976012900 active site 407976012901 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 407976012902 dimer interface [polypeptide binding]; other site 407976012903 active site 407976012904 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 407976012905 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 407976012906 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 407976012907 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 407976012908 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 407976012909 N-terminal plug; other site 407976012910 ligand-binding site [chemical binding]; other site 407976012911 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 407976012912 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 407976012913 Substrate binding site; other site 407976012914 Mg++ binding site; other site 407976012915 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 407976012916 active site 407976012917 substrate binding site [chemical binding]; other site 407976012918 CoA binding site [chemical binding]; other site 407976012919 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 407976012920 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 407976012921 gamma subunit interface [polypeptide binding]; other site 407976012922 epsilon subunit interface [polypeptide binding]; other site 407976012923 LBP interface [polypeptide binding]; other site 407976012924 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 407976012925 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 407976012926 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 407976012927 alpha subunit interaction interface [polypeptide binding]; other site 407976012928 Walker A motif; other site 407976012929 ATP binding site [chemical binding]; other site 407976012930 Walker B motif; other site 407976012931 inhibitor binding site; inhibition site 407976012932 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 407976012933 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 407976012934 core domain interface [polypeptide binding]; other site 407976012935 delta subunit interface [polypeptide binding]; other site 407976012936 epsilon subunit interface [polypeptide binding]; other site 407976012937 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 407976012938 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 407976012939 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 407976012940 beta subunit interaction interface [polypeptide binding]; other site 407976012941 Walker A motif; other site 407976012942 ATP binding site [chemical binding]; other site 407976012943 Walker B motif; other site 407976012944 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 407976012945 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 407976012946 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 407976012947 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 407976012948 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 407976012949 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 407976012950 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 407976012951 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 407976012952 F0F1 ATP synthase subunit I; Validated; Region: PRK05760 407976012953 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 407976012954 ParB-like nuclease domain; Region: ParBc; pfam02195 407976012955 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 407976012956 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 407976012957 P-loop; other site 407976012958 Magnesium ion binding site [ion binding]; other site 407976012959 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 407976012960 Magnesium ion binding site [ion binding]; other site 407976012961 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 407976012962 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 407976012963 S-adenosylmethionine binding site [chemical binding]; other site 407976012964 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 407976012965 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 407976012966 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 407976012967 FMN-binding protein MioC; Provisional; Region: PRK09004 407976012968 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 407976012969 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 407976012970 trmE is a tRNA modification GTPase; Region: trmE; cd04164 407976012971 G1 box; other site 407976012972 GTP/Mg2+ binding site [chemical binding]; other site 407976012973 Switch I region; other site 407976012974 G2 box; other site 407976012975 Switch II region; other site 407976012976 G3 box; other site 407976012977 G4 box; other site 407976012978 G5 box; other site 407976012979 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 407976012980 membrane protein insertase; Provisional; Region: PRK01318 407976012981 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 407976012982 Haemolytic domain; Region: Haemolytic; pfam01809 407976012983 ribonuclease P; Reviewed; Region: rnpA; PRK01732 407976012984 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 407976012985 bifunctional antitoxin/transcriptional repressor RelB; Provisional; Region: PRK11235 407976012986 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 407976012987 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 407976012988 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976012989 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 407976012990 Transposase; Region: DEDD_Tnp_IS110; pfam01548 407976012991 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 407976012992 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 407976012993 Homeodomain-like domain; Region: HTH_32; pfam13565 407976012994 Integrase core domain; Region: rve; pfam00665 407976012995 Integrase core domain; Region: rve_3; cl15866 407976012996 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 407976012997 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 407976012998 Integrase core domain; Region: rve; pfam00665 407976012999 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 407976013000 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 407976013001 catalytic residues [active] 