-- dump date 20140620_064011 -- class Genbank::misc_feature -- table misc_feature_note -- id note 60480000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 60480000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 60480000003 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 60480000004 Walker A motif; other site 60480000005 ATP binding site [chemical binding]; other site 60480000006 Walker B motif; other site 60480000007 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 60480000008 arginine finger; other site 60480000009 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 60480000010 DnaA box-binding interface [nucleotide binding]; other site 60480000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 60480000012 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 60480000013 putative DNA binding surface [nucleotide binding]; other site 60480000014 dimer interface [polypeptide binding]; other site 60480000015 beta-clamp/clamp loader binding surface; other site 60480000016 beta-clamp/translesion DNA polymerase binding surface; other site 60480000017 recombination protein F; Reviewed; Region: recF; PRK00064 60480000018 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480000019 Walker A/P-loop; other site 60480000020 ATP binding site [chemical binding]; other site 60480000021 Q-loop/lid; other site 60480000022 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480000023 ABC transporter signature motif; other site 60480000024 Walker B; other site 60480000025 D-loop; other site 60480000026 H-loop/switch region; other site 60480000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 60480000028 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 60480000029 ATP binding site [chemical binding]; other site 60480000030 Mg2+ binding site [ion binding]; other site 60480000031 G-X-G motif; other site 60480000032 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 60480000033 anchoring element; other site 60480000034 dimer interface [polypeptide binding]; other site 60480000035 ATP binding site [chemical binding]; other site 60480000036 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 60480000037 active site 60480000038 putative metal-binding site [ion binding]; other site 60480000039 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 60480000040 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 60480000041 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 60480000042 putative C-terminal domain interface [polypeptide binding]; other site 60480000043 putative GSH binding site (G-site) [chemical binding]; other site 60480000044 putative dimer interface [polypeptide binding]; other site 60480000045 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 60480000046 putative N-terminal domain interface [polypeptide binding]; other site 60480000047 putative dimer interface [polypeptide binding]; other site 60480000048 putative substrate binding pocket (H-site) [chemical binding]; other site 60480000049 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480000050 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480000051 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 60480000052 dimerization interface [polypeptide binding]; other site 60480000053 HDOD domain; Region: HDOD; pfam08668 60480000054 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480000055 Zn2+ binding site [ion binding]; other site 60480000056 Mg2+ binding site [ion binding]; other site 60480000057 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 60480000058 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 60480000059 dimer interface [polypeptide binding]; other site 60480000060 motif 1; other site 60480000061 active site 60480000062 motif 2; other site 60480000063 motif 3; other site 60480000064 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 60480000065 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 60480000066 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480000067 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 60480000068 Amidohydrolase; Region: Amidohydro_5; pfam13594 60480000069 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 60480000070 active site 60480000071 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 60480000072 MOSC domain; Region: MOSC; pfam03473 60480000073 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 60480000074 CPxP motif; other site 60480000075 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 60480000076 heme-binding site [chemical binding]; other site 60480000077 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480000078 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480000079 metal binding site [ion binding]; metal-binding site 60480000080 active site 60480000081 I-site; other site 60480000082 putative transposase OrfB; Reviewed; Region: PHA02517 60480000083 Integrase core domain; Region: rve; pfam00665 60480000084 Integrase core domain; Region: rve_3; pfam13683 60480000085 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 60480000086 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 60480000087 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 60480000088 dimer interface [polypeptide binding]; other site 60480000089 active site 60480000090 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 60480000091 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 60480000092 substrate binding site [chemical binding]; other site 60480000093 oxyanion hole (OAH) forming residues; other site 60480000094 trimer interface [polypeptide binding]; other site 60480000095 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 60480000096 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 60480000097 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 60480000098 proline dipeptidase; Provisional; Region: PRK13607 60480000099 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 60480000100 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 60480000101 active site 60480000102 hypothetical protein; Provisional; Region: PRK11568 60480000103 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 60480000104 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 60480000105 Cation transport protein; Region: TrkH; cl17365 60480000106 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 60480000107 Flavodoxin domain; Region: Flavodoxin_5; cl17428 60480000108 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 60480000109 dimerization interface [polypeptide binding]; other site 60480000110 putative DNA binding site [nucleotide binding]; other site 60480000111 putative Zn2+ binding site [ion binding]; other site 60480000112 Flavodoxin domain; Region: Flavodoxin_5; cl17428 60480000113 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 60480000114 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 60480000115 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 60480000116 TrkA-N domain; Region: TrkA_N; pfam02254 60480000117 TrkA-C domain; Region: TrkA_C; pfam02080 60480000118 TrkA-N domain; Region: TrkA_N; pfam02254 60480000119 TrkA-C domain; Region: TrkA_C; pfam02080 60480000120 16S rRNA methyltransferase B; Provisional; Region: PRK10901 60480000121 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 60480000122 putative RNA binding site [nucleotide binding]; other site 60480000123 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 60480000124 S-adenosylmethionine binding site [chemical binding]; other site 60480000125 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 60480000126 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 60480000127 putative active site [active] 60480000128 substrate binding site [chemical binding]; other site 60480000129 putative cosubstrate binding site; other site 60480000130 catalytic site [active] 60480000131 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 60480000132 substrate binding site [chemical binding]; other site 60480000133 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 60480000134 active site 60480000135 catalytic residues [active] 60480000136 metal binding site [ion binding]; metal-binding site 60480000137 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 60480000138 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480000139 DNA protecting protein DprA; Region: dprA; TIGR00732 60480000140 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 60480000141 Protein of unknown function (DUF494); Region: DUF494; pfam04361 60480000142 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 60480000143 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 60480000144 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 60480000145 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 60480000146 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 60480000147 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 60480000148 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 60480000149 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 60480000150 apolar tunnel; other site 60480000151 heme binding site [chemical binding]; other site 60480000152 dimerization interface [polypeptide binding]; other site 60480000153 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 60480000154 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 60480000155 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 60480000156 shikimate binding site; other site 60480000157 NAD(P) binding site [chemical binding]; other site 60480000158 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 60480000159 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 60480000160 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 60480000161 trimer interface [polypeptide binding]; other site 60480000162 putative metal binding site [ion binding]; other site 60480000163 Flagellin N-methylase; Region: FliB; cl00497 60480000164 Transcriptional regulator; Region: Rrf2; cl17282 60480000165 Rrf2 family protein; Region: rrf2_super; TIGR00738 60480000166 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 60480000167 NodB motif; other site 60480000168 putative active site [active] 60480000169 putative catalytic site [active] 60480000170 Zn binding site [ion binding]; other site 60480000171 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 60480000172 C-terminal peptidase (prc); Region: prc; TIGR00225 60480000173 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 60480000174 protein binding site [polypeptide binding]; other site 60480000175 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 60480000176 Catalytic dyad [active] 60480000177 phosphoglyceromutase; Provisional; Region: PRK05434 60480000178 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 60480000179 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 60480000180 active site residue [active] 60480000181 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 60480000182 SecA binding site; other site 60480000183 Preprotein binding site; other site 60480000184 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 60480000185 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 60480000186 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 60480000187 HI0933-like protein; Region: HI0933_like; pfam03486 60480000188 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 60480000189 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 60480000190 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 60480000191 TrkA-N domain; Region: TrkA_N; pfam02254 60480000192 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480000193 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480000194 active site 60480000195 phosphorylation site [posttranslational modification] 60480000196 intermolecular recognition site; other site 60480000197 dimerization interface [polypeptide binding]; other site 60480000198 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 60480000199 DNA binding site [nucleotide binding] 60480000200 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 60480000201 dimer interface [polypeptide binding]; other site 60480000202 phosphorylation site [posttranslational modification] 60480000203 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 60480000204 ATP binding site [chemical binding]; other site 60480000205 Mg2+ binding site [ion binding]; other site 60480000206 G-X-G motif; other site 60480000207 Pirin-related protein [General function prediction only]; Region: COG1741 60480000208 Pirin; Region: Pirin; pfam02678 60480000209 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 60480000210 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 60480000211 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 60480000212 GAF domain; Region: GAF_3; pfam13492 60480000213 Histidine kinase; Region: His_kinase; pfam06580 60480000214 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 60480000215 ATP binding site [chemical binding]; other site 60480000216 Mg2+ binding site [ion binding]; other site 60480000217 G-X-G motif; other site 60480000218 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 60480000219 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480000220 active site 60480000221 phosphorylation site [posttranslational modification] 60480000222 intermolecular recognition site; other site 60480000223 dimerization interface [polypeptide binding]; other site 60480000224 LytTr DNA-binding domain; Region: LytTR; pfam04397 60480000225 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 60480000226 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480000227 NlpC/P60 family; Region: NLPC_P60; pfam00877 60480000228 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 60480000229 putative substrate translocation pore; other site 60480000230 Transcriptional regulators [Transcription]; Region: PurR; COG1609 60480000231 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 60480000232 DNA binding site [nucleotide binding] 60480000233 domain linker motif; other site 60480000234 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 60480000235 putative dimerization interface [polypeptide binding]; other site 60480000236 putative ligand binding site [chemical binding]; other site 60480000237 sucrose phosphorylase; Provisional; Region: PRK13840 60480000238 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 60480000239 active site 60480000240 homodimer interface [polypeptide binding]; other site 60480000241 catalytic site [active] 60480000242 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 60480000243 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 60480000244 putative substrate translocation pore; other site 60480000245 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480000246 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 60480000247 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 60480000248 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 60480000249 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 60480000250 putative substrate binding site [chemical binding]; other site 60480000251 putative ATP binding site [chemical binding]; other site 60480000252 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 60480000253 MPT binding site; other site 60480000254 trimer interface [polypeptide binding]; other site 60480000255 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 60480000256 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 60480000257 conserved cys residue [active] 60480000258 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480000259 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480000260 Phage shock protein B; Region: PspB; cl05946 60480000261 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 60480000262 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 60480000263 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 60480000264 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480000265 Walker A/P-loop; other site 60480000266 ATP binding site [chemical binding]; other site 60480000267 Q-loop/lid; other site 60480000268 ABC transporter signature motif; other site 60480000269 Walker B; other site 60480000270 D-loop; other site 60480000271 H-loop/switch region; other site 60480000272 TAP-like protein; Region: Abhydrolase_4; pfam08386 60480000273 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480000274 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480000275 DNA-binding site [nucleotide binding]; DNA binding site 60480000276 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 60480000277 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 60480000278 Walker A/P-loop; other site 60480000279 ATP binding site [chemical binding]; other site 60480000280 Q-loop/lid; other site 60480000281 ABC transporter signature motif; other site 60480000282 Walker B; other site 60480000283 D-loop; other site 60480000284 H-loop/switch region; other site 60480000285 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 60480000286 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 60480000287 acyl-activating enzyme (AAE) consensus motif; other site 60480000288 putative AMP binding site [chemical binding]; other site 60480000289 putative active site [active] 60480000290 putative CoA binding site [chemical binding]; other site 60480000291 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480000292 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480000293 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 60480000294 active site 60480000295 HPP family; Region: HPP; pfam04982 60480000296 Predicted acetyltransferase [General function prediction only]; Region: COG2388 60480000297 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 60480000298 active site 60480000299 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Region: HTH_MerR2; cd04769 60480000300 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 60480000301 DNA binding residues [nucleotide binding] 60480000302 putative dimer interface [polypeptide binding]; other site 60480000303 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 60480000304 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 60480000305 Uncharacterized conserved protein [Function unknown]; Region: COG3791 60480000306 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 60480000307 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 60480000308 DNA binding residues [nucleotide binding] 60480000309 putative dimer interface [polypeptide binding]; other site 60480000310 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 60480000311 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 60480000312 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 60480000313 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 60480000314 Transcriptional regulators [Transcription]; Region: MarR; COG1846 60480000315 MarR family; Region: MarR_2; pfam12802 60480000316 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 60480000317 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 60480000318 FAD binding pocket [chemical binding]; other site 60480000319 FAD binding motif [chemical binding]; other site 60480000320 phosphate binding motif [ion binding]; other site 60480000321 NAD binding pocket [chemical binding]; other site 60480000322 imidazolonepropionase; Validated; Region: PRK09356 60480000323 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 60480000324 active site 60480000325 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 60480000326 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480000327 DNA-binding site [nucleotide binding]; DNA binding site 60480000328 UTRA domain; Region: UTRA; pfam07702 60480000329 urocanate hydratase; Provisional; Region: PRK05414 60480000330 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 60480000331 active sites [active] 60480000332 tetramer interface [polypeptide binding]; other site 60480000333 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 60480000334 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 60480000335 molybdopterin cofactor binding site; other site 60480000336 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 60480000337 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 60480000338 molybdopterin cofactor binding site; other site 60480000339 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 60480000340 4Fe-4S binding domain; Region: Fer4; pfam00037 60480000341 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 60480000342 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 60480000343 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 60480000344 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 60480000345 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 60480000346 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 60480000347 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 60480000348 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 60480000349 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480000350 catalytic residue [active] 60480000351 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 60480000352 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 60480000353 G1 box; other site 60480000354 putative GEF interaction site [polypeptide binding]; other site 60480000355 GTP/Mg2+ binding site [chemical binding]; other site 60480000356 Switch I region; other site 60480000357 G2 box; other site 60480000358 G3 box; other site 60480000359 Switch II region; other site 60480000360 G4 box; other site 60480000361 G5 box; other site 60480000362 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 60480000363 This family represents the domain of elongation factor SelB, homologous to domain III 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 elements:...; Region: selB_III; cd04094 60480000364 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 60480000365 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 60480000366 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 60480000367 putative inner membrane protein; Provisional; Region: PRK11099 60480000368 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 60480000369 CPxP motif; other site 60480000370 Peptidase family M48; Region: Peptidase_M48; cl12018 60480000371 Pilin (bacterial filament); Region: Pilin; pfam00114 60480000372 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 60480000373 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 60480000374 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 60480000375 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 60480000376 Mechanosensitive ion channel; Region: MS_channel; pfam00924 60480000377 LysE type translocator; Region: LysE; cl00565 60480000378 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 60480000379 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 60480000380 putative acyl-acceptor binding pocket; other site 60480000381 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 60480000382 SnoaL-like domain; Region: SnoaL_3; pfam13474 60480000383 NRDE protein; Region: NRDE; cl01315 60480000384 putative antibiotic transporter; Provisional; Region: PRK10739 60480000385 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 60480000386 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 60480000387 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 60480000388 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480000389 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4412 60480000390 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 60480000391 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 60480000392 Chorismate lyase; Region: Chor_lyase; cl01230 60480000393 flagellar basal body-associated protein FliL-like protein; Validated; Region: PRK05697 60480000394 23S rRNA mA1618 methyltransferase; Provisional; Region: PRK11727 60480000395 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 60480000396 Putative hemolysin [General function prediction only]; Region: Hlx; COG3042 60480000397 Domain of unknown function (DUF333); Region: DUF333; pfam03891 60480000398 Inhibitor of apoptosis-promoting Bax1; Region: Bax1-I; pfam01027 60480000399 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 60480000400 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 60480000401 ATP binding site [chemical binding]; other site 60480000402 substrate interface [chemical binding]; other site 60480000403 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 60480000404 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 60480000405 dimer interface [polypeptide binding]; other site 60480000406 putative functional site; other site 60480000407 putative MPT binding site; other site 60480000408 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 60480000409 Ferritin-like domain; Region: Ferritin; pfam00210 60480000410 ferroxidase diiron center [ion binding]; other site 60480000411 Nitrate and nitrite sensing; Region: NIT; pfam08376 60480000412 RNase II stability modulator; Provisional; Region: PRK10060 60480000413 HAMP domain; Region: HAMP; pfam00672 60480000414 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 60480000415 putative active site [active] 60480000416 heme pocket [chemical binding]; other site 60480000417 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480000418 metal binding site [ion binding]; metal-binding site 60480000419 active site 60480000420 I-site; other site 60480000421 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 60480000422 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 60480000423 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 60480000424 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 60480000425 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480000426 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 60480000427 GIY-YIG motif/motif A; other site 60480000428 putative active site [active] 60480000429 putative metal binding site [ion binding]; other site 60480000430 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480000431 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480000432 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 60480000433 dimerization interface [polypeptide binding]; other site 60480000434 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 60480000435 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 60480000436 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 60480000437 nucleoside/Zn binding site; other site 60480000438 dimer interface [polypeptide binding]; other site 60480000439 catalytic motif [active] 60480000440 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 60480000441 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 60480000442 S-adenosylmethionine binding site [chemical binding]; other site 60480000443 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 60480000444 putative active site [active] 60480000445 Zn binding site [ion binding]; other site 60480000446 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 60480000447 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480000448 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 60480000449 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480000450 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 60480000451 ligand binding site [chemical binding]; other site 60480000452 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 60480000453 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 60480000454 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 60480000455 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 60480000456 active site 60480000457 substrate-binding site [chemical binding]; other site 60480000458 metal-binding site [ion binding] 60480000459 ATP binding site [chemical binding]; other site 60480000460 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 60480000461 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 60480000462 dimerization interface [polypeptide binding]; other site 60480000463 domain crossover interface; other site 60480000464 redox-dependent activation switch; other site 60480000465 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 60480000466 RNA binding surface [nucleotide binding]; other site 60480000467 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 60480000468 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 60480000469 type II secretion system protein D; Region: type_II_gspD; TIGR02517 60480000470 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 60480000471 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 60480000472 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 60480000473 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 60480000474 type II secretion system protein E; Region: type_II_gspE; TIGR02533 60480000475 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 60480000476 Walker A motif; other site 60480000477 ATP binding site [chemical binding]; other site 60480000478 Walker B motif; other site 60480000479 type II secretion system protein F; Region: GspF; TIGR02120 60480000480 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 60480000481 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 60480000482 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 60480000483 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 60480000484 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 60480000485 Type II transport protein GspH; Region: GspH; pfam12019 60480000486 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 60480000487 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 60480000488 type II secretion system protein J; Region: gspJ; TIGR01711 60480000489 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 60480000490 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 60480000491 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 60480000492 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 60480000493 GspL periplasmic domain; Region: GspL_C; pfam12693 60480000494 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 60480000495 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 60480000496 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 60480000497 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 60480000498 motif II; other site 60480000499 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 60480000500 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 60480000501 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 60480000502 dimer interface [polypeptide binding]; other site 60480000503 ADP-ribose binding site [chemical binding]; other site 60480000504 active site 60480000505 nudix motif; other site 60480000506 metal binding site [ion binding]; metal-binding site 60480000507 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 60480000508 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 60480000509 active site 60480000510 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 60480000511 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480000512 Coenzyme A binding pocket [chemical binding]; other site 60480000513 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480000514 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480000515 WHG domain; Region: WHG; pfam13305 60480000516 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 60480000517 putative substrate translocation pore; other site 60480000518 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 60480000519 putative acyl-acceptor binding pocket; other site 60480000520 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 60480000521 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 60480000522 active site residue [active] 60480000523 selenophosphate synthetase; Provisional; Region: PRK00943 60480000524 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 60480000525 dimerization interface [polypeptide binding]; other site 60480000526 putative ATP binding site [chemical binding]; other site 60480000527 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 60480000528 Di-iron ligands [ion binding]; other site 60480000529 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 60480000530 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 60480000531 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480000532 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 60480000533 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 60480000534 S-adenosylmethionine binding site [chemical binding]; other site 60480000535 glutamate racemase; Provisional; Region: PRK00865 60480000536 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 60480000537 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 60480000538 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 60480000539 FAD binding domain; Region: FAD_binding_4; pfam01565 60480000540 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 60480000541 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 60480000542 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 60480000543 dimerization interface [polypeptide binding]; other site 60480000544 putative Zn2+ binding site [ion binding]; other site 60480000545 putative DNA binding site [nucleotide binding]; other site 60480000546 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 60480000547 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 60480000548 pantothenate kinase; Provisional; Region: PRK05439 60480000549 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 60480000550 ATP-binding site [chemical binding]; other site 60480000551 CoA-binding site [chemical binding]; other site 60480000552 Mg2+-binding site [ion binding]; other site 60480000553 elongation factor Tu; Reviewed; Region: PRK00049 60480000554 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 60480000555 G1 box; other site 60480000556 GEF interaction site [polypeptide binding]; other site 60480000557 GTP/Mg2+ binding site [chemical binding]; other site 60480000558 Switch I region; other site 60480000559 G2 box; other site 60480000560 G3 box; other site 60480000561 Switch II region; other site 60480000562 G4 box; other site 60480000563 G5 box; other site 60480000564 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 60480000565 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 60480000566 Antibiotic Binding Site [chemical binding]; other site 60480000567 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 60480000568 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 60480000569 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 60480000570 putative homodimer interface [polypeptide binding]; other site 60480000571 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 60480000572 heterodimer interface [polypeptide binding]; other site 60480000573 homodimer interface [polypeptide binding]; other site 60480000574 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 60480000575 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 60480000576 23S rRNA interface [nucleotide binding]; other site 60480000577 L7/L12 interface [polypeptide binding]; other site 60480000578 putative thiostrepton binding site; other site 60480000579 L25 interface [polypeptide binding]; other site 60480000580 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 60480000581 mRNA/rRNA interface [nucleotide binding]; other site 60480000582 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 60480000583 23S rRNA interface [nucleotide binding]; other site 60480000584 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 60480000585 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 60480000586 core dimer interface [polypeptide binding]; other site 60480000587 peripheral dimer interface [polypeptide binding]; other site 60480000588 L10 interface [polypeptide binding]; other site 60480000589 L11 interface [polypeptide binding]; other site 60480000590 putative EF-Tu interaction site [polypeptide binding]; other site 60480000591 putative EF-G interaction site [polypeptide binding]; other site 60480000592 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 60480000593 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 60480000594 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 60480000595 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 60480000596 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 60480000597 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 60480000598 RPB3 interaction site [polypeptide binding]; other site 60480000599 RPB1 interaction site [polypeptide binding]; other site 60480000600 RPB11 interaction site [polypeptide binding]; other site 60480000601 RPB10 interaction site [polypeptide binding]; other site 60480000602 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 60480000603 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 60480000604 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 60480000605 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 60480000606 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 60480000607 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 60480000608 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 60480000609 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 60480000610 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 60480000611 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 60480000612 DNA binding site [nucleotide binding] 60480000613 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 60480000614 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 60480000615 S17 interaction site [polypeptide binding]; other site 60480000616 S8 interaction site; other site 60480000617 16S rRNA interaction site [nucleotide binding]; other site 60480000618 streptomycin interaction site [chemical binding]; other site 60480000619 23S rRNA interaction site [nucleotide binding]; other site 60480000620 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 60480000621 30S ribosomal protein S7; Validated; Region: PRK05302 60480000622 elongation factor G; Reviewed; Region: PRK00007 60480000623 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 60480000624 G1 box; other site 60480000625 putative GEF interaction site [polypeptide binding]; other site 60480000626 GTP/Mg2+ binding site [chemical binding]; other site 60480000627 Switch I region; other site 60480000628 G2 box; other site 60480000629 G3 box; other site 60480000630 Switch II region; other site 60480000631 G4 box; other site 60480000632 G5 box; other site 60480000633 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 60480000634 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 60480000635 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 60480000636 elongation factor