407976013002 catalytic nucleophile [active] 407976013003 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 407976013004 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 407976013005 Integrase core domain; Region: rve; pfam00665 407976013006 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 407976013007 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 407976013008 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 407976013009 P-loop; other site 407976013010 Magnesium ion binding site [ion binding]; other site 407976013011 Peptidase M66; Region: Peptidase_M66; pfam10462 407976013012 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 407976013013 multiple promoter invertase; Provisional; Region: mpi; PRK13413 407976013014 catalytic residues [active] 407976013015 catalytic nucleophile [active] 407976013016 Presynaptic Site I dimer interface [polypeptide binding]; other site 407976013017 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 407976013018 Synaptic Flat tetramer interface [polypeptide binding]; other site 407976013019 Synaptic Site I dimer interface [polypeptide binding]; other site 407976013020 DNA binding site [nucleotide binding] 407976013021 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 407976013022 DNA-binding interface [nucleotide binding]; DNA binding site 407976013023 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 407976013024 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 407976013025 multiple promoter invertase; Provisional; Region: mpi; PRK13413 407976013026 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 407976013027 catalytic residues [active] 407976013028 catalytic nucleophile [active] 407976013029 RES domain; Region: RES; cl02411 407976013030 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 407976013031 RNA binding site [nucleotide binding]; other site 407976013032 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second...; Region: TopoII_MutL_Trans; cl02783 407976013033 ATP binding site [chemical binding]; other site 407976013034 Tic22-like family; Region: Tic22; cl04468 407976013035 MarR family; Region: MarR_2; cl17246 407976013036 ParB family; Region: ParB; pfam08775 407976013037 plasmid partitioning protein RepA; Region: partition_RepA; TIGR03453 407976013038 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 407976013039 P-loop; other site 407976013040 Magnesium ion binding site [ion binding]; other site 407976013041 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 407976013042 Magnesium ion binding site [ion binding]; other site 407976013043 Helix-turn-helix domains; Region: HTH; cl00088 407976013044 TraY domain; Region: TraY; pfam05509 407976013045 TraA; Region: TraA; cl11503 407976013046 TraL protein; Region: TraL; pfam07178 407976013047 TraE protein; Region: TraE; pfam05309 407976013048 TraK protein; Region: TraK; pfam06586 407976013049 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 407976013050 conjugal transfer pilus assembly protein TraB; Provisional; Region: PRK13729 407976013051 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 407976013052 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 407976013053 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 407976013054 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 407976013055 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 407976013056 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 407976013057 Walker A motif; other site 407976013058 ATP binding site [chemical binding]; other site 407976013059 Type-F conjugative transfer system protein (TrbI_Ftype); Region: TrbI_Ftype; pfam09677 407976013060 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 407976013061 TraU protein; Region: TraU; cl06067 407976013062 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 407976013063 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 407976013064 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 407976013065 F plasmid transfer operon protein; Region: TraF; pfam13728 407976013066 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 407976013067 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 407976013068 catalytic residues [active] 407976013069 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 407976013070 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 407976013071 type IV conjugative transfer system coupling protein TraD; Region: TraD_Ftype; TIGR02759 407976013072 F sex factor protein N terminal; Region: TraD_N; pfam12615 407976013073 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 407976013074 Walker A motif; other site 407976013075 ATP binding site [chemical binding]; other site 407976013076 Walker B motif; other site 407976013077 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 407976013078 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 407976013079 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 407976013080 AAA domain; Region: AAA_30; pfam13604 407976013081 Toprim domain; Region: Toprim_3; pfam13362 407976013082 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 407976013083 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 407976013084 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 407976013085 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976013086 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976013087 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 407976013088 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976013089 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 407976013090 active site 407976013091 catalytic residues [active] 407976013092 DNA binding site [nucleotide binding] 407976013093 Int/Topo IB signature motif; other site 407976013094 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 407976013095 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 407976013096 active site 407976013097 DNA binding site [nucleotide binding] 407976013098 Int/Topo IB signature motif; other site 407976013099 polyketide-type polyunsaturated fatty acid synthase PfaA; Region: omega_3_PfaA; TIGR02813 407976013100 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 407976013101 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 407976013102 