Tu; Reviewed; Region: PRK00049 60480000637 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 60480000638 G1 box; other site 60480000639 GEF interaction site [polypeptide binding]; other site 60480000640 GTP/Mg2+ binding site [chemical binding]; other site 60480000641 Switch I region; other site 60480000642 G2 box; other site 60480000643 G3 box; other site 60480000644 Switch II region; other site 60480000645 G4 box; other site 60480000646 G5 box; other site 60480000647 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 60480000648 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 60480000649 Antibiotic Binding Site [chemical binding]; other site 60480000650 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 60480000651 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 60480000652 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 60480000653 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 60480000654 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 60480000655 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 60480000656 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 60480000657 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 60480000658 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 60480000659 putative translocon binding site; other site 60480000660 protein-rRNA interface [nucleotide binding]; other site 60480000661 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 60480000662 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 60480000663 G-X-X-G motif; other site 60480000664 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 60480000665 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 60480000666 23S rRNA interface [nucleotide binding]; other site 60480000667 5S rRNA interface [nucleotide binding]; other site 60480000668 putative antibiotic binding site [chemical binding]; other site 60480000669 L25 interface [polypeptide binding]; other site 60480000670 L27 interface [polypeptide binding]; other site 60480000671 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 60480000672 23S rRNA interface [nucleotide binding]; other site 60480000673 putative translocon interaction site; other site 60480000674 signal recognition particle (SRP54) interaction site; other site 60480000675 L23 interface [polypeptide binding]; other site 60480000676 trigger factor interaction site; other site 60480000677 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 60480000678 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 60480000679 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 60480000680 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 60480000681 RNA binding site [nucleotide binding]; other site 60480000682 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 60480000683 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 60480000684 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 60480000685 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 60480000686 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 60480000687 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 60480000688 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 60480000689 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 60480000690 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 60480000691 5S rRNA interface [nucleotide binding]; other site 60480000692 23S rRNA interface [nucleotide binding]; other site 60480000693 L5 interface [polypeptide binding]; other site 60480000694 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 60480000695 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 60480000696 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 60480000697 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 60480000698 23S rRNA binding site [nucleotide binding]; other site 60480000699 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 60480000700 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 60480000701 SecY translocase; Region: SecY; pfam00344 60480000702 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 60480000703 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 60480000704 30S ribosomal protein S13; Region: bact_S13; TIGR03631 60480000705 30S ribosomal protein S11; Validated; Region: PRK05309 60480000706 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 60480000707 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 60480000708 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 60480000709 RNA binding surface [nucleotide binding]; other site 60480000710 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 60480000711 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 60480000712 alphaNTD homodimer interface [polypeptide binding]; other site 60480000713 alphaNTD - beta interaction site [polypeptide binding]; other site 60480000714 alphaNTD - beta' interaction site [polypeptide binding]; other site 60480000715 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 60480000716 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 60480000717 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13165 60480000718 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 60480000719 heme exporter protein CcmC; Region: ccmC; TIGR01191 60480000720 heme exporter protein CcmB; Region: ccmB; TIGR01190 60480000721 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 60480000722 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480000723 Walker A/P-loop; other site 60480000724 ATP binding site [chemical binding]; other site 60480000725 Q-loop/lid; other site 60480000726 ABC transporter signature motif; other site 60480000727 Walker B; other site 60480000728 D-loop; other site 60480000729 H-loop/switch region; other site 60480000730 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 60480000731 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 60480000732 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 60480000733 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 60480000734 TPR motif; other site 60480000735 binding surface 60480000736 cytochrome c nitrate reductase biogenesis protein NrfE; Region: cyt_nit_nrfE; TIGR03145 60480000737 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 60480000738 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 60480000739 catalytic residues [active] 60480000740 central insert; other site 60480000741 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 60480000742 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 60480000743 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480000744 catalytic residues [active] 60480000745 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 60480000746 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480000747 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 60480000748 ATP binding site [chemical binding]; other site 60480000749 Mg2+ binding site [ion binding]; other site 60480000750 G-X-G motif; other site 60480000751 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480000752 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480000753 active site 60480000754 phosphorylation site [posttranslational modification] 60480000755 intermolecular recognition site; other site 60480000756 dimerization interface [polypeptide binding]; other site 60480000757 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 60480000758 DNA binding site [nucleotide binding] 60480000759 Predicted membrane protein [Function unknown]; Region: COG3212 60480000760 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 60480000761 Dihaem cytochrome c; Region: DHC; pfam09626 60480000762 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 60480000763 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 60480000764 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 60480000765 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480000766 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480000767 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 60480000768 putative effector binding pocket; other site 60480000769 putative dimerization interface [polypeptide binding]; other site 60480000770 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 60480000771 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480000772 NAD(P) binding site [chemical binding]; other site 60480000773 active site 60480000774 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 60480000775 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 60480000776 NAD(P) binding site [chemical binding]; other site 60480000777 catalytic residues [active] 60480000778 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 60480000779 GAF domain; Region: GAF; pfam01590 60480000780 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 60480000781 Walker A motif; other site 60480000782 ATP binding site [chemical binding]; other site 60480000783 Walker B motif; other site 60480000784 arginine finger; other site 60480000785 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480000786 two-component sensor protein; Provisional; Region: cpxA; PRK09470 60480000787 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 60480000788 dimerization interface [polypeptide binding]; other site 60480000789 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 60480000790 dimer interface [polypeptide binding]; other site 60480000791 phosphorylation site [posttranslational modification] 60480000792 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 60480000793 ATP binding site [chemical binding]; other site 60480000794 Mg2+ binding site [ion binding]; other site 60480000795 G-X-G motif; other site 60480000796 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480000797 active site 60480000798 phosphorylation site [posttranslational modification] 60480000799 intermolecular recognition site; other site 60480000800 dimerization interface [polypeptide binding]; other site 60480000801 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 60480000802 DNA binding site [nucleotide binding] 60480000803 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 60480000804 dimer interface [polypeptide binding]; other site 60480000805 Cation efflux family; Region: Cation_efflux; cl00316 60480000806 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 60480000807 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 60480000808 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 60480000809 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480000810 active site 60480000811 phosphorylation site [posttranslational modification] 60480000812 intermolecular recognition site; other site 60480000813 dimerization interface [polypeptide binding]; other site 60480000814 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 60480000815 Walker A motif; other site 60480000816 ATP binding site [chemical binding]; other site 60480000817 Walker B motif; other site 60480000818 arginine finger; other site 60480000819 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480000820 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 60480000821 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 60480000822 dimer interface [polypeptide binding]; other site 60480000823 phosphorylation site [posttranslational modification] 60480000824 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 60480000825 ATP binding site [chemical binding]; other site 60480000826 Mg2+ binding site [ion binding]; other site 60480000827 G-X-G motif; other site 60480000828 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 60480000829 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 60480000830 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 60480000831 dimer interface [polypeptide binding]; other site 60480000832 active site 60480000833 metal binding site [ion binding]; metal-binding site 60480000834 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480000835 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480000836 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 60480000837 5-histidylcysteine sulfoxide synthase; Region: ovoA_Nterm; TIGR04344 60480000838 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 60480000839 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 60480000840 S-adenosylmethionine binding site [chemical binding]; other site 60480000841 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 60480000842 substrate binding site [chemical binding]; other site 60480000843 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 60480000844 ATP binding site [chemical binding]; other site 60480000845 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480000846 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480000847 metal binding site [ion binding]; metal-binding site 60480000848 active site 60480000849 I-site; other site 60480000850 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 60480000851 MOSC domain; Region: MOSC; pfam03473 60480000852 3-alpha domain; Region: 3-alpha; pfam03475 60480000853 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 60480000854 Cache domain; Region: Cache_1; pfam02743 60480000855 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 60480000856 dimerization interface [polypeptide binding]; other site 60480000857 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480000858 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480000859 dimer interface [polypeptide binding]; other site 60480000860 putative CheW interface [polypeptide binding]; other site 60480000861 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 60480000862 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 60480000863 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 60480000864 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 60480000865 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 60480000866 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 60480000867 FeS/SAM binding site; other site 60480000868 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 60480000869 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 60480000870 trimer interface [polypeptide binding]; other site 60480000871 dimer interface [polypeptide binding]; other site 60480000872 putative active site [active] 60480000873 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 60480000874 MoaE interaction surface [polypeptide binding]; other site 60480000875 MoeB interaction surface [polypeptide binding]; other site 60480000876 thiocarboxylated glycine; other site 60480000877 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 60480000878 MoaE homodimer interface [polypeptide binding]; other site 60480000879 MoaD interaction [polypeptide binding]; other site 60480000880 active site residues [active] 60480000881 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 60480000882 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 60480000883 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 60480000884 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 60480000885 dimer interface [polypeptide binding]; other site 60480000886 conserved gate region; other site 60480000887 putative PBP binding loops; other site 60480000888 ABC-ATPase subunit interface; other site 60480000889 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 60480000890 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480000891 Walker A/P-loop; other site 60480000892 ATP binding site [chemical binding]; other site 60480000893 Q-loop/lid; other site 60480000894 ABC transporter signature motif; other site 60480000895 Walker B; other site 60480000896 D-loop; other site 60480000897 H-loop/switch region; other site 60480000898 alkaline phosphatase isozyme conversion aminopeptidase; Provisional; Region: PRK10199 60480000899 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480000900 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480000901 active site 60480000902 phosphorylation site [posttranslational modification] 60480000903 intermolecular recognition site; other site 60480000904 dimerization interface [polypeptide binding]; other site 60480000905 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 60480000906 DNA binding site [nucleotide binding] 60480000907 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480000908 HAMP domain; Region: HAMP; pfam00672 60480000909 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 60480000910 dimer interface [polypeptide binding]; other site 60480000911 phosphorylation site [posttranslational modification] 60480000912 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 60480000913 ATP binding site [chemical binding]; other site 60480000914 Mg2+ binding site [ion binding]; other site 60480000915 G-X-G motif; other site 60480000916 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 60480000917 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 60480000918 active site 60480000919 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480000920 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480000921 metal binding site [ion binding]; metal-binding site 60480000922 active site 60480000923 I-site; other site 60480000924 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 60480000925 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480000926 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 60480000927 N-terminal plug; other site 60480000928 ligand-binding site [chemical binding]; other site 60480000929 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 60480000930 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 60480000931 Peptidase family M23; Region: Peptidase_M23; pfam01551 60480000932 CHAP domain; Region: CHAP; pfam05257 60480000933 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 60480000934 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 60480000935 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480000936 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480000937 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 60480000938 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 60480000939 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK12489 60480000940 Domain of unknown function (DUF1864); Region: DUF1864; pfam08933 60480000941 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 60480000942 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 60480000943 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480000944 catalytic residue [active] 60480000945 Protein of unknown function (DUF1375); Region: DUF1375; cl11456 60480000946 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480000947 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 60480000948 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480000949 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480000950 L-aspartate oxidase; Provisional; Region: PRK06175 60480000951 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 60480000952 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 60480000953 Cupin domain; Region: Cupin_2; cl17218 60480000954 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480000955 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 60480000956 N-terminal plug; other site 60480000957 ligand-binding site [chemical binding]; other site 60480000958 glutamine synthetase; Provisional; Region: glnA; PRK09469 60480000959 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 60480000960 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 60480000961 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 60480000962 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 60480000963 G1 box; other site 60480000964 putative GEF interaction site [polypeptide binding]; other site 60480000965 GTP/Mg2+ binding site [chemical binding]; other site 60480000966 Switch I region; other site 60480000967 G2 box; other site 60480000968 G3 box; other site 60480000969 Switch II region; other site 60480000970 G4 box; other site 60480000971 G5 box; other site 60480000972 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 60480000973 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 60480000974 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 60480000975 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 60480000976 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480000977 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 60480000978 classical (c) SDRs; Region: SDR_c; cd05233 60480000979 NAD(P) binding site [chemical binding]; other site 60480000980 active site 60480000981 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 60480000982 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 60480000983 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH8; cd08262 60480000984 putative NAD(P) binding site [chemical binding]; other site 60480000985 catalytic Zn binding site [ion binding]; other site 60480000986 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 60480000987 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 60480000988 dimer interface [polypeptide binding]; other site 60480000989 active site 60480000990 heme binding site [chemical binding]; other site 60480000991 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 60480000992 4Fe-4S binding domain; Region: Fer4_5; pfam12801 60480000993 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 60480000994 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 60480000995 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 60480000996 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480000997 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480000998 metal binding site [ion binding]; metal-binding site 60480000999 active site 60480001000 I-site; other site 60480001001 Protein of unknown function (DUF2959); Region: DUF2959; pfam11172 60480001002 hypothetical protein; Reviewed; Region: PRK01637 60480001003 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 60480001004 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 60480001005 putative active site [active] 60480001006 dimerization interface [polypeptide binding]; other site 60480001007 putative tRNAtyr binding site [nucleotide binding]; other site 60480001008 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; pfam09500 60480001009 azoreductase; Reviewed; Region: PRK00170 60480001010 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 60480001011 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 60480001012 active site residue [active] 60480001013 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 60480001014 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 60480001015 non-specific DNA binding site [nucleotide binding]; other site 60480001016 salt bridge; other site 60480001017 sequence-specific DNA binding site [nucleotide binding]; other site 60480001018 Cupin domain; Region: Cupin_2; pfam07883 60480001019 Benzoate membrane transport protein; Region: BenE; pfam03594 60480001020 benzoate transporter; Region: benE; TIGR00843 60480001021 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480001022 dimer interface [polypeptide binding]; other site 60480001023 putative CheW interface [polypeptide binding]; other site 60480001024 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 60480001025 Cu(I) binding site [ion binding]; other site 60480001026 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480001027 Coenzyme A binding pocket [chemical binding]; other site 60480001028 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 60480001029 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 60480001030 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 60480001031 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 60480001032 dimer interface [polypeptide binding]; other site 60480001033 active site 60480001034 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 60480001035 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480001036 NAD(P) binding site [chemical binding]; other site 60480001037 active site 60480001038 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 60480001039 putative active site 1 [active] 60480001040 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 60480001041 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 60480001042 dimer interface [polypeptide binding]; other site 60480001043 active site 60480001044 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 60480001045 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 60480001046 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 60480001047 Predicted exporter [General function prediction only]; Region: COG4258 60480001048 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 60480001049 active site 60480001050 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 60480001051 active sites [active] 60480001052 tetramer interface [polypeptide binding]; other site 60480001053 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 60480001054 Ligand binding site; other site 60480001055 Putative Catalytic site; other site 60480001056 DXD motif; other site 60480001057 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 60480001058 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 60480001059 putative acyl-acceptor binding pocket; other site 60480001060 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 60480001061 active site 2 [active] 60480001062 active site 1 [active] 60480001063 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 60480001064 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 60480001065 acyl-activating enzyme (AAE) consensus motif; other site 60480001066 AMP binding site [chemical binding]; other site 60480001067 active site 60480001068 CoA binding site [chemical binding]; other site 60480001069 Predicted membrane protein [Function unknown]; Region: COG4648 60480001070 acyl carrier protein; Provisional; Region: PRK05350 60480001071 Phosphopantetheine attachment site; Region: PP-binding; cl09936 60480001072 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 60480001073 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 60480001074 putative acyl-acceptor binding pocket; other site 60480001075 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 60480001076 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 60480001077 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 60480001078 Y-family of DNA polymerases; Region: PolY; cl12025 60480001079 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 60480001080 generic binding surface II; other site 60480001081 ssDNA binding site; other site 60480001082 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 60480001083 ATP binding site [chemical binding]; other site 60480001084 putative Mg++ binding site [ion binding]; other site 60480001085 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 60480001086 nucleotide binding region [chemical binding]; other site 60480001087 ATP-binding site [chemical binding]; other site 60480001088 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 60480001089 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 60480001090 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001091 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001092 metal binding site [ion binding]; metal-binding site 60480001093 active site 60480001094 I-site; other site 60480001095 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 60480001096 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480001097 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 60480001098 substrate binding pocket [chemical binding]; other site 60480001099 membrane-bound complex binding site; other site 60480001100 hinge residues; other site 60480001101 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 60480001102 Domain of unknown function DUF21; Region: DUF21; pfam01595 60480001103 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 60480001104 Transporter associated domain; Region: CorC_HlyC; smart01091 60480001105 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480001106 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 60480001107 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 60480001108 putative dimerization interface [polypeptide binding]; other site 60480001109 ketol-acid reductoisomerase; Validated; Region: PRK05225 60480001110 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 60480001111 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 60480001112 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 60480001113 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 60480001114 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 60480001115 PYR/PP interface [polypeptide binding]; other site 60480001116 dimer interface [polypeptide binding]; other site 60480001117 TPP binding site [chemical binding]; other site 60480001118 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 60480001119 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 60480001120 TPP-binding site [chemical binding]; other site 60480001121 dimer interface [polypeptide binding]; other site 60480001122 acetolactate synthase 2 regulatory subunit; Provisional; Region: ilvM; PRK11152 60480001123 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 60480001124 threonine dehydratase; Reviewed; Region: PRK09224 60480001125 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 60480001126 tetramer interface [polypeptide binding]; other site 60480001127 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480001128 catalytic residue [active] 60480001129 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 60480001130 putative Ile/Val binding site [chemical binding]; other site 60480001131 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 60480001132 putative Ile/Val binding site [chemical binding]; other site 60480001133 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 60480001134 homodimer interface [polypeptide binding]; other site 60480001135 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480001136 catalytic residue [active] 60480001137 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 60480001138 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 60480001139 active site 60480001140 inner membrane protein; Provisional; Region: PRK11715 60480001141 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 60480001142 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 60480001143 Membrane fusogenic activity; Region: BMFP; pfam04380 60480001144 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 60480001145 Part of AAA domain; Region: AAA_19; pfam13245 60480001146 Family description; Region: UvrD_C_2; pfam13538 60480001147 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480001148 GAF domain; Region: GAF; pfam01590 60480001149 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480001150 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 60480001151 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001152 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001153 metal binding site [ion binding]; metal-binding site 60480001154 active site 60480001155 I-site; other site 60480001156 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 60480001157 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 60480001158 dimerization interface [polypeptide binding]; other site 60480001159 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001160 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001161 metal binding site [ion binding]; metal-binding site 60480001162 active site 60480001163 I-site; other site 60480001164 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 60480001165 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 60480001166 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 60480001167 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480001168 ligand binding site [chemical binding]; other site 60480001169 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 60480001170 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 60480001171 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480001172 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480001173 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 60480001174 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 60480001175 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 60480001176 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 60480001177 Walker A/P-loop; other site 60480001178 ATP binding site [chemical binding]; other site 60480001179 Q-loop/lid; other site 60480001180 ABC transporter signature motif; other site 60480001181 Walker B; other site 60480001182 D-loop; other site 60480001183 H-loop/switch region; other site 60480001184 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 60480001185 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 60480001186 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 60480001187 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 60480001188 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 60480001189 region containing an unresolved number of tandem repeats 60480001190 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 60480001191 HemY protein N-terminus; Region: HemY_N; pfam07219 60480001192 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 60480001193 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 60480001194 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 60480001195 active site 60480001196 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 60480001197 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 60480001198 domain interfaces; other site 60480001199 active site 60480001200 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 60480001201 adenylate cyclase; Provisional; Region: cyaA; PRK09450 60480001202 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 60480001203 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 60480001204 putative iron binding site [ion binding]; other site 60480001205 diaminopimelate decarboxylase; Region: lysA; TIGR01048 60480001206 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 60480001207 active site 60480001208 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 60480001209 substrate binding site [chemical binding]; other site 60480001210 catalytic residues [active] 60480001211 dimer interface [polypeptide binding]; other site 60480001212 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 60480001213 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 60480001214 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 60480001215 Protein of unknown function, DUF484; Region: DUF484; cl17449 60480001216 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 60480001217 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 60480001218 active site 60480001219 Int/Topo IB signature motif; other site 60480001220 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 60480001221 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 60480001222 motif II; other site 60480001223 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 60480001224 Divergent AAA domain; Region: AAA_4; pfam04326 60480001225 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 60480001226 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 60480001227 Hemerythrin-like domain; Region: Hr-like; cd12108 60480001228 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 60480001229 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 60480001230 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 60480001231 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 60480001232 FMN binding site [chemical binding]; other site 60480001233 active site 60480001234 catalytic residues [active] 60480001235 substrate binding site [chemical binding]; other site 60480001236 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 60480001237 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 60480001238 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13554 60480001239 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 60480001240 Iron-sulfur protein interface; other site 60480001241 proximal heme binding site [chemical binding]; other site 60480001242 distal heme binding site [chemical binding]; other site 60480001243 dimer interface [polypeptide binding]; other site 60480001244 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 60480001245 Iron-sulfur protein interface; other site 60480001246 proximal heme binding site [chemical binding]; other site 60480001247 distal heme binding site [chemical binding]; other site 60480001248 dimer interface [polypeptide binding]; other site 60480001249 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 60480001250 L-aspartate oxidase; Provisional; Region: PRK06175 60480001251 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 60480001252 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 60480001253 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 60480001254 Uncharacterized conserved protein [Function unknown]; Region: COG1359 60480001255 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 60480001256 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 60480001257 putative NAD(P) binding site [chemical binding]; other site 60480001258 dimer interface [polypeptide binding]; other site 60480001259 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480001260 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480001261 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 60480001262 putative effector binding pocket; other site 60480001263 dimerization interface [polypeptide binding]; other site 60480001264 transcription termination factor Rho; Provisional; Region: rho; PRK09376 60480001265 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 60480001266 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 60480001267 RNA binding site [nucleotide binding]; other site 60480001268 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 60480001269 multimer interface [polypeptide binding]; other site 60480001270 Walker A motif; other site 60480001271 ATP binding site [chemical binding]; other site 60480001272 Walker B motif; other site 60480001273 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 60480001274 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480001275 catalytic residues [active] 60480001276 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 60480001277 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 60480001278 ATP binding site [chemical binding]; other site 60480001279 Mg++ binding site [ion binding]; other site 60480001280 motif III; other site 60480001281 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 60480001282 nucleotide binding region [chemical binding]; other site 60480001283 ATP-binding site [chemical binding]; other site 60480001284 exopolyphosphatase; Region: exo_poly_only; TIGR03706 60480001285 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 60480001286 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 60480001287 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480001288 catalytic residues [active] 60480001289 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 60480001290 active site 60480001291 8-oxo-dGMP binding site [chemical binding]; other site 60480001292 nudix motif; other site 60480001293 metal binding site [ion binding]; metal-binding site 60480001294 Domain of unknown function (DUF329); Region: DUF329; pfam03884 60480001295 hypothetical protein; Provisional; Region: PRK05287 60480001296 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 60480001297 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 60480001298 CoA-binding site [chemical binding]; other site 60480001299 ATP-binding [chemical binding]; other site 60480001300 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 60480001301 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 60480001302 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 60480001303 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 60480001304 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 60480001305 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 60480001306 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 60480001307 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 60480001308 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 60480001309 Walker A motif; other site 60480001310 ATP binding site [chemical binding]; other site 60480001311 Walker B motif; other site 60480001312 O-Antigen ligase; Region: Wzy_C; pfam04932 60480001313 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 60480001314 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 60480001315 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 60480001316 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 60480001317 dimerization interface [polypeptide binding]; other site 60480001318 active site 60480001319 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 60480001320 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 60480001321 amidase catalytic site [active] 60480001322 Zn binding residues [ion binding]; other site 60480001323 substrate binding site [chemical binding]; other site 60480001324 regulatory protein AmpE; Provisional; Region: PRK10987 60480001325 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 60480001326 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480001327 DNA-binding site [nucleotide binding]; DNA binding site 60480001328 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 60480001329 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 60480001330 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 60480001331 dimer interface [polypeptide binding]; other site 60480001332 TPP-binding site [chemical binding]; other site 60480001333 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 60480001334 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 60480001335 E3 interaction surface; other site 60480001336 lipoyl attachment site [posttranslational modification]; other site 60480001337 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 60480001338 E3 interaction surface; other site 60480001339 lipoyl attachment site [posttranslational modification]; other site 60480001340 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 60480001341 E3 interaction surface; other site 60480001342 lipoyl attachment site [posttranslational modification]; other site 60480001343 e3 binding domain; Region: E3_binding; pfam02817 60480001344 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 60480001345 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 60480001346 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 60480001347 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 60480001348 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 60480001349 PAS fold; Region: PAS_3; pfam08447 60480001350 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 60480001351 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 60480001352 PAS domain; Region: PAS_9; pfam13426 60480001353 putative active site [active] 60480001354 heme pocket [chemical binding]; other site 60480001355 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001356 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001357 metal binding site [ion binding]; metal-binding site 60480001358 active site 60480001359 I-site; other site 60480001360 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 60480001361 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 60480001362 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 60480001363 active site 60480001364 nucleophile elbow; other site 60480001365 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480001366 Surface antigen; Region: Bac_surface_Ag; pfam01103 60480001367 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 60480001368 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 60480001369 active site 60480001370 Zn binding site [ion binding]; other site 60480001371 putative transposase OrfB; Reviewed; Region: PHA02517 60480001372 Integrase core domain; Region: rve; pfam00665 60480001373 Integrase core domain; Region: rve_3; pfam13683 60480001374 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 60480001375 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 60480001376 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 60480001377 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 60480001378 motif II; other site 60480001379 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 60480001380 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 60480001381 substrate binding site [chemical binding]; other site 60480001382 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 60480001383 substrate binding site [chemical binding]; other site 60480001384 ligand binding site [chemical binding]; other site 60480001385 anti-RNA polymerase sigma 70 factor; Provisional; Region: PRK11718 60480001386 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 60480001387 substrate binding site [chemical binding]; other site 60480001388 active site 60480001389 PAS fold; Region: PAS; pfam00989 60480001390 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 60480001391 putative active site [active] 60480001392 heme pocket [chemical binding]; other site 60480001393 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001394 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001395 metal binding site [ion binding]; metal-binding site 60480001396 active site 60480001397 I-site; other site 60480001398 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 60480001399 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs; Region: 11beta-HSD1_like_SDR_c; cd05332 60480001400 short chain dehydrogenase; Provisional; Region: PRK06181 60480001401 NADP binding site [chemical binding]; other site 60480001402 homodimer interface [polypeptide binding]; other site 60480001403 substrate binding site [chemical binding]; other site 60480001404 active site 60480001405 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 60480001406 Peptidase M60-like family; Region: M60-like; pfam13402 60480001407 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 60480001408 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 60480001409 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 60480001410 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 60480001411 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 60480001412 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 60480001413 purine monophosphate binding site [chemical binding]; other site 60480001414 dimer interface [polypeptide binding]; other site 60480001415 putative catalytic residues [active] 60480001416 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 60480001417 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 60480001418 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 60480001419 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 60480001420 DNA binding residues [nucleotide binding] 60480001421 dimer interface [polypeptide binding]; other site 60480001422 metal binding site [ion binding]; metal-binding site 60480001423 Predicted permease; Region: DUF318; cl17795 60480001424 Predicted permease; Region: DUF318; cl17795 60480001425 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 60480001426 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 60480001427 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 60480001428 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 60480001429 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 60480001430 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 60480001431 putative MFS family transporter protein; Provisional; Region: PRK03633 60480001432 putative substrate translocation pore; other site 60480001433 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480001434 GAF domain; Region: GAF; pfam01590 60480001435 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001436 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001437 metal binding site [ion binding]; metal-binding site 60480001438 active site 60480001439 I-site; other site 60480001440 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 60480001441 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 60480001442 transmembrane helices; other site 60480001443 thioredoxin 2; Provisional; Region: PRK10996 60480001444 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 60480001445 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 60480001446 catalytic residues [active] 60480001447 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480001448 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 60480001449 putative active site [active] 60480001450 PAS fold; Region: PAS_3; pfam08447 60480001451 heme pocket [chemical binding]; other site 60480001452 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001453 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001454 metal binding site [ion binding]; metal-binding site 60480001455 active site 60480001456 I-site; other site 60480001457 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 60480001458 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 60480001459 DctM-like transporters; Region: DctM; pfam06808 60480001460 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 60480001461 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 60480001462 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 60480001463 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 60480001464 Predicted metalloprotease [General function prediction only]; Region: COG2321 60480001465 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 60480001466 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 60480001467 nudix motif; other site 60480001468 SEC-C motif; Region: SEC-C; pfam02810 60480001469 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 60480001470 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 60480001471 Walker A motif; other site 60480001472 ATP binding site [chemical binding]; other site 60480001473 Walker B motif; other site 60480001474 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 60480001475 AAA domain; Region: AAA_13; pfam13166 60480001476 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 60480001477 Part of AAA domain; Region: AAA_19; pfam13245 60480001478 Family description; Region: UvrD_C_2; pfam13538 60480001479 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 60480001480 UbiA prenyltransferase family; Region: UbiA; pfam01040 60480001481 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 60480001482 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 60480001483 FMN binding site [chemical binding]; other site 60480001484 substrate binding site [chemical binding]; other site 60480001485 putative catalytic residue [active] 60480001486 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 60480001487 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480001488 catalytic residues [active] 60480001489 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 60480001490 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480001491 catalytic residues [active] 60480001492 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 60480001493 Domain of unknown function DUF20; Region: UPF0118; pfam01594 60480001494 Pathogenicity locus; Region: Cdd1; pfam11731 60480001495 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 60480001496 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001497 active site 60480001498 phosphorylation site [posttranslational modification] 60480001499 intermolecular recognition site; other site 60480001500 dimerization interface [polypeptide binding]; other site 60480001501 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480001502 Zn2+ binding site [ion binding]; other site 60480001503 Mg2+ binding site [ion binding]; other site 60480001504 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 60480001505 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 60480001506 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 60480001507 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480001508 substrate binding pocket [chemical binding]; other site 60480001509 membrane-bound complex binding site; other site 60480001510 hinge residues; other site 60480001511 PAS domain S-box; Region: sensory_box; TIGR00229 60480001512 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 60480001513 putative active site [active] 60480001514 heme pocket [chemical binding]; other site 60480001515 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 60480001516 dimer interface [polypeptide binding]; other site 60480001517 phosphorylation site [posttranslational modification] 60480001518 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 60480001519 ATP binding site [chemical binding]; other site 60480001520 Mg2+ binding site [ion binding]; other site 60480001521 G-X-G motif; other site 60480001522 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001523 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001524 active site 60480001525 phosphorylation site [posttranslational modification] 60480001526 intermolecular recognition site; other site 60480001527 dimerization interface [polypeptide binding]; other site 60480001528 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 60480001529 putative binding surface; other site 60480001530 active site 60480001531 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001532 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001533 active site 60480001534 phosphorylation site [posttranslational modification] 60480001535 intermolecular recognition site; other site 60480001536 dimerization interface [polypeptide binding]; other site 60480001537 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001538 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001539 active site 60480001540 phosphorylation site [posttranslational modification] 60480001541 intermolecular recognition site; other site 60480001542 dimerization interface [polypeptide binding]; other site 60480001543 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480001544 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 60480001545 ATP binding site [chemical binding]; other site 60480001546 Mg2+ binding site [ion binding]; other site 60480001547 G-X-G motif; other site 60480001548 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 60480001549 metal binding site [ion binding]; metal-binding site 60480001550 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 60480001551 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480001552 catalytic residues [active] 60480001553 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 60480001554 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 60480001555 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 60480001556 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 60480001557 active site residue [active] 60480001558 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 60480001559 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 60480001560 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480001561 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 60480001562 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 60480001563 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 60480001564 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 60480001565 NosL; Region: NosL; pfam05573 60480001566 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 60480001567 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 60480001568 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 60480001569 Walker A/P-loop; other site 60480001570 ATP binding site [chemical binding]; other site 60480001571 Q-loop/lid; other site 60480001572 ABC transporter signature motif; other site 60480001573 Walker B; other site 60480001574 D-loop; other site 60480001575 H-loop/switch region; other site 60480001576 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 60480001577 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 60480001578 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480001579 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 60480001580 DNA binding site [nucleotide binding] 60480001581 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 60480001582 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 60480001583 active site 60480001584 Zn binding site [ion binding]; other site 60480001585 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 60480001586 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 60480001587 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 60480001588 active site 60480001589 catalytic triad [active] 60480001590 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 60480001591 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480001592 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 60480001593 catalytic residues [active] 60480001594 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 60480001595 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 60480001596 Transposase; Region: DEDD_Tnp_IS110; pfam01548 60480001597 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 60480001598 FMN reductase; Validated; Region: fre; PRK08051 60480001599 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 60480001600 FAD binding pocket [chemical binding]; other site 60480001601 FAD binding motif [chemical binding]; other site 60480001602 phosphate binding motif [ion binding]; other site 60480001603 beta-alpha-beta structure motif; other site 60480001604 NAD binding pocket [chemical binding]; other site 60480001605 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 60480001606 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 60480001607 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480001608 putative substrate translocation pore; other site 60480001609 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480001610 short chain dehydrogenase; Provisional; Region: PRK07454 60480001611 NAD(P) binding site [chemical binding]; other site 60480001612 active site 60480001613 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 60480001614 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 60480001615 carboxyltransferase (CT) interaction site; other site 60480001616 biotinylation site [posttranslational modification]; other site 60480001617 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 60480001618 Dehydroquinase class II; Region: DHquinase_II; pfam01220 60480001619 active site 60480001620 trimer interface [polypeptide binding]; other site 60480001621 dimer interface [polypeptide binding]; other site 60480001622 hypothetical protein; Provisional; Region: PRK09256 60480001623 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 60480001624 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 60480001625 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 60480001626 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 60480001627 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480001628 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 60480001629 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480001630 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 60480001631 Protein export membrane protein; Region: SecD_SecF; cl14618 60480001632 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 60480001633 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 60480001634 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 60480001635 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480001636 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480001637 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 60480001638 putative effector binding pocket; other site 60480001639 dimerization interface [polypeptide binding]; other site 60480001640 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 60480001641 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480001642 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480001643 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 60480001644 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 60480001645 putative substrate translocation pore; other site 60480001646 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480001647 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 60480001648 Coenzyme A binding pocket [chemical binding]; other site 60480001649 Uncharacterized conserved protein [Function unknown]; Region: COG1359 60480001650 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 60480001651 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 60480001652 Walker A motif; other site 60480001653 ATP binding site [chemical binding]; other site 60480001654 Walker B motif; other site 60480001655 arginine finger; other site 60480001656 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480001657 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 60480001658 Radical SAM superfamily; Region: Radical_SAM; pfam04055 60480001659 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 60480001660 FeS/SAM binding site; other site 60480001661 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480001662 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 60480001663 N-terminal plug; other site 60480001664 ligand-binding site [chemical binding]; other site 60480001665 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 60480001666 dimerization interface [polypeptide binding]; other site 60480001667 putative DNA binding site [nucleotide binding]; other site 60480001668 putative Zn2+ binding site [ion binding]; other site 60480001669 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 60480001670 arsenical-resistance protein; Region: acr3; TIGR00832 60480001671 Predicted permeases [General function prediction only]; Region: COG0701 60480001672 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 60480001673 catalytic residues [active] 60480001674 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 60480001675 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 60480001676 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 60480001677 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 60480001678 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 60480001679 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 60480001680 Beta-Casp domain; Region: Beta-Casp; smart01027 60480001681 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 60480001682 conserved hypothetical protein; Region: QEGLA; TIGR02421 60480001683 CHASE domain; Region: CHASE; pfam03924 60480001684 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 60480001685 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 60480001686 putative active site [active] 60480001687 heme pocket [chemical binding]; other site 60480001688 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 60480001689 dimer interface [polypeptide binding]; other site 60480001690 phosphorylation site [posttranslational modification] 60480001691 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 60480001692 ATP binding site [chemical binding]; other site 60480001693 Mg2+ binding site [ion binding]; other site 60480001694 G-X-G motif; other site 60480001695 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001696 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001697 active site 60480001698 phosphorylation site [posttranslational modification] 60480001699 intermolecular recognition site; other site 60480001700 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480001701 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001702 active site 60480001703 phosphorylation site [posttranslational modification] 60480001704 intermolecular recognition site; other site 60480001705 dimerization interface [polypeptide binding]; other site 60480001706 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001707 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001708 metal binding site [ion binding]; metal-binding site 60480001709 active site 60480001710 I-site; other site 60480001711 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 60480001712 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 60480001713 RimK-like ATP-grasp domain; Region: RimK; pfam08443 60480001714 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 60480001715 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 60480001716 IHF dimer interface [polypeptide binding]; other site 60480001717 IHF - DNA interface [nucleotide binding]; other site 60480001718 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001719 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001720 active site 60480001721 phosphorylation site [posttranslational modification] 60480001722 intermolecular recognition site; other site 60480001723 dimerization interface [polypeptide binding]; other site 60480001724 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001725 active site 60480001726 phosphorylation site [posttranslational modification] 60480001727 intermolecular recognition site; other site 60480001728 dimerization interface [polypeptide binding]; other site 60480001729 Protein of unknown function (DUF4240); Region: DUF4240; pfam14024 60480001730 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 60480001731 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 60480001732 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 60480001733 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001734 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001735 metal binding site [ion binding]; metal-binding site 60480001736 active site 60480001737 I-site; other site 60480001738 TraB family; Region: TraB; pfam01963 60480001739 Methyltransferase domain; Region: Methyltransf_31; pfam13847 60480001740 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 60480001741 S-adenosylmethionine binding site [chemical binding]; other site 60480001742 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 60480001743 active site 2 [active] 60480001744 active site 1 [active] 60480001745 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 60480001746 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 60480001747 active site 60480001748 catalytic tetrad [active] 60480001749 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 60480001750 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 60480001751 Potassium binding sites [ion binding]; other site 60480001752 Cesium cation binding sites [ion binding]; other site 60480001753 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 60480001754 Mechanosensitive ion channel; Region: MS_channel; pfam00924 60480001755 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 60480001756 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 60480001757 putative ligand binding site [chemical binding]; other site 60480001758 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 60480001759 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 60480001760 putative acyl-acceptor binding pocket; other site 60480001761 RNase E inhibitor protein; Provisional; Region: PRK11191 60480001762 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 60480001763 PAS domain; Region: PAS_9; pfam13426 60480001764 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480001765 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480001766 metal binding site [ion binding]; metal-binding site 60480001767 active site 60480001768 I-site; other site 60480001769 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001770 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001771 active site 60480001772 phosphorylation site [posttranslational modification] 60480001773 intermolecular recognition site; other site 60480001774 dimerization interface [polypeptide binding]; other site 60480001775 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 60480001776 enoyl-CoA hydratase; Provisional; Region: PRK07509 60480001777 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 60480001778 substrate binding site [chemical binding]; other site 60480001779 oxyanion hole (OAH) forming residues; other site 60480001780 trimer interface [polypeptide binding]; other site 60480001781 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 60480001782 ATP-dependent helicase HepA; Validated; Region: PRK04914 60480001783 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 60480001784 ATP binding site [chemical binding]; other site 60480001785 putative Mg++ binding site [ion binding]; other site 60480001786 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 60480001787 nucleotide binding region [chemical binding]; other site 60480001788 ATP-binding site [chemical binding]; other site 60480001789 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 60480001790 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 60480001791 putative active site [active] 60480001792 PhoH-like protein; Region: PhoH; pfam02562 60480001793 Cache domain; Region: Cache_1; pfam02743 60480001794 PAS fold; Region: PAS_4; pfam08448 60480001795 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 60480001796 putative active site [active] 60480001797 heme pocket [chemical binding]; other site 60480001798 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 60480001799 PAS fold; Region: PAS_3; pfam08447 60480001800 putative active site [active] 60480001801 heme pocket [chemical binding]; other site 60480001802 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 60480001803 dimer interface [polypeptide binding]; other site 60480001804 phosphorylation site [posttranslational modification] 60480001805 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 60480001806 ATP binding site [chemical binding]; other site 60480001807 Mg2+ binding site [ion binding]; other site 60480001808 G-X-G motif; other site 60480001809 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480001810 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001811 active site 60480001812 phosphorylation site [posttranslational modification] 60480001813 intermolecular recognition site; other site 60480001814 dimerization interface [polypeptide binding]; other site 60480001815 Response regulator receiver domain; Region: Response_reg; pfam00072 60480001816 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001817 active site 60480001818 phosphorylation site [posttranslational modification] 60480001819 intermolecular recognition site; other site 60480001820 dimerization interface [polypeptide binding]; other site 60480001821 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 60480001822 active site 60480001823 Catalytic domain of Protein Kinases; Region: PKc; cd00180 60480001824 active site 60480001825 ATP binding site [chemical binding]; other site 60480001826 substrate binding site [chemical binding]; other site 60480001827 activation loop (A-loop); other site 60480001828 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 60480001829 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 60480001830 S-adenosylmethionine binding site [chemical binding]; other site 60480001831 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 60480001832 PAS domain; Region: PAS_9; pfam13426 60480001833 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 60480001834 putative active site [active] 60480001835 heme pocket [chemical binding]; other site 60480001836 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480001837 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480001838 dimer interface [polypeptide binding]; other site 60480001839 putative CheW interface [polypeptide binding]; other site 60480001840 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 60480001841 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 60480001842 NAD binding site [chemical binding]; other site 60480001843 ligand binding site [chemical binding]; other site 60480001844 catalytic site [active] 60480001845 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 60480001846 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 60480001847 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 60480001848 active site 60480001849 catalytic site [active] 60480001850 metal binding site [ion binding]; metal-binding site 60480001851 putative mechanosensitive channel protein; Provisional; Region: PRK10929 60480001852 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 60480001853 Mechanosensitive ion channel; Region: MS_channel; pfam00924 60480001854 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 60480001855 EamA-like transporter family; Region: EamA; pfam00892 60480001856 EamA-like transporter family; Region: EamA; pfam00892 60480001857 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 60480001858 GTPase RsgA; Reviewed; Region: PRK12288 60480001859 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 60480001860 RNA binding site [nucleotide binding]; other site 60480001861 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 60480001862 GTPase/Zn-binding domain interface [polypeptide binding]; other site 60480001863 GTP/Mg2+ binding site [chemical binding]; other site 60480001864 G4 box; other site 60480001865 G5 box; other site 60480001866 G1 box; other site 60480001867 Switch I region; other site 60480001868 G2 box; other site 60480001869 G3 box; other site 60480001870 Switch II region; other site 60480001871 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 60480001872 catalytic site [active] 60480001873 putative active site [active] 60480001874 putative substrate binding site [chemical binding]; other site 60480001875 dimer interface [polypeptide binding]; other site 60480001876 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 60480001877 dinuclear metal binding motif [ion binding]; other site 60480001878 putative carbohydrate kinase; Provisional; Region: PRK10565 60480001879 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 60480001880 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 60480001881 putative substrate binding site [chemical binding]; other site 60480001882 putative ATP binding site [chemical binding]; other site 60480001883 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 60480001884 AMIN domain; Region: AMIN; pfam11741 60480001885 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 60480001886 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 60480001887 active site 60480001888 metal binding site [ion binding]; metal-binding site 60480001889 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 60480001890 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480001891 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 60480001892 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 60480001893 ATP binding site [chemical binding]; other site 60480001894 Mg2+ binding site [ion binding]; other site 60480001895 G-X-G motif; other site 60480001896 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 60480001897 ATP binding site [chemical binding]; other site 60480001898 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 60480001899 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 60480001900 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 60480001901 bacterial Hfq-like; Region: Hfq; cd01716 60480001902 hexamer interface [polypeptide binding]; other site 60480001903 Sm1 motif; other site 60480001904 RNA binding site [nucleotide binding]; other site 60480001905 Sm2 motif; other site 60480001906 GTPase HflX; Provisional; Region: PRK11058 60480001907 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 60480001908 HflX GTPase family; Region: HflX; cd01878 60480001909 G1 box; other site 60480001910 GTP/Mg2+ binding site [chemical binding]; other site 60480001911 Switch I region; other site 60480001912 G2 box; other site 60480001913 G3 box; other site 60480001914 Switch II region; other site 60480001915 G4 box; other site 60480001916 G5 box; other site 60480001917 FtsH protease regulator HflK; Provisional; Region: PRK10930 60480001918 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 60480001919 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 60480001920 FtsH protease regulator HflC; Provisional; Region: PRK11029 60480001921 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 60480001922 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 60480001923 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 60480001924 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 60480001925 [2Fe-2S] cluster binding site [ion binding]; other site 60480001926 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 60480001927 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 60480001928 Qi binding site; other site 60480001929 intrachain domain interface; other site 60480001930 interchain domain interface [polypeptide binding]; other site 60480001931 heme bH binding site [chemical binding]; other site 60480001932 heme bL binding site [chemical binding]; other site 60480001933 Qo binding site; other site 60480001934 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 60480001935 interchain domain interface [polypeptide binding]; other site 60480001936 intrachain domain interface; other site 60480001937 Qi binding site; other site 60480001938 Qo binding site; other site 60480001939 