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 407976013103 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 407976013104 Protein of unknown function (DUF1778); Region: DUF1778; pfam08681 407976013105 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 407976013106 ParB-like nuclease domain; Region: ParB; smart00470 407976013107 Transposase; Region: HTH_Tnp_1; pfam01527 407976013108 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 407976013109 putative transposase OrfB; Reviewed; Region: PHA02517 407976013110 HTH-like domain; Region: HTH_21; pfam13276 407976013111 Integrase core domain; Region: rve; pfam00665 407976013112 Integrase core domain; Region: rve_2; pfam13333 407976013113 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 407976013114 Integrase core domain; Region: rve; pfam00665 407976013115 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 407976013116 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 407976013117 Walker A motif; other site 407976013118 ATP binding site [chemical binding]; other site 407976013119 Walker B motif; other site 407976013120 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 407976013121 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 407976013122 P-loop; other site 407976013123 Magnesium ion binding site [ion binding]; other site 407976013124 Peptidase M66; Region: Peptidase_M66; pfam10462 407976013125 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 407976013126 multiple promoter invertase; Provisional; Region: mpi; PRK13413 407976013127 catalytic residues [active] 407976013128 catalytic nucleophile [active] 407976013129 Presynaptic Site I dimer interface [polypeptide binding]; other site 407976013130 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 407976013131 Synaptic Flat tetramer interface [polypeptide binding]; other site 407976013132 Synaptic Site I dimer interface [polypeptide binding]; other site 407976013133 DNA binding site [nucleotide binding] 407976013134 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 407976013135 DNA-binding interface [nucleotide binding]; DNA binding site 407976013136 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 407976013137 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 407976013138 Hok/gef family; Region: HOK_GEF; pfam01848 407976013139 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 407976013140 non-specific DNA binding site [nucleotide binding]; other site 407976013141 Predicted transcriptional regulator [Transcription]; Region: COG2932 407976013142 salt bridge; other site 407976013143 sequence-specific DNA binding site [nucleotide binding]; other site 407976013144 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 407976013145 Catalytic site [active] 407976013146 TraY domain; Region: TraY; pfam05509 407976013147 type IV conjugative transfer system pilin TraA; Region: TraA_TIGR; TIGR02758 407976013148 TraL protein; Region: TraL; pfam07178 407976013149 TraE protein; Region: TraE; pfam05309 407976013150 TraK protein; Region: TraK; pfam06586 407976013151 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 407976013152 conjugal transfer pilus assembly protein TraB; Provisional; Region: PRK13729 407976013153 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 407976013154 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 407976013155 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 407976013156 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 407976013157 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 407976013158 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 407976013159 Walker A motif; other site 407976013160 ATP binding site [chemical binding]; other site 407976013161 Type-F conjugative transfer system protein (TrbI_Ftype); Region: TrbI_Ftype; pfam09677 407976013162 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 407976013163 TraU protein; Region: TraU; cl06067 407976013164 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 407976013165 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 407976013166 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 407976013167 F plasmid transfer operon protein; Region: TraF; pfam13728 407976013168 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 407976013169 catalytic residues [active] 407976013170 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 407976013171 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 407976013172 type IV conjugative transfer system coupling protein TraD; Region: TraD_Ftype; TIGR02759 407976013173 F sex factor protein N terminal; Region: TraD_N; pfam12615 407976013174 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 407976013175 Walker A motif; other site 407976013176 ATP binding site [chemical binding]; other site 407976013177 Walker B motif; other site 407976013178 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 407976013179 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 407976013180 AAA domain; Region: AAA_30; pfam13604 407976013181 Toprim domain; Region: Toprim_3; pfam13362 407976013182 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 407976013183 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 407976013184 Protein of unknown function, DUF462; Region: DUF462; cl01190 407976013185 ParB-like nuclease domain; Region: ParBc; pfam02195 407976013186 Domain of unknown function (DUF3560); Region: DUF3560; pfam12083 407976013187 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 407976013188 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 407976013189 Protein of unknown function, DUF462; Region: DUF462; cl01190 407976013190 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 407976013191 Helix-turn-helix domain; Region: HTH_38; pfam13936 407976013192 Integrase core domain; Region: rve; pfam00665 407976013193 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 407976013194 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 407976013195 AAA domain; Region: AAA_30; pfam13604 407976013196 AAA domain; Region: AAA_30; pfam13604 407976013197 Toprim domain; Region: Toprim_3; pfam13362 407976013198 type IV conjugative transfer system coupling protein TraD; Region: TraD_Ftype; TIGR02759 407976013199 F sex factor protein N terminal; Region: TraD_N; pfam12615 