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 60480001940 stringent starvation protein A; Provisional; Region: sspA; PRK09481 60480001941 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 60480001942 C-terminal domain interface [polypeptide binding]; other site 60480001943 putative GSH binding site (G-site) [chemical binding]; other site 60480001944 dimer interface [polypeptide binding]; other site 60480001945 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 60480001946 dimer interface [polypeptide binding]; other site 60480001947 N-terminal domain interface [polypeptide binding]; other site 60480001948 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 60480001949 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 60480001950 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 60480001951 glutamine binding [chemical binding]; other site 60480001952 catalytic triad [active] 60480001953 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480001954 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480001955 HDOD domain; Region: HDOD; pfam08668 60480001956 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 60480001957 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 60480001958 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 60480001959 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 60480001960 inhibitor-cofactor binding pocket; inhibition site 60480001961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480001962 catalytic residue [active] 60480001963 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 60480001964 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 60480001965 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 60480001966 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 60480001967 NAD(P) binding site [chemical binding]; other site 60480001968 catalytic residues [active] 60480001969 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 60480001970 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480001971 HAMP domain; Region: HAMP; pfam00672 60480001972 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 60480001973 dimer interface [polypeptide binding]; other site 60480001974 phosphorylation site [posttranslational modification] 60480001975 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 60480001976 ATP binding site [chemical binding]; other site 60480001977 Mg2+ binding site [ion binding]; other site 60480001978 G-X-G motif; other site 60480001979 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480001980 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480001981 active site 60480001982 phosphorylation site [posttranslational modification] 60480001983 intermolecular recognition site; other site 60480001984 dimerization interface [polypeptide binding]; other site 60480001985 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 60480001986 DNA binding site [nucleotide binding] 60480001987 Predicted membrane protein [Function unknown]; Region: COG3212 60480001988 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 60480001989 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 60480001990 ligand binding site [chemical binding]; other site 60480001991 flexible hinge region; other site 60480001992 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 60480001993 putative switch regulator; other site 60480001994 non-specific DNA interactions [nucleotide binding]; other site 60480001995 DNA binding site [nucleotide binding] 60480001996 sequence specific DNA binding site [nucleotide binding]; other site 60480001997 putative cAMP binding site [chemical binding]; other site 60480001998 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 60480001999 Sel1-like repeats; Region: SEL1; smart00671 60480002000 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 60480002001 binding surface 60480002002 TPR motif; other site 60480002003 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 60480002004 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 60480002005 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480002006 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480002007 metal binding site [ion binding]; metal-binding site 60480002008 active site 60480002009 I-site; other site 60480002010 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 60480002011 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 60480002012 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 60480002013 N-terminal plug; other site 60480002014 ligand-binding site [chemical binding]; other site 60480002015 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 60480002016 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 60480002017 ATP binding site [chemical binding]; other site 60480002018 putative Mg++ binding site [ion binding]; other site 60480002019 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 60480002020 nucleotide binding region [chemical binding]; other site 60480002021 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 60480002022 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 60480002023 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 60480002024 Transglycosylase; Region: Transgly; pfam00912 60480002025 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 60480002026 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 60480002027 OsmC-like protein; Region: OsmC; cl00767 60480002028 Regulator of replication initiation timing [Replication, recombination, and repair]; Region: COG4467; cl01853 60480002029 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 60480002030 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 60480002031 N-terminal plug; other site 60480002032 ligand-binding site [chemical binding]; other site 60480002033 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 60480002034 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 60480002035 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480002036 putative active site [active] 60480002037 heme pocket [chemical binding]; other site 60480002038 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 60480002039 putative active site [active] 60480002040 heme pocket [chemical binding]; other site 60480002041 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480002042 dimer interface [polypeptide binding]; other site 60480002043 putative CheW interface [polypeptide binding]; other site 60480002044 tetrathionate reductase subunit A; Provisional; Region: PRK14991 60480002045 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 60480002046 molybdopterin cofactor binding site; other site 60480002047 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 60480002048 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 60480002049 putative molybdopterin cofactor binding site; other site 60480002050 tetrathionate reductase subunit C; Provisional; Region: PRK14992 60480002051 tetrathionate reductase subunit B; Provisional; Region: PRK14993 60480002052 4Fe-4S binding domain; Region: Fer4; pfam00037 60480002053 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 60480002054 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 60480002055 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 60480002056 dimer interface [polypeptide binding]; other site 60480002057 phosphorylation site [posttranslational modification] 60480002058 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 60480002059 ATP binding site [chemical binding]; other site 60480002060 Mg2+ binding site [ion binding]; other site 60480002061 G-X-G motif; other site 60480002062 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 60480002063 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002064 active site 60480002065 phosphorylation site [posttranslational modification] 60480002066 intermolecular recognition site; other site 60480002067 dimerization interface [polypeptide binding]; other site 60480002068 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 60480002069 DNA binding residues [nucleotide binding] 60480002070 dimerization interface [polypeptide binding]; other site 60480002071 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 60480002072 Pleckstrin homology-like domain; Region: PH-like; cl17171 60480002073 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 60480002074 active site 60480002075 metal binding site [ion binding]; metal-binding site 60480002076 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480002077 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 60480002078 putative transposase OrfB; Reviewed; Region: PHA02517 60480002079 Integrase core domain; Region: rve; pfam00665 60480002080 Integrase core domain; Region: rve_3; pfam13683 60480002081 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 60480002082 hypothetical protein; Provisional; Region: PRK05208 60480002083 Nuclease-related domain; Region: NERD; pfam08378 60480002084 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 60480002085 AMP binding site [chemical binding]; other site 60480002086 metal binding site [ion binding]; metal-binding site 60480002087 active site 60480002088 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 60480002089 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480002090 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480002091 two-component response regulator; Provisional; Region: PRK11173 60480002092 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002093 active site 60480002094 phosphorylation site [posttranslational modification] 60480002095 intermolecular recognition site; other site 60480002096 dimerization interface [polypeptide binding]; other site 60480002097 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 60480002098 DNA binding site [nucleotide binding] 60480002099 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 60480002100 aspartate kinase III; Validated; Region: PRK09084 60480002101 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 60480002102 nucleotide binding site [chemical binding]; other site 60480002103 substrate binding site [chemical binding]; other site 60480002104 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 60480002105 dimer interface [polypeptide binding]; other site 60480002106 allosteric regulatory binding pocket; other site 60480002107 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 60480002108 dimer interface [polypeptide binding]; other site 60480002109 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 60480002110 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 60480002111 active site 60480002112 Zn binding site [ion binding]; other site 60480002113 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 60480002114 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 60480002115 Cl binding site [ion binding]; other site 60480002116 oligomer interface [polypeptide binding]; other site 60480002117 Uncharacterized protein family (UPF0231); Region: UPF0231; pfam06062 60480002118 transcriptional regulator NarL; Provisional; Region: PRK10651 60480002119 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002120 active site 60480002121 phosphorylation site [posttranslational modification] 60480002122 intermolecular recognition site; other site 60480002123 dimerization interface [polypeptide binding]; other site 60480002124 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 60480002125 DNA binding residues [nucleotide binding] 60480002126 dimerization interface [polypeptide binding]; other site 60480002127 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 60480002128 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 60480002129 HAMP domain; Region: HAMP; pfam00672 60480002130 dimerization interface [polypeptide binding]; other site 60480002131 Histidine kinase; Region: HisKA_3; pfam07730 60480002132 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 60480002133 ATP binding site [chemical binding]; other site 60480002134 Mg2+ binding site [ion binding]; other site 60480002135 G-X-G motif; other site 60480002136 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 60480002137 GAF domain; Region: GAF; pfam01590 60480002138 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480002139 metal binding site [ion binding]; metal-binding site 60480002140 active site 60480002141 I-site; other site 60480002142 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 60480002143 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 60480002144 active site 60480002145 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 60480002146 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 60480002147 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 60480002148 ATP binding site [chemical binding]; other site 60480002149 Transposase; Region: HTH_Tnp_1; cl17663 60480002150 putative outer membrane lipoprotein; Provisional; Region: PRK10510 60480002151 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480002152 ligand binding site [chemical binding]; other site 60480002153 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 60480002154 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional; Region: PRK03537 60480002155 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 60480002156 MgtE intracellular N domain; Region: MgtE_N; smart00924 60480002157 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 60480002158 Divalent cation transporter; Region: MgtE; pfam01769 60480002159 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 60480002160 dimerization domain swap beta strand [polypeptide binding]; other site 60480002161 regulatory protein interface [polypeptide binding]; other site 60480002162 active site 60480002163 regulatory phosphorylation site [posttranslational modification]; other site 60480002164 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 60480002165 AAA domain; Region: AAA_18; pfam13238 60480002166 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 60480002167 active site 60480002168 phosphorylation site [posttranslational modification] 60480002169 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 60480002170 30S subunit binding site; other site 60480002171 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 60480002172 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 60480002173 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 60480002174 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 60480002175 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 60480002176 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 60480002177 Walker A/P-loop; other site 60480002178 ATP binding site [chemical binding]; other site 60480002179 Q-loop/lid; other site 60480002180 ABC transporter signature motif; other site 60480002181 Walker B; other site 60480002182 D-loop; other site 60480002183 H-loop/switch region; other site 60480002184 OstA-like protein; Region: OstA; cl00844 60480002185 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 60480002186 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 60480002187 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 60480002188 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 60480002189 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 60480002190 active site 60480002191 motif I; other site 60480002192 motif II; other site 60480002193 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 60480002194 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 60480002195 putative active site [active] 60480002196 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 60480002197 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 60480002198 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 60480002199 Walker A/P-loop; other site 60480002200 ATP binding site [chemical binding]; other site 60480002201 Q-loop/lid; other site 60480002202 ABC transporter signature motif; other site 60480002203 Walker B; other site 60480002204 D-loop; other site 60480002205 H-loop/switch region; other site 60480002206 Permease; Region: Permease; cl00510 60480002207 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 60480002208 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 60480002209 mce related protein; Region: MCE; pfam02470 60480002210 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 60480002211 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 60480002212 anti sigma factor interaction site; other site 60480002213 regulatory phosphorylation site [posttranslational modification]; other site 60480002214 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 60480002215 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 60480002216 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 60480002217 hinge; other site 60480002218 active site 60480002219 Protein with unknown function (DUF469); Region: DUF469; pfam04320 60480002220 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 60480002221 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 60480002222 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 60480002223 S-adenosylmethionine binding site [chemical binding]; other site 60480002224 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 60480002225 dimer interface [polypeptide binding]; other site 60480002226 Alkaline phosphatase homologues; Region: alkPPc; smart00098 60480002227 active site 60480002228 glutathione synthetase; Provisional; Region: PRK05246 60480002229 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 60480002230 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 60480002231 RNA methyltransferase, RsmE family; Region: TIGR00046 60480002232 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 60480002233 Endonuclease I [DNA replication, recombination, and repair]; Region: EndA; COG2356 60480002234 hypothetical protein; Provisional; Region: PRK04860 60480002235 Zn-dependent metalloprotease, SprT family [General function prediction only]; Region: SprT; COG3091 60480002236 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 60480002237 putative substrate binding pocket [chemical binding]; other site 60480002238 AC domain interface; other site 60480002239 catalytic triad [active] 60480002240 AB domain interface; other site 60480002241 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 60480002242 LysR family transcriptional regulator; Provisional; Region: PRK14997 60480002243 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480002244 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 60480002245 putative effector binding pocket; other site 60480002246 dimerization interface [polypeptide binding]; other site 60480002247 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 60480002248 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 60480002249 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 60480002250 ATP-grasp domain; Region: ATP-grasp_4; cl17255 60480002251 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 60480002252 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 60480002253 carboxyltransferase (CT) interaction site; other site 60480002254 biotinylation site [posttranslational modification]; other site 60480002255 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 60480002256 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 60480002257 substrate binding pocket [chemical binding]; other site 60480002258 membrane-bound complex binding site; other site 60480002259 hinge residues; other site 60480002260 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480002261 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480002262 metal binding site [ion binding]; metal-binding site 60480002263 active site 60480002264 I-site; other site 60480002265 elongation factor G; Reviewed; Region: PRK00007 60480002266 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 60480002267 G1 box; other site 60480002268 putative GEF interaction site [polypeptide binding]; other site 60480002269 GTP/Mg2+ binding site [chemical binding]; other site 60480002270 Switch I region; other site 60480002271 G2 box; other site 60480002272 G3 box; other site 60480002273 Switch II region; other site 60480002274 G4 box; other site 60480002275 G5 box; other site 60480002276 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 60480002277 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 60480002278 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 60480002279 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480002280 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480002281 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 60480002282 putative dimerization interface [polypeptide binding]; other site 60480002283 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 60480002284 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 60480002285 4Fe-4S binding domain; Region: Fer4_5; pfam12801 60480002286 4Fe-4S binding domain; Region: Fer4_5; pfam12801 60480002287 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 60480002288 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 60480002289 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 60480002290 [4Fe-4S] binding site [ion binding]; other site 60480002291 molybdopterin cofactor binding site; other site 60480002292 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 60480002293 molybdopterin cofactor binding site; other site 60480002294 NapD protein; Region: NapD; pfam03927 60480002295 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 60480002296 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 60480002297 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 60480002298 Type II transport protein GspH; Region: GspH; pfam12019 60480002299 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 60480002300 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 60480002301 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 60480002302 FtsX-like permease family; Region: FtsX; pfam02687 60480002303 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 60480002304 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 60480002305 Walker A/P-loop; other site 60480002306 ATP binding site [chemical binding]; other site 60480002307 Q-loop/lid; other site 60480002308 ABC transporter signature motif; other site 60480002309 Walker B; other site 60480002310 D-loop; other site 60480002311 H-loop/switch region; other site 60480002312 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 60480002313 amino acid carrier protein; Region: agcS; TIGR00835 60480002314 Cache domain; Region: Cache_1; pfam02743 60480002315 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480002316 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 60480002317 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480002318 putative active site [active] 60480002319 heme pocket [chemical binding]; other site 60480002320 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480002321 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 60480002322 putative active site [active] 60480002323 heme pocket [chemical binding]; other site 60480002324 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 60480002325 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480002326 putative active site [active] 60480002327 heme pocket [chemical binding]; other site 60480002328 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 60480002329 putative active site [active] 60480002330 heme pocket [chemical binding]; other site 60480002331 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480002332 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 60480002333 dimer interface [polypeptide binding]; other site 60480002334 phosphorylation site [posttranslational modification] 60480002335 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 60480002336 ATP binding site [chemical binding]; other site 60480002337 Mg2+ binding site [ion binding]; other site 60480002338 G-X-G motif; other site 60480002339 Response regulator receiver domain; Region: Response_reg; pfam00072 60480002340 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002341 active site 60480002342 phosphorylation site [posttranslational modification] 60480002343 intermolecular recognition site; other site 60480002344 dimerization interface [polypeptide binding]; other site 60480002345 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002346 Response regulator receiver domain; Region: Response_reg; pfam00072 60480002347 active site 60480002348 phosphorylation site [posttranslational modification] 60480002349 intermolecular recognition site; other site 60480002350 dimerization interface [polypeptide binding]; other site 60480002351 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 60480002352 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 60480002353 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002354 active site 60480002355 phosphorylation site [posttranslational modification] 60480002356 intermolecular recognition site; other site 60480002357 dimerization interface [polypeptide binding]; other site 60480002358 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480002359 Zn2+ binding site [ion binding]; other site 60480002360 Mg2+ binding site [ion binding]; other site 60480002361 putative global regulator; Reviewed; Region: PRK09559 60480002362 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 60480002363 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 60480002364 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 60480002365 ligand binding site [chemical binding]; other site 60480002366 NAD binding site [chemical binding]; other site 60480002367 tetramer interface [polypeptide binding]; other site 60480002368 catalytic site [active] 60480002369 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 60480002370 L-serine binding site [chemical binding]; other site 60480002371 ACT domain interface; other site 60480002372 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 60480002373 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480002374 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 60480002375 DNA binding residues [nucleotide binding] 60480002376 dimerization interface [polypeptide binding]; other site 60480002377 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 60480002378 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 60480002379 Curlin associated repeat; Region: Curlin_rpt; pfam07012 60480002380 major curlin subunit; Provisional; Region: csgA; PRK10051 60480002381 Curlin associated repeat; Region: Curlin_rpt; pfam07012 60480002382 Curlin associated repeat; Region: Curlin_rpt; pfam07012 60480002383 Curlin associated repeat; Region: Curlin_rpt; pfam07012 60480002384 Curlin associated repeat; Region: Curlin_rpt; pfam07012 60480002385 Curlin associated repeat; Region: Curlin_rpt; pfam07012 60480002386 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 60480002387 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 60480002388 catalytic triad [active] 60480002389 putative active site [active] 60480002390 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 60480002391 FOG: PKD repeat [General function prediction only]; Region: COG3291 60480002392 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 60480002393 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 60480002394 Pantoate-beta-alanine ligase; Region: PanC; cd00560 60480002395 pantoate--beta-alanine ligase; Region: panC; TIGR00018 60480002396 active site 60480002397 ATP-binding site [chemical binding]; other site 60480002398 pantoate-binding site; other site 60480002399 HXXH motif; other site 60480002400 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 60480002401 oligomerization interface [polypeptide binding]; other site 60480002402 active site 60480002403 metal binding site [ion binding]; metal-binding site 60480002404 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 60480002405 catalytic center binding site [active] 60480002406 ATP binding site [chemical binding]; other site 60480002407 poly(A) polymerase; Region: pcnB; TIGR01942 60480002408 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 60480002409 active site 60480002410 NTP binding site [chemical binding]; other site 60480002411 metal binding triad [ion binding]; metal-binding site 60480002412 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 60480002413 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 60480002414 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 60480002415 active site 60480002416 nucleotide binding site [chemical binding]; other site 60480002417 HIGH motif; other site 60480002418 KMSKS motif; other site 60480002419 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 60480002420 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 60480002421 aminopeptidase B; Provisional; Region: PRK05015 60480002422 Peptidase; Region: DUF3663; pfam12404 60480002423 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 60480002424 interface (dimer of trimers) [polypeptide binding]; other site 60480002425 Substrate-binding/catalytic site; other site 60480002426 Zn-binding sites [ion binding]; other site 60480002427 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 60480002428 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480002429 Coenzyme A binding pocket [chemical binding]; other site 60480002430 phosphoribulokinase; Provisional; Region: PRK15453 60480002431 active site 60480002432 Uncharacterized protein family (UPF0270); Region: UPF0270; pfam06794 60480002433 putative hydrolase; Provisional; Region: PRK10985 60480002434 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 60480002435 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 60480002436 Uncharacterized conserved protein [Function unknown]; Region: COG3791 60480002437 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 60480002438 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 60480002439 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480002440 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480002441 ABC transporter; Region: ABC_tran_2; pfam12848 60480002442 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480002443 conserved hypothetical metal-binding protein; Region: TIGR02443 60480002444 Domain of unknown function (DUF4041); Region: DUF4041; pfam13250 60480002445 This entry represents the putative helicase A859L; Region: T5orf172; smart00974 60480002446 Pirin-related protein [General function prediction only]; Region: COG1741 60480002447 Pirin; Region: Pirin; pfam02678 60480002448 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 60480002449 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 60480002450 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 60480002451 ATP binding site [chemical binding]; other site 60480002452 Mg++ binding site [ion binding]; other site 60480002453 motif III; other site 60480002454 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 60480002455 nucleotide binding region [chemical binding]; other site 60480002456 ATP-binding site [chemical binding]; other site 60480002457 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 60480002458 putative RNA binding site [nucleotide binding]; other site 60480002459 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480002460 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 60480002461 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 60480002462 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 60480002463 active site 60480002464 catalytic tetrad [active] 60480002465 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 60480002466 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 60480002467 E3 interaction surface; other site 60480002468 lipoyl attachment site [posttranslational modification]; other site 60480002469 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 60480002470 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 60480002471 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 60480002472 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 60480002473 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 60480002474 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 60480002475 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 60480002476 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 60480002477 catalytic loop [active] 60480002478 iron binding site [ion binding]; other site 60480002479 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 60480002480 FAD binding pocket [chemical binding]; other site 60480002481 FAD binding motif [chemical binding]; other site 60480002482 phosphate binding motif [ion binding]; other site 60480002483 beta-alpha-beta structure motif; other site 60480002484 NAD binding pocket [chemical binding]; other site 60480002485 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 60480002486 Transposase; Region: DEDD_Tnp_IS110; pfam01548 60480002487 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 60480002488 Beta-lactamase; Region: Beta-lactamase; pfam00144 60480002489 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 60480002490 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 60480002491 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 60480002492 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 60480002493 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 60480002494 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 60480002495 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 60480002496 MarR family; Region: MarR; pfam01047 60480002497 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 60480002498 inosine/xanthosine triphosphatase; Reviewed; Region: PRK05074 60480002499 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 60480002500 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 60480002501 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 60480002502 active site 60480002503 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 60480002504 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 60480002505 serine transporter; Region: stp; TIGR00814 60480002506 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480002507 Coenzyme A binding pocket [chemical binding]; other site 60480002508 Domain of unknown function (DUF4234); Region: DUF4234; pfam14018 60480002509 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480002510 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 60480002511 META domain; Region: META; pfam03724 60480002512 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480002513 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480002514 metal binding site [ion binding]; metal-binding site 60480002515 active site 60480002516 I-site; other site 60480002517 Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]; Region: CelB; COG1455 60480002518 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 60480002519 S-adenosylmethionine synthetase; Validated; Region: PRK05250 60480002520 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 60480002521 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 60480002522 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 60480002523 transketolase; Reviewed; Region: PRK12753 60480002524 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 60480002525 TPP-binding site [chemical binding]; other site 60480002526 dimer interface [polypeptide binding]; other site 60480002527 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 60480002528 PYR/PP interface [polypeptide binding]; other site 60480002529 dimer interface [polypeptide binding]; other site 60480002530 TPP binding site [chemical binding]; other site 60480002531 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 60480002532 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 60480002533 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 60480002534 Phosphoglycerate kinase; Region: PGK; pfam00162 60480002535 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 60480002536 substrate binding site [chemical binding]; other site 60480002537 hinge regions; other site 60480002538 ADP binding site [chemical binding]; other site 60480002539 catalytic site [active] 60480002540 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 60480002541 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 60480002542 intersubunit interface [polypeptide binding]; other site 60480002543 active site 60480002544 zinc binding site [ion binding]; other site 60480002545 Na+ binding site [ion binding]; other site 60480002546 Protein of unknown function, DUF481; Region: DUF481; pfam04338 60480002547 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 60480002548 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 60480002549 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 60480002550 DNA binding site [nucleotide binding] 60480002551 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 60480002552 DNA binding site [nucleotide binding] 60480002553 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 60480002554 PAS domain; Region: PAS_9; pfam13426 60480002555 putative active site [active] 60480002556 heme pocket [chemical binding]; other site 60480002557 PAS domain; Region: PAS_9; pfam13426 60480002558 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480002559 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 60480002560 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 60480002561 FeS/SAM binding site; other site 60480002562 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480002563 Protein export membrane protein; Region: SecD_SecF; cl14618 60480002564 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480002565 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480002566 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 60480002567 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480002568 ATP binding site [chemical binding]; other site 60480002569 Mg++ binding site [ion binding]; other site 60480002570 motif III; other site 60480002571 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 60480002572 nucleotide binding region [chemical binding]; other site 60480002573 ATP-binding site [chemical binding]; other site 60480002574 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 60480002575 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 60480002576 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 60480002577 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 60480002578 PAS domain S-box; Region: sensory_box; TIGR00229 60480002579 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 60480002580 putative active site [active] 60480002581 heme pocket [chemical binding]; other site 60480002582 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 60480002583 PAS fold; Region: PAS_3; pfam08447 60480002584 putative active site [active] 60480002585 heme pocket [chemical binding]; other site 60480002586 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480002587 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 60480002588 dimer interface [polypeptide binding]; other site 60480002589 phosphorylation site [posttranslational modification] 60480002590 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 60480002591 ATP binding site [chemical binding]; other site 60480002592 Mg2+ binding site [ion binding]; other site 60480002593 G-X-G motif; other site 60480002594 Response regulator receiver domain; Region: Response_reg; pfam00072 60480002595 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002596 active site 60480002597 phosphorylation site [posttranslational modification] 60480002598 intermolecular recognition site; other site 60480002599 dimerization interface [polypeptide binding]; other site 60480002600 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 60480002601 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 60480002602 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002603 active site 60480002604 phosphorylation site [posttranslational modification] 60480002605 intermolecular recognition site; other site 60480002606 dimerization interface [polypeptide binding]; other site 60480002607 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480002608 Zn2+ binding site [ion binding]; other site 60480002609 Mg2+ binding site [ion binding]; other site 60480002610 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 60480002611 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 60480002612 S-adenosylmethionine binding site [chemical binding]; other site 60480002613 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 60480002614 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 60480002615 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 60480002616 active site 60480002617 Int/Topo IB signature motif; other site 60480002618 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 60480002619 dimerization domain [polypeptide binding]; other site 60480002620 dimer interface [polypeptide binding]; other site 60480002621 catalytic residues [active] 60480002622 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 60480002623 DHH family; Region: DHH; pfam01368 60480002624 DHHA1 domain; Region: DHHA1; pfam02272 60480002625 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 60480002626 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480002627 Coenzyme A binding pocket [chemical binding]; other site 60480002628 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 60480002629 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 60480002630 catalytic residue [active] 60480002631 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 60480002632 catalytic residues [active] 60480002633 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480002634 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 60480002635 peroxiredoxin; Region: AhpC; TIGR03137 60480002636 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 60480002637 dimer interface [polypeptide binding]; other site 60480002638 decamer (pentamer of dimers) interface [polypeptide binding]; other site 60480002639 catalytic triad [active] 60480002640 peroxidatic and resolving cysteines [active] 60480002641 multifunctional aminopeptidase A; Provisional; Region: PRK00913 60480002642 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 60480002643 interface (dimer of trimers) [polypeptide binding]; other site 60480002644 Substrate-binding/catalytic site; other site 60480002645 Zn-binding sites [ion binding]; other site 60480002646 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 60480002647 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 60480002648 Mechanosensitive ion channel; Region: MS_channel; pfam00924 60480002649 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 60480002650 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 60480002651 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 60480002652 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 60480002653 putative ligand binding site [chemical binding]; other site 60480002654 putative NAD binding site [chemical binding]; other site 60480002655 catalytic site [active] 60480002656 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 60480002657 heme-binding residues [chemical binding]; other site 60480002658 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 60480002659 L-aspartate oxidase; Provisional; Region: PRK06175 60480002660 tellurite resistance protein TehB; Provisional; Region: PRK11207 60480002661 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 60480002662 S-adenosylmethionine binding site [chemical binding]; other site 60480002663 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 60480002664 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 60480002665 Transcriptional regulators [Transcription]; Region: MarR; COG1846 60480002666 MarR family; Region: MarR; pfam01047 60480002667 FAD dependent oxidoreductase; Region: DAO; pfam01266 60480002668 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 60480002669 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 60480002670 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 60480002671 dimer interface [polypeptide binding]; other site 60480002672 phosphorylation site [posttranslational modification] 60480002673 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 60480002674 ATP binding site [chemical binding]; other site 60480002675 Mg2+ binding site [ion binding]; other site 60480002676 G-X-G motif; other site 60480002677 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480002678 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002679 active site 60480002680 phosphorylation site [posttranslational modification] 60480002681 intermolecular recognition site; other site 60480002682 dimerization interface [polypeptide binding]; other site 60480002683 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 60480002684 DNA binding site [nucleotide binding] 60480002685 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 60480002686 MltA-interacting protein MipA; Region: MipA; cl01504 60480002687 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 60480002688 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 60480002689 active site 60480002690 catalytic triad [active] 60480002691 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 60480002692 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480002693 Peptidase S8 family domain in Vpr-like proteins; Region: Peptidases_S8_subtilisin_Vpr-like; cd07474 60480002694 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 60480002695 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 60480002696 Chromate transporter; Region: Chromate_transp; pfam02417 60480002697 Cache domain; Region: Cache_2; pfam08269 60480002698 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 60480002699 dimerization interface [polypeptide binding]; other site 60480002700 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480002701 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480002702 dimer interface [polypeptide binding]; other site 60480002703 putative CheW interface [polypeptide binding]; other site 60480002704 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 60480002705 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 60480002706 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480002707 4Fe-4S binding domain; Region: Fer4_6; pfam12837 60480002708 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 60480002709 4Fe-4S binding domain; Region: Fer4; pfam00037 60480002710 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 60480002711 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 60480002712 [4Fe-4S] binding site [ion binding]; other site 60480002713 molybdopterin cofactor binding site; other site 60480002714 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 60480002715 molybdopterin cofactor binding site; other site 60480002716 peptide chain release factor 2; Validated; Region: prfB; PRK00578 60480002717 This domain is found in peptide chain release factors; Region: PCRF; smart00937 60480002718 RF-1 domain; Region: RF-1; pfam00472 60480002719 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 60480002720 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 60480002721 dimer interface [polypeptide binding]; other site 60480002722 putative anticodon binding site; other site 60480002723 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 60480002724 motif 1; other site 60480002725 active site 60480002726 motif 2; other site 60480002727 motif 3; other site 60480002728 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 60480002729 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 60480002730 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 60480002731 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480002732 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480002733 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480002734 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480002735 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480002736 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480002737 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 60480002738 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480002739 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480002740 AAA ATPase domain; Region: AAA_15; pfam13175 60480002741 Walker A/P-loop; other site 60480002742 ATP binding site [chemical binding]; other site 60480002743 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480002744 ABC transporter signature motif; other site 60480002745 Walker B; other site 60480002746 D-loop; other site 60480002747 H-loop/switch region; other site 60480002748 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 60480002749 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 60480002750 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 60480002751 substrate binding pocket [chemical binding]; other site 60480002752 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 60480002753 B12 binding site [chemical binding]; other site 60480002754 cobalt ligand [ion binding]; other site 60480002755 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 60480002756 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 60480002757 catalytic core [active] 60480002758 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 60480002759 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 60480002760 Walker A/P-loop; other site 60480002761 ATP binding site [chemical binding]; other site 60480002762 Q-loop/lid; other site 60480002763 ABC transporter signature motif; other site 60480002764 Walker B; other site 60480002765 D-loop; other site 60480002766 H-loop/switch region; other site 60480002767 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 60480002768 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 60480002769 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 60480002770 ABC-ATPase subunit interface; other site 60480002771 dimer interface [polypeptide binding]; other site 60480002772 putative PBP binding regions; other site 60480002773 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 60480002774 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 60480002775 active site pocket [active] 60480002776 putative dimer interface [polypeptide binding]; other site 60480002777 putative cataytic base [active] 60480002778 cobalamin synthase; Reviewed; Region: cobS; PRK00235 60480002779 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 60480002780 homotrimer interface [polypeptide binding]; other site 60480002781 Walker A motif; other site 60480002782 GTP binding site [chemical binding]; other site 60480002783 Walker B motif; other site 60480002784 cobyric acid synthase; Provisional; Region: PRK00784 60480002785 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 60480002786 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 60480002787 catalytic triad [active] 60480002788 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 60480002789 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 60480002790 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 60480002791 homodimer interface [polypeptide binding]; other site 60480002792 Walker A motif; other site 60480002793 ATP binding site [chemical binding]; other site 60480002794 hydroxycobalamin binding site [chemical binding]; other site 60480002795 Walker B motif; other site 60480002796 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 60480002797 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 60480002798 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 60480002799 cobalamin binding residues [chemical binding]; other site 60480002800 putative BtuC binding residues; other site 60480002801 dimer interface [polypeptide binding]; other site 60480002802 MAPEG family; Region: MAPEG; cl09190 60480002803 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 60480002804 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 60480002805 Type II transport protein GspH; Region: GspH; pfam12019 60480002806 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 60480002807 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 60480002808 PilX N-terminal; Region: PilX_N; pfam14341 60480002809 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 60480002810 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 60480002811 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 60480002812 active site 60480002813 substrate binding pocket [chemical binding]; other site 60480002814 dimer interface [polypeptide binding]; other site 60480002815 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480002816 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480002817 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480002818 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 60480002819 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 60480002820 Walker A/P-loop; other site 60480002821 ATP binding site [chemical binding]; other site 60480002822 Q-loop/lid; other site 60480002823 ABC transporter signature motif; other site 60480002824 Walker B; other site 60480002825 D-loop; other site 60480002826 H-loop/switch region; other site 60480002827 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 60480002828 FtsX-like permease family; Region: FtsX; pfam02687 60480002829 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 60480002830 FtsX-like permease family; Region: FtsX; pfam02687 60480002831 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 60480002832 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480002833 active site 60480002834 phosphorylation site [posttranslational modification] 60480002835 intermolecular recognition site; other site 60480002836 dimerization interface [polypeptide binding]; other site 60480002837 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 60480002838 Walker A motif; other site 60480002839 ATP binding site [chemical binding]; other site 60480002840 Walker B motif; other site 60480002841 arginine finger; other site 60480002842 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480002843 HAMP domain; Region: HAMP; pfam00672 60480002844 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 60480002845 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 60480002846 ATP binding site [chemical binding]; other site 60480002847 Mg2+ binding site [ion binding]; other site 60480002848 G-X-G motif; other site 60480002849 Curli assembly protein CsgE; Region: CsgE; pfam10627 60480002850 Type VIII secretion system (T8SS), CsgF protein; Region: CsgF; cl08082 60480002851 Curli production assembly/transport component CsgG; Region: CsgG; pfam03783 60480002852 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480002853 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480002854 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 60480002855 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 60480002856 NAD(P) binding site [chemical binding]; other site 60480002857 catalytic residues [active] 60480002858 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 60480002859 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 60480002860 Ligand Binding Site [chemical binding]; other site 60480002861 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 60480002862 Ligand Binding Site [chemical binding]; other site 60480002863 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480002864 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 60480002865 membrane-bound complex binding site; other site 60480002866 hinge residues; other site 60480002867 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 60480002868 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; pfam09904 60480002869 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 60480002870 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 60480002871 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 60480002872 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 60480002873 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 60480002874 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480002875 Walker A/P-loop; other site 60480002876 ATP binding site [chemical binding]; other site 60480002877 Q-loop/lid; other site 60480002878 ABC transporter signature motif; other site 60480002879 Walker B; other site 60480002880 D-loop; other site 60480002881 H-loop/switch region; other site 60480002882 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 60480002883 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 60480002884 acyl-activating enzyme (AAE) consensus motif; other site 60480002885 putative AMP binding site [chemical binding]; other site 60480002886 putative active site [active] 60480002887 putative CoA binding site [chemical binding]; other site 60480002888 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 60480002889 active site 60480002890 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 60480002891 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 60480002892 4Fe-4S binding domain; Region: Fer4_5; pfam12801 60480002893 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 60480002894 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 60480002895 PAS domain S-box; Region: sensory_box; TIGR00229 60480002896 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 60480002897 putative active site [active] 60480002898 heme pocket [chemical binding]; other site 60480002899 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 60480002900 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 60480002901 Walker A motif; other site 60480002902 ATP binding site [chemical binding]; other site 60480002903 Walker B motif; other site 60480002904 arginine finger; other site 60480002905 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480002906 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 60480002907 DsbD alpha interface [polypeptide binding]; other site 60480002908 catalytic residues [active] 60480002909 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 60480002910 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 60480002911 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 60480002912 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 60480002913 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 60480002914 ligand binding site [chemical binding]; other site 60480002915 active site 60480002916 UGI interface [polypeptide binding]; other site 60480002917 catalytic site [active] 60480002918 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 60480002919 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 60480002920 substrate binding pocket [chemical binding]; other site 60480002921 chain length determination region; other site 60480002922 substrate-Mg2+ binding site; other site 60480002923 catalytic residues [active] 60480002924 aspartate-rich region 1; other site 60480002925 active site lid residues [active] 60480002926 aspartate-rich region 2; other site 60480002927 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 60480002928 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 60480002929 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 60480002930 GTPase CgtA; Reviewed; Region: obgE; PRK12298 60480002931 GTP1/OBG; Region: GTP1_OBG; pfam01018 60480002932 Obg GTPase; Region: Obg; cd01898 60480002933 G1 box; other site 60480002934 GTP/Mg2+ binding site [chemical binding]; other site 60480002935 Switch I region; other site 60480002936 G2 box; other site 60480002937 G3 box; other site 60480002938 Switch II region; other site 60480002939 G4 box; other site 60480002940 G5 box; other site 60480002941 Uncharacterized conserved protein [Function unknown]; Region: COG2966 60480002942 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 60480002943 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 60480002944 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 60480002945 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 60480002946 NADP+ binding site [chemical binding]; other site 60480002947 folate binding site [chemical binding]; other site 60480002948 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 60480002949 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 60480002950 dimerization interface [polypeptide binding]; other site 60480002951 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480002952 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480002953 dimer interface [polypeptide binding]; other site 60480002954 putative CheW interface [polypeptide binding]; other site 60480002955 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 60480002956 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 60480002957 active site 60480002958 metal binding site [ion binding]; metal-binding site 60480002959 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 60480002960 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 60480002961 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 60480002962 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 60480002963 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 60480002964 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 60480002965 SurA N-terminal domain; Region: SurA_N; pfam09312 60480002966 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 60480002967 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 60480002968 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 60480002969 OstA-like protein; Region: OstA; cl00844 60480002970 Organic solvent tolerance protein; Region: OstA_C; pfam04453 60480002971 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 60480002972 Phosphotransferase enzyme family; Region: APH; pfam01636 60480002973 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 60480002974 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 60480002975 Substrate binding site; other site 60480002976 metal-binding site 60480002977 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 60480002978 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 60480002979 putative metal binding site [ion binding]; other site 60480002980 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 60480002981 HSP70 interaction site [polypeptide binding]; other site 60480002982 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 60480002983 glycerate dehydrogenase; Provisional; Region: PRK06487 60480002984 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 60480002985 putative ligand binding site [chemical binding]; other site 60480002986 putative NAD binding site [chemical binding]; other site 60480002987 catalytic site [active] 60480002988 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 60480002989 Transposase; Region: DEDD_Tnp_IS110; pfam01548 60480002990 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 60480002991 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 60480002992 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480002993 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 60480002994 ligand binding site [chemical binding]; other site 60480002995 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 60480002996 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 60480002997 RNA binding surface [nucleotide binding]; other site 60480002998 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 60480002999 probable active site [active] 60480003000 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 60480003001 FMN-binding domain; Region: FMN_bind; pfam04205 60480003002 ApbE family; Region: ApbE; pfam02424 60480003003 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 60480003004 dimerization interface [polypeptide binding]; other site 60480003005 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480003006 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480003007 dimer interface [polypeptide binding]; other site 60480003008 putative CheW interface [polypeptide binding]; other site 60480003009 EamA-like transporter family; Region: EamA; pfam00892 60480003010 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 60480003011 EamA-like transporter family; Region: EamA; pfam00892 60480003012 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 60480003013 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 60480003014 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 60480003015 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 60480003016 homodimer interface [polypeptide binding]; other site 60480003017 substrate-cofactor binding pocket; other site 60480003018 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480003019 catalytic residue [active] 60480003020 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 60480003021 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 60480003022 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 60480003023 S-adenosylmethionine binding site [chemical binding]; other site 60480003024 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 60480003025 BolA-like protein; Region: BolA; cl00386 60480003026 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 60480003027 S-ribosylhomocysteinase; Provisional; Region: PRK02260 60480003028 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480003029 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 60480003030 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 60480003031 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 60480003032 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 60480003033 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 60480003034 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 60480003035 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 60480003036 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 60480003037 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 60480003038 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 60480003039 FAD binding pocket [chemical binding]; other site 60480003040 FAD binding motif [chemical binding]; other site 60480003041 phosphate binding motif [ion binding]; other site 60480003042 beta-alpha-beta structure motif; other site 60480003043 NAD binding pocket [chemical binding]; other site 60480003044 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 60480003045 ApbE family; Region: ApbE; pfam02424 60480003046 Protein of unknown function (DUF539); Region: DUF539; cl01129 60480003047 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 60480003048 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 60480003049 heme binding site [chemical binding]; other site 60480003050 ferroxidase pore; other site 60480003051 ferroxidase diiron center [ion binding]; other site 60480003052 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 60480003053 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 60480003054 heme binding site [chemical binding]; other site 60480003055 ferroxidase pore; other site 60480003056 ferroxidase diiron center [ion binding]; other site 60480003057 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480003058 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 60480003059 dimerization interface [polypeptide binding]; other site 60480003060 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480003061 dimer interface [polypeptide binding]; other site 60480003062 putative CheW interface [polypeptide binding]; other site 60480003063 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 60480003064 active site 60480003065 DNA polymerase IV; Validated; Region: PRK02406 60480003066 DNA binding site [nucleotide binding] 60480003067 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 60480003068 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 60480003069 metal binding site [ion binding]; metal-binding site 60480003070 dimer interface [polypeptide binding]; other site 60480003071 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 60480003072 interface (dimer of trimers) [polypeptide binding]; other site 60480003073 Substrate-binding/catalytic site; other site 60480003074 Zn-binding sites [ion binding]; other site 60480003075 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 60480003076 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 60480003077 N-terminal plug; other site 60480003078 ligand-binding site [chemical binding]; other site 60480003079 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 60480003080 gamma-glutamyl kinase; Provisional; Region: PRK05429 60480003081 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 60480003082 nucleotide binding site [chemical binding]; other site 60480003083 homotetrameric interface [polypeptide binding]; other site 60480003084 putative phosphate binding site [ion binding]; other site 60480003085 putative allosteric binding site; other site 60480003086 PUA domain; Region: PUA; pfam01472 60480003087 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 60480003088 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 60480003089 putative catalytic cysteine [active] 60480003090 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 60480003091 putative deacylase active site [active] 60480003092 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 60480003093 EamA-like transporter family; Region: EamA; pfam00892 60480003094 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 60480003095 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 60480003096 nucleotide binding site [chemical binding]; other site 60480003097 chaperone protein DnaJ; Provisional; Region: PRK10767 60480003098 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 60480003099 HSP70 interaction site [polypeptide binding]; other site 60480003100 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 60480003101 substrate binding site [polypeptide binding]; other site 60480003102 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 60480003103 Zn binding sites [ion binding]; other site 60480003104 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 60480003105 dimer interface [polypeptide binding]; other site 60480003106 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 60480003107 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 60480003108 ATP binding site [chemical binding]; other site 60480003109 putative Mg++ binding site [ion binding]; other site 60480003110 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 60480003111 nucleotide binding region [chemical binding]; other site 60480003112 ATP-binding site [chemical binding]; other site 60480003113 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 60480003114 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 60480003115 Peptidase family M48; Region: Peptidase_M48; pfam01435 60480003116 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 60480003117 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 60480003118 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480003119 dihydrodipicolinate reductase; Provisional; Region: PRK00048 60480003120 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 60480003121 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 60480003122 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 60480003123 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 60480003124 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 60480003125 catalytic site [active] 60480003126 subunit interface [polypeptide binding]; other site 60480003127 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 60480003128 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 60480003129 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 60480003130 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 60480003131 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 60480003132 ATP-grasp domain; Region: ATP-grasp_4; cl17255 60480003133 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 60480003134 IMP binding site; other site 60480003135 dimer interface [polypeptide binding]; other site 60480003136 interdomain contacts; other site 60480003137 partial ornithine binding site; other site 60480003138 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480003139 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 60480003140 substrate binding pocket [chemical binding]; other site 60480003141 membrane-bound complex binding site; other site 60480003142 hinge residues; other site 60480003143 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480003144 dimer interface [polypeptide binding]; other site 60480003145 putative CheW interface [polypeptide binding]; other site 60480003146 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 60480003147 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 60480003148 putative catalytic site [active] 60480003149 putative metal binding site [ion binding]; other site 60480003150 putative phosphate binding site [ion binding]; other site 60480003151 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 60480003152 putative catalytic site [active] 60480003153 putative phosphate binding site [ion binding]; other site 60480003154 putative metal binding site [ion binding]; other site 60480003155 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 60480003156 hypothetical protein; Provisional; Region: PRK05409 60480003157 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 60480003158 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 60480003159 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 60480003160 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 60480003161 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 60480003162 putative RNA binding site [nucleotide binding]; other site 60480003163 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 60480003164 S-adenosylmethionine binding site [chemical binding]; other site 60480003165 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 60480003166 tetramer (dimer of dimers) interface [polypeptide binding]; other site 60480003167 active site 60480003168 dimer interface [polypeptide binding]; other site 60480003169 Protein of unknown function (DUF808); Region: DUF808; pfam05661 60480003170 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 60480003171 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 60480003172 catalytic site [active] 60480003173 putative active site [active] 60480003174 putative substrate binding site [chemical binding]; other site 60480003175 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480003176 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 60480003177 N-terminal plug; other site 60480003178 ligand-binding site [chemical binding]; other site 60480003179 Predicted membrane protein [Function unknown]; Region: COG3503 60480003180 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 60480003181 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 60480003182 dimerization interface [polypeptide binding]; other site 60480003183 DPS ferroxidase diiron center [ion binding]; other site 60480003184 ion pore; other site 60480003185 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 60480003186 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 60480003187 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480003188 Coenzyme A binding pocket [chemical binding]; other site 60480003189 lipoyl synthase; Provisional; Region: PRK05481 60480003190 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 60480003191 FeS/SAM binding site; other site 60480003192 lipoate-protein ligase B; Provisional; Region: PRK14342 60480003193 hypothetical protein; Provisional; Region: PRK04998 60480003194 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 60480003195 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 60480003196 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 60480003197 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 60480003198 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 60480003199 Sporulation related domain; Region: SPOR; pfam05036 60480003200 Transglycosylase SLT domain; Region: SLT_2; pfam13406 60480003201 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 60480003202 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480003203 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 60480003204 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 60480003205 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 60480003206 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 60480003207 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 60480003208 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 60480003209 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 60480003210 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 60480003211 active site 60480003212 (T/H)XGH motif; other site 60480003213 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 60480003214 DNA polymerase III, delta subunit; Region: holA; TIGR01128 60480003215 Lipopolysaccharide-assembly; Region: LptE; cl01125 60480003216 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 60480003217 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 60480003218 HIGH motif; other site 60480003219 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 60480003220 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 60480003221 active site 60480003222 KMSKS motif; other site 60480003223 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 60480003224 tRNA binding