407976013200 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 407976013201 Walker A motif; other site 407976013202 ATP binding site [chemical binding]; other site 407976013203 Walker B motif; other site 407976013204 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 407976013205 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 407976013206 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 407976013207 catalytic residues [active] 407976013208 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 407976013209 F plasmid transfer operon protein; Region: TraF; pfam13728 407976013210 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 407976013211 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 407976013212 TraU protein; Region: TraU; cl06067 407976013213 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 407976013214 Type-F conjugative transfer system protein (TrbI_Ftype); Region: TrbI_Ftype; pfam09677 407976013215 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 407976013216 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 407976013217 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 407976013218 Walker A motif; other site 407976013219 ATP binding site [chemical binding]; other site 407976013220 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 407976013221 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 407976013222 conjugal transfer pilus assembly protein TraB; Provisional; Region: PRK13729 407976013223 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 407976013224 TraK protein; Region: TraK; pfam06586 407976013225 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 407976013226 TraE protein; Region: TraE; pfam05309 407976013227 TraL protein; Region: TraL; pfam07178 407976013228 type IV conjugative transfer system pilin TraA; Region: TraA_TIGR; TIGR02758 407976013229 TraY domain; Region: TraY; pfam05509 407976013230 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 407976013231 non-specific DNA binding site [nucleotide binding]; other site 407976013232 salt bridge; other site 407976013233 sequence-specific DNA binding site [nucleotide binding]; other site 407976013234 Predicted transcriptional regulator [Transcription]; Region: COG2932 407976013235 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 407976013236 Catalytic site [active] 407976013237 Hok/gef family; Region: HOK_GEF; pfam01848 407976013238 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 407976013239 S-adenosylmethionine binding site [chemical binding]; other site 407976013240 SIR2-like domain; Region: SIR2_2; pfam13289 407976013241 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976013242 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 407976013243 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976013244 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 407976013245 Methyltransferase domain; Region: Methyltransf_26; pfam13659 407976013246 AAA domain; Region: AAA_21; pfam13304 407976013247 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 407976013248 ABC transporter signature motif; other site 407976013249 Walker B; other site 407976013250 D-loop; other site 407976013251 H-loop/switch region; other site 407976013252 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 407976013253 DEAD-like helicases superfamily; Region: DEXDc; smart00487 407976013254 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 407976013255 ATP binding site [chemical binding]; other site 407976013256 putative Mg++ binding site [ion binding]; other site 407976013257 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; cl17351 407976013258 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 407976013259 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 407976013260 non-specific DNA binding site [nucleotide binding]; other site 407976013261 salt bridge; other site 407976013262 sequence-specific DNA binding site [nucleotide binding]; other site 407976013263 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 407976013264 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 407976013265 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 407976013266 catalytic residues [active] 407976013267 catalytic nucleophile [active] 407976013268 ParA-like protein; Provisional; Region: PHA02518 407976013269 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 407976013270 P-loop; other site 407976013271 Magnesium ion binding site [ion binding]; other site 407976013272 bifunctional antitoxin/transcriptional repressor RelB; Provisional; Region: PRK11235 407976013273 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 407976013274 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 407976013275 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 407976013276 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 407976013277 ATP binding site [chemical binding]; other site 407976013278 putative Mg++ binding site [ion binding]; other site 407976013279 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 407976013280 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_4; pfam14281 407976013281 Domain of unknown function (DUF4268); Region: DUF4268; pfam14088 407976013282 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976013283 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 407976013284 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 407976013285 HsdM N-terminal domain; Region: HsdM_N; pfam12161 407976013286 HsdM N-terminal domain; Region: HsdM_N; pfam12161 407976013287 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 407976013288 Methyltransferase domain; Region: Methyltransf_26; pfam13659 407976013289 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 407976013290 active site 407976013291 catalytic residues [active] 407976013292 DNA binding site [nucleotide binding] 407976013293 Int/Topo IB signature motif; other site 407976013294 Abi-like protein; Region: Abi_2; pfam07751 407976013295 H-NS histone family; Region: Histone_HNS; pfam00816 407976013296 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 407976013297 ParB-like nuclease domain; Region: ParBc; pfam02195 407976013298 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 407976013299 HicB family; Region: HicB; pfam05534