surface [nucleotide binding]; other site 60480003225 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 60480003226 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 60480003227 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 60480003228 putative active site [active] 60480003229 catalytic triad [active] 60480003230 putative dimer interface [polypeptide binding]; other site 60480003231 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 60480003232 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 60480003233 Transporter associated domain; Region: CorC_HlyC; smart01091 60480003234 metal-binding heat shock protein; Provisional; Region: PRK00016 60480003235 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 60480003236 PhoH-like protein; Region: PhoH; pfam02562 60480003237 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 60480003238 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 60480003239 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 60480003240 FeS/SAM binding site; other site 60480003241 TRAM domain; Region: TRAM; pfam01938 60480003242 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 60480003243 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 60480003244 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 60480003245 putative active site [active] 60480003246 catalytic residue [active] 60480003247 GTP-binding protein YchF; Reviewed; Region: PRK09601 60480003248 YchF GTPase; Region: YchF; cd01900 60480003249 G1 box; other site 60480003250 GTP/Mg2+ binding site [chemical binding]; other site 60480003251 Switch I region; other site 60480003252 G2 box; other site 60480003253 Switch II region; other site 60480003254 G3 box; other site 60480003255 G4 box; other site 60480003256 G5 box; other site 60480003257 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 60480003258 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 60480003259 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 60480003260 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 60480003261 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 60480003262 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 60480003263 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 60480003264 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 60480003265 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 60480003266 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 60480003267 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 60480003268 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 60480003269 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 60480003270 Protein export membrane protein; Region: SecD_SecF; pfam02355 60480003271 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 60480003272 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 60480003273 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 60480003274 S-adenosylmethionine binding site [chemical binding]; other site 60480003275 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 60480003276 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 60480003277 Walker A motif; other site 60480003278 ATP binding site [chemical binding]; other site 60480003279 Walker B motif; other site 60480003280 arginine finger; other site 60480003281 Peptidase family M41; Region: Peptidase_M41; pfam01434 60480003282 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 60480003283 dihydropteroate synthase; Region: DHPS; TIGR01496 60480003284 substrate binding pocket [chemical binding]; other site 60480003285 dimer interface [polypeptide binding]; other site 60480003286 inhibitor binding site; inhibition site 60480003287 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 60480003288 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 60480003289 active site 60480003290 substrate binding site [chemical binding]; other site 60480003291 metal binding site [ion binding]; metal-binding site 60480003292 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 60480003293 triosephosphate isomerase; Provisional; Region: PRK14567 60480003294 substrate binding site [chemical binding]; other site 60480003295 dimer interface [polypeptide binding]; other site 60480003296 catalytic triad [active] 60480003297 Preprotein translocase SecG subunit; Region: SecG; pfam03840 60480003298 ribosome maturation protein RimP; Reviewed; Region: PRK00092 60480003299 Sm and related proteins; Region: Sm_like; cl00259 60480003300 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 60480003301 putative oligomer interface [polypeptide binding]; other site 60480003302 putative RNA binding site [nucleotide binding]; other site 60480003303 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 60480003304 NusA N-terminal domain; Region: NusA_N; pfam08529 60480003305 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 60480003306 RNA binding site [nucleotide binding]; other site 60480003307 homodimer interface [polypeptide binding]; other site 60480003308 NusA-like KH domain; Region: KH_5; pfam13184 60480003309 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 60480003310 G-X-X-G motif; other site 60480003311 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 60480003312 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 60480003313 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 60480003314 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 60480003315 translation initiation factor IF-2; Region: IF-2; TIGR00487 60480003316 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 60480003317 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 60480003318 G1 box; other site 60480003319 putative GEF interaction site [polypeptide binding]; other site 60480003320 GTP/Mg2+ binding site [chemical binding]; other site 60480003321 Switch I region; other site 60480003322 G2 box; other site 60480003323 G3 box; other site 60480003324 Switch II region; other site 60480003325 G4 box; other site 60480003326 G5 box; other site 60480003327 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 60480003328 Translation-initiation factor 2; Region: IF-2; pfam11987 60480003329 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 60480003330 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 60480003331 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 60480003332 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 60480003333 RNA binding site [nucleotide binding]; other site 60480003334 active site 60480003335 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 60480003336 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 60480003337 16S/18S rRNA binding site [nucleotide binding]; other site 60480003338 S13e-L30e interaction site [polypeptide binding]; other site 60480003339 25S rRNA binding site [nucleotide binding]; other site 60480003340 biofilm formation regulator HmsP; Provisional; Region: PRK11829 60480003341 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480003342 metal binding site [ion binding]; metal-binding site 60480003343 active site 60480003344 I-site; other site 60480003345 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 60480003346 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 60480003347 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 60480003348 RNase E interface [polypeptide binding]; other site 60480003349 trimer interface [polypeptide binding]; other site 60480003350 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 60480003351 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 60480003352 RNase E interface [polypeptide binding]; other site 60480003353 trimer interface [polypeptide binding]; other site 60480003354 active site 60480003355 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 60480003356 putative nucleic acid binding region [nucleotide binding]; other site 60480003357 G-X-X-G motif; other site 60480003358 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 60480003359 RNA binding site [nucleotide binding]; other site 60480003360 domain interface; other site 60480003361 lipoprotein NlpI; Provisional; Region: PRK11189 60480003362 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 60480003363 TPR motif; other site 60480003364 binding surface 60480003365 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 60480003366 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 60480003367 G1 box; other site 60480003368 putative GEF interaction site [polypeptide binding]; other site 60480003369 GTP/Mg2+ binding site [chemical binding]; other site 60480003370 Switch I region; other site 60480003371 G2 box; other site 60480003372 G3 box; other site 60480003373 Switch II region; other site 60480003374 G4 box; other site 60480003375 G5 box; other site 60480003376 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 60480003377 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 60480003378 active site 60480003379 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 60480003380 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 60480003381 Nucleoside recognition; Region: Gate; pfam07670 60480003382 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 60480003383 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; pfam03502 60480003384 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 60480003385 intersubunit interface [polypeptide binding]; other site 60480003386 active site 60480003387 catalytic residue [active] 60480003388 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 60480003389 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 60480003390 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 60480003391 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 60480003392 phosphopentomutase; Provisional; Region: PRK05362 60480003393 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 60480003394 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 60480003395 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 60480003396 phosphoserine phosphatase SerB; Region: serB; TIGR00338 60480003397 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 60480003398 motif II; other site 60480003399 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 60480003400 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480003401 PilZ domain; Region: PilZ; pfam07238 60480003402 PilZ domain; Region: PilZ; pfam07238 60480003403 DNA repair protein RadA; Provisional; Region: PRK11823 60480003404 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 60480003405 Walker A motif/ATP binding site; other site 60480003406 ATP binding site [chemical binding]; other site 60480003407 Walker B motif; other site 60480003408 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 60480003409 PilZ domain; Region: PilZ; pfam07238 60480003410 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 60480003411 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480003412 active site 60480003413 phosphorylation site [posttranslational modification] 60480003414 intermolecular recognition site; other site 60480003415 dimerization interface [polypeptide binding]; other site 60480003416 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 60480003417 DNA binding site [nucleotide binding] 60480003418 TMAO reductase system periplasmic protein TorT; Provisional; Region: PRK10936 60480003419 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 60480003420 putative ligand binding site [chemical binding]; other site 60480003421 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 60480003422 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 60480003423 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 60480003424 ATP binding site [chemical binding]; other site 60480003425 Mg2+ binding site [ion binding]; other site 60480003426 G-X-G motif; other site 60480003427 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480003428 active site 60480003429 phosphorylation site [posttranslational modification] 60480003430 intermolecular recognition site; other site 60480003431 dimerization interface [polypeptide binding]; other site 60480003432 Hpt domain; Region: Hpt; pfam01627 60480003433 putative binding surface; other site 60480003434 active site 60480003435 chaperone protein TorD; Validated; Region: torD; PRK04976 60480003436 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 60480003437 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 60480003438 molybdopterin cofactor binding site [chemical binding]; other site 60480003439 substrate binding site [chemical binding]; other site 60480003440 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 60480003441 molybdopterin cofactor binding site; other site 60480003442 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 60480003443 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 60480003444 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 60480003445 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 60480003446 FOG: CBS domain [General function prediction only]; Region: COG0517 60480003447 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 60480003448 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 60480003449 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 60480003450 putative acyl-acceptor binding pocket; other site 60480003451 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 60480003452 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 60480003453 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 60480003454 putative active site [active] 60480003455 putative metal binding site [ion binding]; other site 60480003456 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 60480003457 Nucleoside recognition; Region: Gate; pfam07670 60480003458 putative protease; Provisional; Region: PRK15447 60480003459 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 60480003460 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 60480003461 Peptidase family U32; Region: Peptidase_U32; pfam01136 60480003462 SCP-2 sterol transfer family; Region: SCP2; cl01225 60480003463 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 60480003464 putative protease; Provisional; Region: PRK15452 60480003465 Peptidase family U32; Region: Peptidase_U32; pfam01136 60480003466 HDOD domain; Region: HDOD; pfam08668 60480003467 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480003468 metal binding site [ion binding]; metal-binding site 60480003469 active site 60480003470 I-site; other site 60480003471 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 60480003472 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 60480003473 active site 60480003474 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 60480003475 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 60480003476 GDP-binding site [chemical binding]; other site 60480003477 ACT binding site; other site 60480003478 IMP binding site; other site 60480003479 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480003480 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480003481 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 60480003482 dimerization interface [polypeptide binding]; other site 60480003483 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480003484 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 60480003485 substrate binding pocket [chemical binding]; other site 60480003486 membrane-bound complex binding site; other site 60480003487 hinge residues; other site 60480003488 OsmC-like protein; Region: OsmC; pfam02566 60480003489 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480003490 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480003491 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480003492 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480003493 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480003494 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 60480003495 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480003496 Zn2+ binding site [ion binding]; other site 60480003497 Mg2+ binding site [ion binding]; other site 60480003498 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 60480003499 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480003500 Zn2+ binding site [ion binding]; other site 60480003501 Mg2+ binding site [ion binding]; other site 60480003502 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 60480003503 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480003504 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480003505 metal binding site [ion binding]; metal-binding site 60480003506 active site 60480003507 I-site; other site 60480003508 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 60480003509 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 60480003510 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 60480003511 apolar tunnel; other site 60480003512 heme binding site [chemical binding]; other site 60480003513 dimerization interface [polypeptide binding]; other site 60480003514 Uncharacterized conserved protein [Function unknown]; Region: COG1432 60480003515 LabA_like proteins; Region: LabA; cd10911 60480003516 putative metal binding site [ion binding]; other site 60480003517 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 60480003518 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 60480003519 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480003520 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 60480003521 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480003522 putative substrate translocation pore; other site 60480003523 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480003524 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480003525 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480003526 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480003527 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 60480003528 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480003529 substrate binding pocket [chemical binding]; other site 60480003530 membrane-bound complex binding site; other site 60480003531 hinge residues; other site 60480003532 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 60480003533 Shewanella-like phosphatases, metallophosphatase domain; Region: MPP_Shelphs; cd07425 60480003534 active site 60480003535 metal binding site [ion binding]; metal-binding site 60480003536 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 60480003537 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 60480003538 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 60480003539 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 60480003540 catalytic residues [active] 60480003541 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 60480003542 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480003543 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480003544 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 60480003545 putative effector binding pocket; other site 60480003546 dimerization interface [polypeptide binding]; other site 60480003547 Domain of unknown function (DUF389); Region: DUF389; pfam04087 60480003548 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 60480003549 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480003550 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480003551 ABC transporter; Region: ABC_tran_2; pfam12848 60480003552 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480003553 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 60480003554 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 60480003555 dimer interface [polypeptide binding]; other site 60480003556 active site 60480003557 glycine-pyridoxal phosphate binding site [chemical binding]; other site 60480003558 folate binding site [chemical binding]; other site 60480003559 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 60480003560 ATP cone domain; Region: ATP-cone; pfam03477 60480003561 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 60480003562 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 60480003563 catalytic motif [active] 60480003564 Zn binding site [ion binding]; other site 60480003565 RibD C-terminal domain; Region: RibD_C; cl17279 60480003566 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 60480003567 Lumazine binding domain; Region: Lum_binding; pfam00677 60480003568 Lumazine binding domain; Region: Lum_binding; pfam00677 60480003569 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 60480003570 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 60480003571 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 60480003572 dimerization interface [polypeptide binding]; other site 60480003573 active site 60480003574 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 60480003575 homopentamer interface [polypeptide binding]; other site 60480003576 active site 60480003577 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 60480003578 putative RNA binding site [nucleotide binding]; other site 60480003579 thiamine monophosphate kinase; Provisional; Region: PRK05731 60480003580 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 60480003581 ATP binding site [chemical binding]; other site 60480003582 dimerization interface [polypeptide binding]; other site 60480003583 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 60480003584 tetramer interfaces [polypeptide binding]; other site 60480003585 binuclear metal-binding site [ion binding]; other site 60480003586 universal stress protein UspE; Provisional; Region: PRK11175 60480003587 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 60480003588 Ligand Binding Site [chemical binding]; other site 60480003589 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 60480003590 Ligand Binding Site [chemical binding]; other site 60480003591 recombination and repair protein; Provisional; Region: PRK10869 60480003592 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 60480003593 Walker A/P-loop; other site 60480003594 ATP binding site [chemical binding]; other site 60480003595 Q-loop/lid; other site 60480003596 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 60480003597 ABC transporter signature motif; other site 60480003598 Walker B; other site 60480003599 D-loop; other site 60480003600 H-loop/switch region; other site 60480003601 Predicted permeases [General function prediction only]; Region: COG0679 60480003602 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480003603 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480003604 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 60480003605 putative effector binding pocket; other site 60480003606 dimerization interface [polypeptide binding]; other site 60480003607 Protein of unknown function (DUF3319); Region: DUF3319; pfam11782 60480003608 Protein of unknown function (DUF416); Region: DUF416; pfam04222 60480003609 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 60480003610 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 60480003611 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 60480003612 dimerization interface [polypeptide binding]; other site 60480003613 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 60480003614 dimer interface [polypeptide binding]; other site 60480003615 phosphorylation site [posttranslational modification] 60480003616 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 60480003617 ATP binding site [chemical binding]; other site 60480003618 Mg2+ binding site [ion binding]; other site 60480003619 G-X-G motif; other site 60480003620 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480003621 active site 60480003622 phosphorylation site [posttranslational modification] 60480003623 intermolecular recognition site; other site 60480003624 dimerization interface [polypeptide binding]; other site 60480003625 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 60480003626 putative binding surface; other site 60480003627 active site 60480003628 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 60480003629 TRAM domain; Region: TRAM; pfam01938 60480003630 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 60480003631 S-adenosylmethionine binding site [chemical binding]; other site 60480003632 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 60480003633 HD domain; Region: HD_4; pfam13328 60480003634 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 60480003635 synthetase active site [active] 60480003636 NTP binding site [chemical binding]; other site 60480003637 metal binding site [ion binding]; metal-binding site 60480003638 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 60480003639 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 60480003640 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 60480003641 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 60480003642 homodimer interface [polypeptide binding]; other site 60480003643 metal binding site [ion binding]; metal-binding site 60480003644 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 60480003645 homodimer interface [polypeptide binding]; other site 60480003646 active site 60480003647 putative chemical substrate binding site [chemical binding]; other site 60480003648 metal binding site [ion binding]; metal-binding site 60480003649 CTP synthetase; Validated; Region: pyrG; PRK05380 60480003650 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 60480003651 Catalytic site [active] 60480003652 active site 60480003653 UTP binding site [chemical binding]; other site 60480003654 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 60480003655 active site 60480003656 putative oxyanion hole; other site 60480003657 catalytic triad [active] 60480003658 enolase; Provisional; Region: eno; PRK00077 60480003659 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 60480003660 dimer interface [polypeptide binding]; other site 60480003661 metal binding site [ion binding]; metal-binding site 60480003662 substrate binding pocket [chemical binding]; other site 60480003663 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 60480003664 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 60480003665 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 60480003666 substrate binding site; other site 60480003667 dimer interface; other site 60480003668 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 60480003669 homotrimer interaction site [polypeptide binding]; other site 60480003670 zinc binding site [ion binding]; other site 60480003671 CDP-binding sites; other site 60480003672 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 60480003673 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 60480003674 Permutation of conserved domain; other site 60480003675 active site 60480003676 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 60480003677 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 60480003678 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 60480003679 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 60480003680 S-adenosylmethionine binding site [chemical binding]; other site 60480003681 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 60480003682 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480003683 Peptidase family M23; Region: Peptidase_M23; pfam01551 60480003684 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 60480003685 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 60480003686 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480003687 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 60480003688 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 60480003689 DNA binding residues [nucleotide binding] 60480003690 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 60480003691 MutS domain I; Region: MutS_I; pfam01624 60480003692 MutS domain II; Region: MutS_II; pfam05188 60480003693 MutS domain III; Region: MutS_III; pfam05192 60480003694 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 60480003695 Walker A/P-loop; other site 60480003696 ATP binding site [chemical binding]; other site 60480003697 Q-loop/lid; other site 60480003698 ABC transporter signature motif; other site 60480003699 Walker B; other site 60480003700 D-loop; other site 60480003701 H-loop/switch region; other site 60480003702 recombinase A; Provisional; Region: recA; PRK09354 60480003703 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 60480003704 hexamer interface [polypeptide binding]; other site 60480003705 Walker A motif; other site 60480003706 ATP binding site [chemical binding]; other site 60480003707 Walker B motif; other site 60480003708 RecX family; Region: RecX; pfam02631 60480003709 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 60480003710 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 60480003711 motif 1; other site 60480003712 active site 60480003713 motif 2; other site 60480003714 motif 3; other site 60480003715 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 60480003716 DHHA1 domain; Region: DHHA1; pfam02272 60480003717 aspartate kinase; Reviewed; Region: PRK06635 60480003718 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 60480003719 putative nucleotide binding site [chemical binding]; other site 60480003720 putative catalytic residues [active] 60480003721 putative Mg ion binding site [ion binding]; other site 60480003722 putative aspartate binding site [chemical binding]; other site 60480003723 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 60480003724 putative allosteric regulatory residue; other site 60480003725 carbon storage regulator; Provisional; Region: PRK01712 60480003726 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 60480003727 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 60480003728 HIGH motif; other site 60480003729 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 60480003730 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 60480003731 active site 60480003732 KMSKS motif; other site 60480003733 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 60480003734 tRNA binding surface [nucleotide binding]; other site 60480003735 anticodon binding site; other site 60480003736 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 60480003737 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 60480003738 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 60480003739 30S subunit binding site; other site 60480003740 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 60480003741 Cytochrome C' Region: Cytochrom_C_2; pfam01322 60480003742 Trp repressor protein; Region: Trp_repressor; pfam01371 60480003743 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 60480003744 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480003745 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 60480003746 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 60480003747 putative catalytic residues [active] 60480003748 putative nucleotide binding site [chemical binding]; other site 60480003749 putative aspartate binding site [chemical binding]; other site 60480003750 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 60480003751 dimer interface [polypeptide binding]; other site 60480003752 putative threonine allosteric regulatory site; other site 60480003753 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 60480003754 putative threonine allosteric regulatory site; other site 60480003755 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 60480003756 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 60480003757 homoserine kinase; Provisional; Region: PRK01212 60480003758 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 60480003759 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 60480003760 threonine synthase; Validated; Region: PRK09225 60480003761 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 60480003762 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480003763 catalytic residue [active] 60480003764 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 60480003765 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480003766 substrate binding pocket [chemical binding]; other site 60480003767 membrane-bound complex binding site; other site 60480003768 hinge residues; other site 60480003769 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 60480003770 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480003771 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 60480003772 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 60480003773 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 60480003774 protein binding site [polypeptide binding]; other site 60480003775 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 60480003776 Domain interface; other site 60480003777 Peptide binding site; other site 60480003778 Active site tetrad [active] 60480003779 OsmC-like protein; Region: OsmC; cl00767 60480003780 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 60480003781 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 60480003782 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 60480003783 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 60480003784 PAS domain; Region: PAS_9; pfam13426 60480003785 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 60480003786 putative active site [active] 60480003787 heme pocket [chemical binding]; other site 60480003788 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480003789 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480003790 dimer interface [polypeptide binding]; other site 60480003791 putative CheW interface [polypeptide binding]; other site 60480003792 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 60480003793 30S subunit binding site; other site 60480003794 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480003795 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480003796 active site 60480003797 phosphorylation site [posttranslational modification] 60480003798 intermolecular recognition site; other site 60480003799 dimerization interface [polypeptide binding]; other site 60480003800 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 60480003801 DNA binding residues [nucleotide binding] 60480003802 dimerization interface [polypeptide binding]; other site 60480003803 Histidine kinase; Region: HisKA_3; pfam07730 60480003804 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 60480003805 ATP binding site [chemical binding]; other site 60480003806 Mg2+ binding site [ion binding]; other site 60480003807 G-X-G motif; other site 60480003808 Isochorismatase family; Region: Isochorismatase; pfam00857 60480003809 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 60480003810 catalytic triad [active] 60480003811 conserved cis-peptide bond; other site 60480003812 hypothetical protein; Provisional; Region: PRK12378 60480003813 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480003814 dimer interface [polypeptide binding]; other site 60480003815 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 60480003816 putative CheW interface [polypeptide binding]; other site 60480003817 Protein of unknown function (DUF2375); Region: DUF2375; pfam09558 60480003818 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480003819 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480003820 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 60480003821 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 60480003822 FMN binding site [chemical binding]; other site 60480003823 active site 60480003824 substrate binding site [chemical binding]; other site 60480003825 catalytic residue [active] 60480003826 AAA domain; Region: AAA_32; pfam13654 60480003827 ATP-dependent protease Lon; Provisional; Region: PRK13765 60480003828 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 60480003829 PAS domain; Region: PAS_9; pfam13426 60480003830 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 60480003831 PAS domain; Region: PAS_9; pfam13426 60480003832 putative active site [active] 60480003833 heme pocket [chemical binding]; other site 60480003834 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480003835 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480003836 metal binding site [ion binding]; metal-binding site 60480003837 active site 60480003838 I-site; other site 60480003839 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 60480003840 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 60480003841 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480003842 ATP binding site [chemical binding]; other site 60480003843 Mg++ binding site [ion binding]; other site 60480003844 motif III; other site 60480003845 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 60480003846 nucleotide binding region [chemical binding]; other site 60480003847 ATP-binding site [chemical binding]; other site 60480003848 Protein of unknown function (DUF523); Region: DUF523; pfam04463 60480003849 Uncharacterized conserved protein [Function unknown]; Region: COG3272 60480003850 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 60480003851 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 60480003852 DNA binding residues [nucleotide binding] 60480003853 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 60480003854 DNA photolyase; Region: DNA_photolyase; pfam00875 60480003855 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 60480003856 SnoaL-like domain; Region: SnoaL_2; pfam12680 60480003857 short chain dehydrogenase; Provisional; Region: PRK06101 60480003858 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480003859 NAD(P) binding site [chemical binding]; other site 60480003860 active site 60480003861 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 60480003862 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 60480003863 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 60480003864 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 60480003865 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 60480003866 S-adenosylmethionine binding site [chemical binding]; other site 60480003867 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 60480003868 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 60480003869 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 60480003870 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 60480003871 hypothetical protein; Provisional; Region: PRK03757 60480003872 oxidative damage protection protein; Provisional; Region: PRK05408 60480003873 adenine DNA glycosylase; Provisional; Region: PRK10880 60480003874 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 60480003875 minor groove reading motif; other site 60480003876 helix-hairpin-helix signature motif; other site 60480003877 substrate binding pocket [chemical binding]; other site 60480003878 active site 60480003879 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 60480003880 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 60480003881 DNA binding and oxoG recognition site [nucleotide binding] 60480003882 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 60480003883 S-adenosylmethionine binding site [chemical binding]; other site 60480003884 hypothetical protein; Provisional; Region: PRK11702 60480003885 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 60480003886 glutaminase; Provisional; Region: PRK00971 60480003887 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 60480003888 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480003889 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480003890 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 60480003891 putative effector binding pocket; other site 60480003892 dimerization interface [polypeptide binding]; other site 60480003893 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 60480003894 HemN family oxidoreductase; Provisional; Region: PRK05660 60480003895 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 60480003896 FeS/SAM binding site; other site 60480003897 HemN C-terminal domain; Region: HemN_C; pfam06969 60480003898 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 60480003899 active site 60480003900 dimerization interface [polypeptide binding]; other site 60480003901 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 60480003902 hypothetical protein; Validated; Region: PRK05090 60480003903 YGGT family; Region: YGGT; pfam02325 60480003904 YGGT family; Region: YGGT; pfam02325 60480003905 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 60480003906 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 60480003907 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 60480003908 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 60480003909 catalytic residue [active] 60480003910 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 60480003911 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 60480003912 Walker A motif; other site 60480003913 ATP binding site [chemical binding]; other site 60480003914 Walker B motif; other site 60480003915 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 60480003916 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 60480003917 Walker A motif; other site 60480003918 ATP binding site [chemical binding]; other site 60480003919 Walker B motif; other site 60480003920 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 60480003921 catalytic residues [active] 60480003922 dimer interface [polypeptide binding]; other site 60480003923 ferrochelatase; Reviewed; Region: hemH; PRK00035 60480003924 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 60480003925 C-terminal domain interface [polypeptide binding]; other site 60480003926 active site 60480003927 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 60480003928 active site 60480003929 N-terminal domain interface [polypeptide binding]; other site 60480003930 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 60480003931 hypothetical protein; Validated; Region: PRK00228 60480003932 translation initiation factor Sui1; Validated; Region: PRK06824 60480003933 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 60480003934 putative rRNA binding site [nucleotide binding]; other site 60480003935 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 60480003936 Predicted membrane protein [Function unknown]; Region: COG2860 60480003937 UPF0126 domain; Region: UPF0126; pfam03458 60480003938 UPF0126 domain; Region: UPF0126; pfam03458 60480003939 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 60480003940 dimer interface [polypeptide binding]; other site 60480003941 catalytic triad [active] 60480003942 peroxidatic and resolving cysteines [active] 60480003943 Conserved TM helix; Region: TM_helix; pfam05552 60480003944 mechanosensitive channel MscS; Provisional; Region: PRK10334 60480003945 Mechanosensitive ion channel; Region: MS_channel; pfam00924 60480003946 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 60480003947 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480003948 ligand binding site [chemical binding]; other site 60480003949 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 60480003950 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 60480003951 tetramer interface [polypeptide binding]; other site 60480003952 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480003953 catalytic residue [active] 60480003954 HDOD domain; Region: HDOD; pfam08668 60480003955 GAF domain; Region: GAF_3; pfam13492 60480003956 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 60480003957 SnoaL-like domain; Region: SnoaL_3; pfam13474 60480003958 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 60480003959 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 60480003960 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480003961 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480003962 metal binding site [ion binding]; metal-binding site 60480003963 active site 60480003964 I-site; other site 60480003965 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 60480003966 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 60480003967 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 60480003968 ParA-like protein; Provisional; Region: PHA02518 60480003969 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 60480003970 P-loop; other site 60480003971 Magnesium ion binding site [ion binding]; other site 60480003972 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480003973 Coenzyme A binding pocket [chemical binding]; other site 60480003974 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 60480003975 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 60480003976 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480003977 Coenzyme A binding pocket [chemical binding]; other site 60480003978 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 60480003979 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480003980 Coenzyme A binding pocket [chemical binding]; other site 60480003981 Pirin-related protein [General function prediction only]; Region: COG1741 60480003982 Pirin; Region: Pirin; pfam02678 60480003983 DoxX; Region: DoxX; pfam07681 60480003984 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480003985 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 60480003986 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 60480003987 putative dimerization interface [polypeptide binding]; other site 60480003988 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 60480003989 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 60480003990 active site 60480003991 metal binding site [ion binding]; metal-binding site 60480003992 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 60480003993 Domain of unknown function DUF21; Region: DUF21; pfam01595 60480003994 FOG: CBS domain [General function prediction only]; Region: COG0517 60480003995 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 60480003996 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 60480003997 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 60480003998 FeS/SAM binding site; other site 60480003999 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 60480004000 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 60480004001 binding surface 60480004002 TPR motif; other site 60480004003 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 60480004004 binding surface 60480004005 TPR motif; other site 60480004006 cytoskeletal protein RodZ; Provisional; Region: PRK10856 60480004007 Helix-turn-helix domain; Region: HTH_25; pfam13413 60480004008 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 60480004009 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 60480004010 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 60480004011 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 60480004012 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 60480004013 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 60480004014 dimer interface [polypeptide binding]; other site 60480004015 motif 1; other site 60480004016 active site 60480004017 motif 2; other site 60480004018 motif 3; other site 60480004019 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 60480004020 anticodon binding site; other site 60480004021 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 60480004022 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 60480004023 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 60480004024 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 60480004025 Trp docking motif [polypeptide binding]; other site 60480004026 active site 60480004027 GTP-binding protein Der; Reviewed; Region: PRK00093 60480004028 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 60480004029 G1 box; other site 60480004030 GTP/Mg2+ binding site [chemical binding]; other site 60480004031 Switch I region; other site 60480004032 G2 box; other site 60480004033 Switch II region; other site 60480004034 G3 box; other site 60480004035 G4 box; other site 60480004036 G5 box; other site 60480004037 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 60480004038 G1 box; other site 60480004039 GTP/Mg2+ binding site [chemical binding]; other site 60480004040 Switch I region; other site 60480004041 G2 box; other site 60480004042 G3 box; other site 60480004043 Switch II region; other site 60480004044 G4 box; other site 60480004045 G5 box; other site 60480004046 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 60480004047 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 60480004048 generic binding surface II; other site 60480004049 generic binding surface I; other site 60480004050 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 60480004051 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 60480004052 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 60480004053 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 60480004054 active site 60480004055 GMP synthase; Reviewed; Region: guaA; PRK00074 60480004056 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 60480004057 AMP/PPi binding site [chemical binding]; other site 60480004058 candidate oxyanion hole; other site 60480004059 catalytic triad [active] 60480004060 potential glutamine specificity residues [chemical binding]; other site 60480004061 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 60480004062 ATP Binding subdomain [chemical binding]; other site 60480004063 Ligand Binding sites [chemical binding]; other site 60480004064 Dimerization subdomain; other site 60480004065 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 60480004066 nucleoside/Zn binding site; other site 60480004067 dimer interface [polypeptide binding]; other site 60480004068 catalytic motif [active] 60480004069 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 60480004070 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 60480004071 substrate binding pocket [chemical binding]; other site 60480004072 membrane-bound complex binding site; other site 60480004073 hinge residues; other site 60480004074 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 60480004075 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480004076 catalytic residue [active] 60480004077 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 60480004078 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 60480004079 dimerization interface [polypeptide binding]; other site 60480004080 ATP binding site [chemical binding]; other site 60480004081 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 60480004082 dimerization interface [polypeptide binding]; other site 60480004083 ATP binding site [chemical binding]; other site 60480004084 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 60480004085 putative active site [active] 60480004086 catalytic triad [active] 60480004087 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 60480004088 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 60480004089 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 60480004090 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 60480004091 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 60480004092 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 60480004093 dimerization interface [polypeptide binding]; other site 60480004094 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480004095 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480004096 dimer interface [polypeptide binding]; other site 60480004097 putative CheW interface [polypeptide binding]; other site 60480004098 Protein of unknown function (DUF465); Region: DUF465; pfam04325 60480004099 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480004100 Protein export membrane protein; Region: SecD_SecF; cl14618 60480004101 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480004102 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480004103 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480004104 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480004105 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480004106 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 60480004107 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 60480004108 LPP20 lipoprotein; Region: LPP20; pfam02169 60480004109 FlgN protein; Region: FlgN; pfam05130 60480004110 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 60480004111 SAF-like; Region: SAF_2; pfam13144 60480004112 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 60480004113 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 60480004114 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480004115 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004116 active site 60480004117 phosphorylation site [posttranslational modification] 60480004118 intermolecular recognition site; other site 60480004119 dimerization interface [polypeptide binding]; other site 60480004120 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 60480004121 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 60480004122 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 60480004123 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 60480004124 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 60480004125 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 60480004126 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 60480004127 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 60480004128 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK12634 60480004129 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 60480004130 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 60480004131 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 60480004132 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 60480004133 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 60480004134 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 60480004135 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 60480004136 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 60480004137 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 60480004138 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 60480004139 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 60480004140 Flagellar L-ring protein; Region: FlgH; pfam02107 60480004141 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 60480004142 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 60480004143 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 60480004144 flagellar rod assembly protein/muramidase FlgJ; Provisional; Region: flgJ; PRK12712 60480004145 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 60480004146 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08871 60480004147 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 60480004148 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 60480004149 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 60480004150 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 60480004151 flagellin; Provisional; Region: PRK12806 60480004152 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 60480004153 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 60480004154 flagellin; Provisional; Region: PRK12806 60480004155 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 60480004156 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 60480004157 FlaG protein; Region: FlaG; pfam03646 60480004158 flagellar capping protein; Reviewed; Region: fliD; PRK08032 60480004159 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 60480004160 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 60480004161 flagellar protein FliS; Validated; Region: fliS; PRK05685 60480004162 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 60480004163 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 60480004164 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 60480004165 Walker A motif; other site 60480004166 ATP binding site [chemical binding]; other site 60480004167 Walker B motif; other site 60480004168 arginine finger; other site 60480004169 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480004170 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 60480004171 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 60480004172 putative active site [active] 60480004173 heme pocket [chemical binding]; other site 60480004174 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 60480004175 dimer interface [polypeptide binding]; other site 60480004176 phosphorylation site [posttranslational modification] 60480004177 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 60480004178 ATP binding site [chemical binding]; other site 60480004179 Mg2+ binding site [ion binding]; other site 60480004180 G-X-G motif; other site 60480004181 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 60480004182 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004183 active site 60480004184 phosphorylation site [posttranslational modification] 60480004185 intermolecular recognition site; other site 60480004186 dimerization interface [polypeptide binding]; other site 60480004187 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 60480004188 Walker A motif; other site 60480004189 ATP binding site [chemical binding]; other site 60480004190 Walker B motif; other site 60480004191 arginine finger; other site 60480004192 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480004193 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 60480004194 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 60480004195 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 60480004196 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 60480004197 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 60480004198 MgtE intracellular N domain; Region: MgtE_N; smart00924 60480004199 FliG C-terminal domain; Region: FliG_C; pfam01706 60480004200 flagellar assembly protein H; Validated; Region: fliH; PRK05687 60480004201 Flagellar assembly protein FliH; Region: FliH; pfam02108 60480004202 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 60480004203 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 60480004204 Walker A motif/ATP binding site; other site 60480004205 Walker B motif; other site 60480004206 Flagellar FliJ protein; Region: FliJ; pfam02050 60480004207 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 60480004208 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 60480004209 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK05696 60480004210 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 60480004211 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 60480004212 flagellar motor switch protein; Validated; Region: fliN; PRK08983 60480004213 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 60480004214 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 60480004215 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 60480004216 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 60480004217 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 60480004218 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 60480004219 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 60480004220 FHIPEP family; Region: FHIPEP; pfam00771 60480004221 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 60480004222 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 60480004223 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 60480004224 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 60480004225 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 60480004226 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 60480004227 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480004228 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 60480004229 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 60480004230 DNA binding residues [nucleotide binding] 60480004231 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 60480004232 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004233 active site 60480004234 phosphorylation site [posttranslational modification] 60480004235 intermolecular recognition site; other site 60480004236 dimerization interface [polypeptide binding]; other site 60480004237 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 60480004238 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 60480004239 putative binding surface; other site 60480004240 active site 60480004241 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 60480004242 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 60480004243 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 60480004244 ATP binding site [chemical binding]; other site 60480004245 Mg2+ binding site [ion binding]; other site 60480004246 G-X-G motif; other site 60480004247 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 60480004248 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 60480004249 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004250 active site 60480004251 phosphorylation site [posttranslational modification] 60480004252 intermolecular recognition site; other site 60480004253 CheB methylesterase; Region: CheB_methylest; pfam01339 60480004254 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 60480004255 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 60480004256 P-loop; other site 60480004257 Magnesium ion binding site [ion binding]; other site 60480004258 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 60480004259 Magnesium ion binding site [ion binding]; other site 60480004260 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 60480004261 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 60480004262 putative CheA interaction surface; other site 60480004263 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 60480004264 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 60480004265 VacJ like lipoprotein; Region: VacJ; cl01073 60480004266 Response regulator receiver domain; Region: Response_reg; pfam00072 60480004267 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004268 active site 60480004269 phosphorylation site [posttranslational modification] 60480004270 intermolecular recognition site; other site 60480004271 dimerization interface [polypeptide binding]; other site 60480004272 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 60480004273 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 60480004274 putative substrate translocation pore; other site 60480004275 POT family; Region: PTR2; cl17359 60480004276 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 60480004277 transcriptional activator RfaH; Region: RfaH; TIGR01955 60480004278 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 60480004279 heterodimer interface [polypeptide binding]; other site 60480004280 homodimer interface [polypeptide binding]; other site 60480004281 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 60480004282 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 60480004283 SLBB domain; Region: SLBB; pfam10531 60480004284 SLBB domain; Region: SLBB; pfam10531 60480004285 SLBB domain; Region: SLBB; pfam10531 60480004286 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 60480004287 SLBB domain; Region: SLBB; pfam10531 60480004288 hypothetical protein; Reviewed; Region: PRK12275 60480004289 four helix bundle protein; Region: TIGR02436 60480004290 Chain length determinant protein; Region: Wzz; pfam02706 60480004291 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 60480004292 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 60480004293 NAD binding site [chemical binding]; other site 60480004294 substrate binding site [chemical binding]; other site 60480004295 homodimer interface [polypeptide binding]; other site 60480004296 active site 60480004297 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 60480004298 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 60480004299 substrate binding site; other site 60480004300 tetramer interface; other site 60480004301 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 60480004302 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 60480004303 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 60480004304 inhibitor-cofactor binding pocket; inhibition site 60480004305 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480004306 catalytic residue [active] 60480004307 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 60480004308 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 60480004309 trimer interface [polypeptide binding]; other site 60480004310 active site 60480004311 substrate binding site [chemical binding]; other site 60480004312 CoA binding site [chemical binding]; other site 60480004313 4-alpha-L-fucosyltransferase glycosyl transferase group 56; Region: Glyco_transf_56; cl07929 60480004314 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 60480004315 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 60480004316 active site 60480004317 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 60480004318 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 60480004319 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 60480004320 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 60480004321 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 60480004322 Substrate binding site; other site 60480004323 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 60480004324 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 60480004325 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 60480004326 active site 60480004327 substrate binding site [chemical binding]; other site 60480004328 metal binding site [ion binding]; metal-binding site 60480004329 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 60480004330 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 60480004331 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 60480004332 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 60480004333 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 60480004334 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 60480004335 Mg++ binding site [ion binding]; other site 60480004336 putative catalytic motif [active] 60480004337 substrate binding site [chemical binding]; other site 60480004338 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 60480004339 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 60480004340 Mg++ binding site [ion binding]; other site 60480004341 putative catalytic motif [active] 60480004342 substrate binding site [chemical binding]; other site 60480004343 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 60480004344 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 60480004345 active site 60480004346 substrate binding site [chemical binding]; other site 60480004347 metal binding site [ion binding]; metal-binding site 60480004348 HutD; Region: HutD; pfam05962 60480004349 Uncharacterized lipoprotein NlpE involved in copper resistance [Cell envelope biogenesis, outer membrane / Inorganic ion transport and metabolism]; Region: CutF; COG3015 60480004350 NlpE N-terminal domain; Region: NlpE; pfam04170 60480004351 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480004352 GAF domain; Region: GAF; pfam01590 60480004353 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480004354 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 60480004355 ATP binding site [chemical binding]; other site 60480004356 Mg2+ binding site [ion binding]; other site 60480004357 G-X-G motif; other site 60480004358 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 60480004359 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 60480004360 substrate binding site; other site 60480004361 tetramer interface; other site 60480004362 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 60480004363 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 60480004364 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 60480004365 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 60480004366 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 60480004367 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 60480004368 nucleophile elbow; other site 60480004369 prolyl-tRNA synthetase; Provisional; Region: PRK09194 60480004370 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 60480004371 dimer interface [polypeptide binding]; other site 60480004372 motif 1; other site 60480004373 active site 60480004374 motif 2; other site 60480004375 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 60480004376 putative deacylase active site [active] 60480004377 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 60480004378 active site 60480004379 motif 3; other site 60480004380 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 60480004381 anticodon binding site; other site 60480004382 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 60480004383 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 60480004384 putative CoA binding site [chemical binding]; other site 60480004385 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 60480004386 trimer interface [polypeptide binding]; other site 60480004387 active site 60480004388 substrate binding site [chemical binding]; other site 60480004389 CoA binding site [chemical binding]; other site 60480004390 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 60480004391 homodimer interaction site [polypeptide binding]; other site 60480004392 cofactor binding site; other site 60480004393 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 60480004394 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 60480004395 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 60480004396 active site 60480004397 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 60480004398 active site 60480004399 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 60480004400 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 60480004401 active site 60480004402 Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA; Region: Topoisomer_IB_N; cl02774 60480004403 DNA-binding protein H-NS [General function prediction only]; Region: Hns; COG2916 60480004404 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 60480004405 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 60480004406 Ligand binding site [chemical binding]; other site 60480004407 Electron transfer flavoprotein domain; Region: ETF; pfam01012 60480004408 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 60480004409 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 60480004410 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 60480004411 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 60480004412 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 60480004413 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 60480004414 active site 60480004415 Zn binding site [ion binding]; other site 60480004416 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 60480004417 thymidine kinase; Provisional; Region: PRK04296 60480004418 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 60480004419 Transglycosylase; Region: Transgly; cl17702 60480004420 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 60480004421 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004422 active site 60480004423 phosphorylation site [posttranslational modification] 60480004424 intermolecular recognition site; other site 60480004425 dimerization interface [polypeptide binding]; other site 60480004426 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 60480004427 Walker A motif; other site 60480004428 ATP binding site [chemical binding]; other site 60480004429 Walker B motif; other site 60480004430 arginine finger; other site 60480004431 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480004432 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 60480004433 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 60480004434 dimer interface [polypeptide binding]; other site 60480004435 phosphorylation site [posttranslational modification] 60480004436 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 60480004437 ATP binding site [chemical binding]; other site 60480004438 Mg2+ binding site [ion binding]; other site 60480004439 G-X-G motif; other site 60480004440 DctM-like transporters; Region: DctM; pfam06808 60480004441 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 60480004442 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 60480004443 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 60480004444 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 60480004445 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 60480004446 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 60480004447 active site 60480004448 HIGH motif; other site 60480004449 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 60480004450 active site 60480004451 KMSKS motif; other site 60480004452 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 60480004453 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 60480004454 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 60480004455 Walker A/P-loop; other site 60480004456 ATP binding site [chemical binding]; other site 60480004457 Q-loop/lid; other site 60480004458 ABC transporter signature motif; other site 60480004459 Walker B; other site 60480004460 D-loop; other site 60480004461 H-loop/switch region; other site 60480004462 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 60480004463 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 60480004464 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480004465 AlkA N-terminal domain; Region: AlkA_N; smart01009 60480004466 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 60480004467 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 60480004468 minor groove reading motif; other site 60480004469 helix-hairpin-helix signature motif; other site 60480004470 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 60480004471 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 60480004472 DNA binding site [nucleotide binding] 60480004473 active site 60480004474 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 60480004475 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 60480004476 ATP binding site [chemical binding]; other site 60480004477 putative Mg++ binding site [ion binding]; other site 60480004478 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 60480004479 nucleotide binding region [chemical binding]; other site 60480004480 ATP-binding site [chemical binding]; other site 60480004481 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 60480004482 active site 60480004483 catalytic residues [active] 60480004484 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 60480004485 PLD-like domain; Region: PLDc_2; pfam13091 60480004486 putative active site [active] 60480004487 catalytic site [active] 60480004488 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 60480004489 PLD-like domain; Region: PLDc_2; pfam13091 60480004490 putative active site [active] 60480004491 catalytic site [active] 60480004492 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 60480004493 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480004494 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480004495 active site 60480004496 phosphorylation site [posttranslational modification] 60480004497 intermolecular recognition site; other site 60480004498 dimerization interface [polypeptide binding]; other site 60480004499 serine/threonine transporter SstT; Provisional; Region: PRK13628 60480004500 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480004501 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 60480004502 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 60480004503 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 60480004504 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 60480004505 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 60480004506 active site 60480004507 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 60480004508 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480004509 catalytic residues [active] 60480004510 Protein of unknown function, DUF479; Region: DUF479; pfam04336 60480004511 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 60480004512 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 60480004513 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 60480004514 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 60480004515 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 60480004516 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 60480004517 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 60480004518 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 60480004519 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 60480004520 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 60480004521 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 60480004522 Protein export membrane protein; Region: SecD_SecF; pfam02355 60480004523 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 60480004524 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 60480004525 active site residue [active] 60480004526 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 60480004527 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 60480004528 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 60480004529 YaeQ protein; Region: YaeQ; pfam07152 60480004530 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 60480004531 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 60480004532 active site 60480004533 catalytic residues [active] 60480004534 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 60480004535 PA/subtilisin-like domain interface [polypeptide binding]; other site 60480004536 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 60480004537 catalytic residues [active] 60480004538 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 60480004539 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 60480004540 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 60480004541 active site residue [active] 60480004542 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 60480004543 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480004544 Protein export membrane protein; Region: SecD_SecF; cl14618 60480004545 Protein export membrane protein; Region: SecD_SecF; cl14618 60480004546 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480004547 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480004548 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 60480004549 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 60480004550 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 60480004551 active site 60480004552 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 60480004553 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 60480004554 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 60480004555 Na binding site [ion binding]; other site 60480004556 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 60480004557 RNA polymerase sigma factor; Provisional; Region: PRK12517 60480004558 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480004559 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 60480004560 DNA binding residues [nucleotide binding] 60480004561 Oxygen tolerance; Region: BatD; pfam13584 60480004562 von Willebrand factor type A domain; Region: VWA_2; pfam13519 60480004563 metal ion-dependent adhesion site (MIDAS); other site 60480004564 Tetratricopeptide repeat; Region: TPR_16; pfam13432 60480004565 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 60480004566 TPR motif; other site 60480004567 binding surface 60480004568 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 60480004569 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 60480004570 metal ion-dependent adhesion site (MIDAS); other site 60480004571 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 60480004572 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 60480004573 Protein of unknown function DUF58; Region: DUF58; pfam01882 60480004574 MoxR-like ATPases [General function prediction only]; Region: COG0714 60480004575 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 60480004576 Walker A motif; other site 60480004577 ATP binding site [chemical binding]; other site 60480004578 Walker B motif; other site 60480004579 arginine finger; other site 60480004580 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 60480004581 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 60480004582 dimer interface [polypeptide binding]; other site 60480004583 active site 60480004584 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 60480004585 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 60480004586 substrate binding site [chemical binding]; other site 60480004587 oxyanion hole (OAH) forming residues; other site 60480004588 trimer interface [polypeptide binding]; other site 60480004589 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 60480004590 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 60480004591 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 60480004592 Two component regulator propeller; Region: Reg_prop; pfam07494 60480004593 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 60480004594 Cytokine receptor motif; other site 60480004595 PAS fold; Region: PAS_3; pfam08447 60480004596 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 60480004597 PAS domain; Region: PAS_9; pfam13426 60480004598 putative active site [active] 60480004599 heme pocket [chemical binding]; other site 60480004600 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480004601 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480004602 metal binding site [ion binding]; metal-binding site 60480004603 active site 60480004604 I-site; other site 60480004605 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 60480004606 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 60480004607 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480004608 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480004609 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480004610 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 60480004611 catalytic core [active] 60480004612 hypothetical protein; Provisional; Region: PRK04946 60480004613 Smr domain; Region: Smr; pfam01713 60480004614 HemK family putative methylases; Region: hemK_fam; TIGR00536 60480004615 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 60480004616 S-adenosylmethionine binding site [chemical binding]; other site 60480004617 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 60480004618 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 60480004619 Tetramer interface [polypeptide binding]; other site 60480004620 active site 60480004621 FMN-binding site [chemical binding]; other site 60480004622 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 60480004623 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 60480004624 putative substrate translocation pore; other site 60480004625 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 60480004626 ATP-NAD kinase; Region: NAD_kinase; pfam01513 60480004627 YfcL protein; Region: YfcL; pfam08891 60480004628 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 60480004629 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 60480004630 tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain; Region: MnmC_Cterm; TIGR03197 60480004631 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 60480004632 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 60480004633 dimer interface [polypeptide binding]; other site 60480004634 active site 60480004635 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 60480004636 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 60480004637 ligand binding site [chemical binding]; other site 60480004638 NAD binding site [chemical binding]; other site 60480004639 catalytic site [active] 60480004640 homodimer interface [polypeptide binding]; other site 60480004641 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 60480004642 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 60480004643 FimV N-terminal domain; Region: FimV_core; TIGR03505 60480004644 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 60480004645 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 60480004646 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 60480004647 dimerization interface 3.5A [polypeptide binding]; other site 60480004648 active site 60480004649 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 60480004650 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 60480004651 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 60480004652 cell division protein DedD; Provisional; Region: PRK11633 60480004653 Sporulation related domain; Region: SPOR; pfam05036 60480004654 Colicin V production protein; Region: Colicin_V; cl00567 60480004655 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 60480004656 amidophosphoribosyltransferase; Provisional; Region: PRK09246 60480004657 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 60480004658 active site 60480004659 tetramer interface [polypeptide binding]; other site 60480004660 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480004661 active site 60480004662 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 60480004663 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 60480004664 DNA topoisomerase III; Provisional; Region: PRK07726 60480004665 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 60480004666 active site 60480004667 putative interdomain interaction site [polypeptide binding]; other site 60480004668 putative metal-binding site [ion binding]; other site 60480004669 putative nucleotide binding site [chemical binding]; other site 60480004670 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 60480004671 domain I; other site 60480004672 DNA binding groove [nucleotide binding] 60480004673 phosphate binding site [ion binding]; other site 60480004674 domain II; other site 60480004675 domain III; other site 60480004676 nucleotide binding site [chemical binding]; other site 60480004677 catalytic site [active] 60480004678 domain IV; other site 60480004679 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 60480004680 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 60480004681 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480004682 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 60480004683 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480004684 dimer interface [polypeptide binding]; other site 60480004685 putative CheW interface [polypeptide binding]; other site 60480004686 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 60480004687 XdhC Rossmann domain; Region: XdhC_C; pfam13478 60480004688 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 60480004689 Ligand binding site; other site 60480004690 metal-binding site 60480004691 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 60480004692 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 60480004693 catalytic loop [active] 60480004694 iron binding site [ion binding]; other site 60480004695 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 60480004696 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 60480004697 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 60480004698 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 60480004699 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 60480004700 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 60480004701 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 60480004702 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 60480004703 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480004704 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480004705 dimer interface [polypeptide binding]; other site 60480004706 putative CheW interface [polypeptide binding]; other site 60480004707 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 60480004708 Transposase; Region: DDE_Tnp_ISL3; pfam01610 60480004709 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 60480004710 Restriction endonuclease; Region: Mrr_cat; pfam04471 60480004711 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 60480004712 putative catalytic site [active] 60480004713 putative phosphate binding site [ion binding]; other site 60480004714 active site 60480004715 metal binding site A [ion binding]; metal-binding site 60480004716 DNA binding site [nucleotide binding] 60480004717 putative AP binding site [nucleotide binding]; other site 60480004718 putative metal binding site B [ion binding]; other site 60480004719 YciI-like protein; Reviewed; Region: PRK11370 60480004720 intracellular septation protein A; Reviewed; Region: PRK00259 60480004721 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 60480004722 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 60480004723 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 60480004724 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 60480004725 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 60480004726 N-terminal plug; other site 60480004727 ligand-binding site [chemical binding]; other site 60480004728 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 60480004729 IucA / IucC family; Region: IucA_IucC; pfam04183 60480004730 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 60480004731 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 60480004732 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 60480004733 L-lysine 6-monooxygenase (NADPH-requiring); Region: K_oxygenase; pfam13434 60480004734 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480004735 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 60480004736 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 60480004737 substrate binding site [chemical binding]; other site 60480004738 active site 60480004739 catalytic residues [active] 60480004740 heterodimer interface [polypeptide binding]; other site 60480004741 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 60480004742 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 60480004743 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480004744 catalytic residue [active] 60480004745 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 60480004746 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 60480004747 active site 60480004748 ribulose/triose binding site [chemical binding]; other site 60480004749 phosphate binding site [ion binding]; other site 60480004750 substrate (anthranilate) binding pocket [chemical binding]; other site 60480004751 product (indole) binding pocket [chemical binding]; other site 60480004752 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 60480004753 active site 60480004754 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 60480004755 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 60480004756 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 60480004757 Glutamine amidotransferase class-I; Region: GATase; pfam00117 60480004758 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 60480004759 glutamine binding [chemical binding]; other site 60480004760 catalytic triad [active] 60480004761 anthranilate synthase component I; Provisional; Region: PRK13564 60480004762 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 60480004763 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 60480004764 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 60480004765 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 60480004766 active site 60480004767 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 60480004768 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 60480004769 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 60480004770 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 60480004771 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 60480004772 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 60480004773 RNA binding surface [nucleotide binding]; other site 60480004774 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 60480004775 probable active site [active] 60480004776 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 60480004777 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480004778 NAD(P) binding site [chemical binding]; other site 60480004779 active site 60480004780 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 60480004781 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 60480004782 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 60480004783 putative inner membrane peptidase; Provisional; Region: PRK11778 60480004784 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 60480004785 tandem repeat interface [polypeptide binding]; other site 60480004786 oligomer interface [polypeptide binding]; other site 60480004787 active site residues [active] 60480004788 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 60480004789 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 60480004790 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 60480004791 conserved hypothetical protein, HNE_0200 family; Region: chp_HNE_0200; TIGR03806 60480004792 Planctomycete cytochrome C; Region: PSCyt1; pfam07635 60480004793 parallel beta-helix repeat-containing protein; Region: beta_helix_1; TIGR03805 60480004794 conserved hypothetical protein, HNE_0200 family; Region: chp_HNE_0200; TIGR03806 60480004795 Planctomycete cytochrome C; Region: PSCyt1; pfam07635 60480004796 Predicted integral membrane protein [Function unknown]; Region: COG0392 60480004797 Uncharacterized conserved protein [Function unknown]; Region: COG2898 60480004798 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 60480004799 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 60480004800 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480004801 Protein of unknown function (DUF3083); Region: DUF3083; pfam11281 60480004802 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 60480004803 active site 60480004804 catalytic triad [active] 60480004805 oxyanion hole [active] 60480004806 switch loop; other site 60480004807 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 60480004808 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 60480004809 Walker A/P-loop; other site 60480004810 ATP binding site [chemical binding]; other site 60480004811 Q-loop/lid; other site 60480004812 ABC transporter signature motif; other site 60480004813 Walker B; other site 60480004814 D-loop; other site 60480004815 H-loop/switch region; other site 60480004816 FtsX-like permease family; Region: FtsX; pfam02687 60480004817 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 60480004818 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 60480004819 Catalytic site [active] 60480004820 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 60480004821 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 60480004822 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 60480004823 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 60480004824 putative NAD(P) binding site [chemical binding]; other site 60480004825 putative active site [active] 60480004826 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 60480004827 homooctamer interface [polypeptide binding]; other site 60480004828 active site 60480004829 Domain of unknown function DUF20; Region: UPF0118; pfam01594 60480004830 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 60480004831 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 60480004832 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 60480004833 S-adenosylmethionine binding site [chemical binding]; other site 60480004834 phosphate acetyltransferase; Reviewed; Region: PRK05632 60480004835 DRTGG domain; Region: DRTGG; pfam07085 60480004836 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 60480004837 propionate/acetate kinase; Provisional; Region: PRK12379 60480004838 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 60480004839 nucleotide binding site [chemical binding]; other site 60480004840 butyrate kinase; Provisional; Region: PRK03011 60480004841 Protein of unknown function, DUF412; Region: DUF412; pfam04217 60480004842 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 60480004843 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 60480004844 FeS/SAM binding site; other site 60480004845 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 60480004846 Pyruvate formate lyase 1; Region: PFL1; cd01678 60480004847 coenzyme A binding site [chemical binding]; other site 60480004848 active site 60480004849 catalytic residues [active] 60480004850 glycine loop; other site 60480004851 formate transporter FocA; Region: formate_focA; TIGR04060 60480004852 hypothetical protein; Provisional; Region: PRK11588 60480004853 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 60480004854 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480004855 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 60480004856 N-terminal plug; other site 60480004857 ligand-binding site [chemical binding]; other site 60480004858 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 60480004859 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 60480004860 gating phenylalanine in ion channel; other site 60480004861 O-methyltransferase; Region: Methyltransf_2; pfam00891 60480004862 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 60480004863 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 60480004864 dimer interface [polypeptide binding]; other site 60480004865 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480004866 catalytic residue [active] 60480004867 RDD family; Region: RDD; pfam06271 60480004868 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 60480004869 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 60480004870 dimer interface [polypeptide binding]; other site 60480004871 active site 60480004872 CoA binding pocket [chemical binding]; other site 60480004873 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_2; cd09618 60480004874 putative ligand binding site [chemical binding]; other site 60480004875 putative sulfate transport protein CysZ; Validated; Region: PRK04949 60480004876 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 60480004877 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 60480004878 Walker A/P-loop; other site 60480004879 ATP binding site [chemical binding]; other site 60480004880 Q-loop/lid; other site 60480004881 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 60480004882 ABC transporter signature motif; other site 60480004883 Walker B; other site 60480004884 D-loop; other site 60480004885 H-loop/switch region; other site 60480004886 cell division protein ZipA; Provisional; Region: PRK03427 60480004887 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 60480004888 FtsZ protein binding site [polypeptide binding]; other site 60480004889 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 60480004890 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 60480004891 nucleotide binding pocket [chemical binding]; other site 60480004892 K-X-D-G motif; other site 60480004893 catalytic site [active] 60480004894 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 60480004895 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 60480004896 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 60480004897 Dimer interface [polypeptide binding]; other site 60480004898 BRCT sequence motif; other site 60480004899 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 60480004900 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 60480004901 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 60480004902 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480004903 Zn2+ binding site [ion binding]; other site 60480004904 Mg2+ binding site [ion binding]; other site 60480004905 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 60480004906 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 60480004907 putative NAD(P) binding site [chemical binding]; other site 60480004908 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 60480004909 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 60480004910 catalytic residues [active] 60480004911 hinge region; other site 60480004912 alpha helical domain; other site 60480004913 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 60480004914 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 60480004915 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 60480004916 Na binding site [ion binding]; other site 60480004917 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 60480004918 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 60480004919 ligand binding site [chemical binding]; other site 60480004920 flexible hinge region; other site 60480004921 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 60480004922 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 60480004923 metal binding triad; other site 60480004924 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 60480004925 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 60480004926 active site 60480004927 catalytic site [active] 60480004928 substrate binding site [chemical binding]; other site 60480004929 MarR family; Region: MarR_2; cl17246 60480004930 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 60480004931 Prostaglandin dehydrogenases; Region: PGDH; cd05288 60480004932 NAD(P) binding site [chemical binding]; other site 60480004933 substrate binding site [chemical binding]; other site 60480004934 dimer interface [polypeptide binding]; other site 60480004935 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 60480004936 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 60480004937 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 60480004938 dimer interface [polypeptide binding]; other site 60480004939 active site 60480004940 CoA binding pocket [chemical binding]; other site 60480004941 Transcriptional regulators [Transcription]; Region: GntR; COG1802 60480004942 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480004943 DNA-binding site [nucleotide binding]; DNA binding site 60480004944 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 60480004945 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 60480004946 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 60480004947 active site 60480004948 motif I; other site 60480004949 motif II; other site 60480004950 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 60480004951 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 60480004952 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 60480004953 active site 60480004954 metal binding site [ion binding]; metal-binding site 60480004955 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 60480004956 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 60480004957 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 60480004958 active site 60480004959 Zn binding site [ion binding]; other site 60480004960 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 60480004961 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 60480004962 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 60480004963 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 60480004964 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 60480004965 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480004966 Coenzyme A binding pocket [chemical binding]; other site 60480004967 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 60480004968 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 60480004969 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 60480004970 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 60480004971 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 60480004972 generic binding surface II; other site 60480004973 generic binding surface I; other site 60480004974 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 60480004975 putative active site [active] 60480004976 putative catalytic site [active] 60480004977 putative Mg binding site IVb [ion binding]; other site 60480004978 putative phosphate binding site [ion binding]; other site 60480004979 putative DNA binding site [nucleotide binding]; other site 60480004980 putative Mg binding site IVa [ion binding]; other site 60480004981 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 60480004982 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 60480004983 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 60480004984 HSP70 interaction site [polypeptide binding]; other site 60480004985 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 60480004986 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 60480004987 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 60480004988 S-adenosylmethionine binding site [chemical binding]; other site 60480004989 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 60480004990 S-adenosylmethionine binding site [chemical binding]; other site 60480004991 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 60480004992 ABC transporter ATPase component; Reviewed; Region: PRK11147 60480004993 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480004994 Walker A/P-loop; other site 60480004995 ATP binding site [chemical binding]; other site 60480004996 Q-loop/lid; other site 60480004997 ABC transporter signature motif; other site 60480004998 Walker B; other site 60480004999 D-loop; other site 60480005000 H-loop/switch region; other site 60480005001 ABC transporter; Region: ABC_tran_2; pfam12848 60480005002 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480005003 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 60480005004 ribosome modulation factor; Provisional; Region: PRK14563 60480005005 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 60480005006 active site 1 [active] 60480005007 dimer interface [polypeptide binding]; other site 60480005008 active site 2 [active] 60480005009 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 60480005010 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 60480005011 response regulator; Provisional; Region: PRK09483 60480005012 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480005013 active site 60480005014 phosphorylation site [posttranslational modification] 60480005015 intermolecular recognition site; other site 60480005016 dimerization interface [polypeptide binding]; other site 60480005017 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 60480005018 DNA binding residues [nucleotide binding] 60480005019 dimerization interface [polypeptide binding]; other site 60480005020 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 60480005021 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 60480005022 GIY-YIG motif/motif A; other site 60480005023 active site 60480005024 catalytic site [active] 60480005025 putative DNA binding site [nucleotide binding]; other site 60480005026 metal binding site [ion binding]; metal-binding site 60480005027 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 60480005028 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 60480005029 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 60480005030 IHF dimer interface [polypeptide binding]; other site 60480005031 IHF - DNA interface [nucleotide binding]; other site 60480005032 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 60480005033 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480005034 Walker A/P-loop; other site 60480005035 ATP binding site [chemical binding]; other site 60480005036 Q-loop/lid; other site 60480005037 ABC transporter signature motif; other site 60480005038 Walker B; other site 60480005039 D-loop; other site 60480005040 H-loop/switch region; other site 60480005041 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 60480005042 hypothetical protein; Provisional; Region: PRK11239 60480005043 Protein of unknown function, DUF480; Region: DUF480; pfam04337 60480005044 rod-segment of the talin C-terminal domain; Region: talin-RS; cd12150 60480005045 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 60480005046 S1 domain; Region: S1_2; pfam13509 60480005047 arginine decarboxylase; Provisional; Region: PRK05354 60480005048 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 60480005049 dimer interface [polypeptide binding]; other site 60480005050 active site 60480005051 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 60480005052 catalytic residues [active] 60480005053 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 60480005054 Adenosylmethionine decarboxylase; Region: SAM_decarbox; cl03253 60480005055 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 60480005056 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 60480005057 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 60480005058 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 60480005059 YceI-like domain; Region: YceI; pfam04264 60480005060 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 60480005061 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 60480005062 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 60480005063 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 60480005064 Cache domain; Region: Cache_1; pfam02743 60480005065 PAS fold; Region: PAS_4; pfam08448 60480005066 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 60480005067 putative active site [active] 60480005068 heme pocket [chemical binding]; other site 60480005069 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 60480005070 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 60480005071 ATP binding site [chemical binding]; other site 60480005072 Mg2+ binding site [ion binding]; other site 60480005073 G-X-G motif; other site 60480005074 disulfide bond formation protein B; Provisional; Region: PRK01749 60480005075 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 60480005076 fatty acid metabolism regulator; Provisional; Region: PRK04984 60480005077 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480005078 DNA-binding site [nucleotide binding]; DNA binding site 60480005079 FadR C-terminal domain; Region: FadR_C; pfam07840 60480005080 SpoVR family protein; Provisional; Region: PRK11767 60480005081 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 60480005082 hypothetical protein; Provisional; Region: PRK05325 60480005083 superoxide dismutase; Provisional; Region: PRK10543 60480005084 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 60480005085 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 60480005086 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 60480005087 putative GSH binding site [chemical binding]; other site 60480005088 catalytic residues [active] 60480005089 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 60480005090 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 60480005091 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 60480005092 DNA replication initiation factor; Provisional; Region: PRK08084 60480005093 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 60480005094 Walker A motif; other site 60480005095 ATP binding site [chemical binding]; other site 60480005096 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 60480005097 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 60480005098 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480005099 Zn2+ binding site [ion binding]; other site 60480005100 Mg2+ binding site [ion binding]; other site 60480005101 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 60480005102 sensor protein PhoQ; Provisional; Region: PRK10815 60480005103 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 60480005104 ATP binding site [chemical binding]; other site 60480005105 Mg2+ binding site [ion binding]; other site 60480005106 G-X-G motif; other site 60480005107 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 60480005108 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480005109 active site 60480005110 phosphorylation site [posttranslational modification] 60480005111 intermolecular recognition site; other site 60480005112 dimerization interface [polypeptide binding]; other site 60480005113 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 60480005114 DNA binding site [nucleotide binding] 60480005115 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480005116 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 60480005117 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 60480005118 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 60480005119 succinylarginine dihydrolase; Provisional; Region: PRK13281 60480005120 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 60480005121 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 60480005122 active site 60480005123 interdomain interaction site; other site 60480005124 putative metal-binding site [ion binding]; other site 60480005125 nucleotide binding site [chemical binding]; other site 60480005126 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 60480005127 domain I; other site 60480005128 DNA binding groove [nucleotide binding] 60480005129 phosphate binding site [ion binding]; other site 60480005130 domain II; other site 60480005131 domain III; other site 60480005132 nucleotide binding site [chemical binding]; other site 60480005133 catalytic site [active] 60480005134 domain IV; other site 60480005135 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 60480005136 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 60480005137 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 60480005138 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 60480005139 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 60480005140 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480005141 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 60480005142 substrate binding site [chemical binding]; other site 60480005143 dimerization interface [polypeptide binding]; other site 60480005144 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480005145 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480005146 active site 60480005147 phosphorylation site [posttranslational modification] 60480005148 intermolecular recognition site; other site 60480005149 dimerization interface [polypeptide binding]; other site 60480005150 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 60480005151 DNA binding residues [nucleotide binding] 60480005152 dimerization interface [polypeptide binding]; other site 60480005153 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 60480005154 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12756 60480005155 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 60480005156 PEP synthetase regulatory protein; Provisional; Region: PRK05339 60480005157 phosphoenolpyruvate synthase; Validated; Region: PRK06464 60480005158 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 60480005159 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 60480005160 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 60480005161 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 60480005162 FAD binding domain; Region: FAD_binding_4; pfam01565 60480005163 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 60480005164 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 60480005165 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 60480005166 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 60480005167 MarR family; Region: MarR; pfam01047 60480005168 Peptidase S8 family domain, uncharacterized subfamily 6; Region: Peptidases_S8_6; cd07490 60480005169 active site 60480005170 catalytic triad [active] 60480005171 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cl08238 60480005172 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480005173 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 60480005174 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 60480005175 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 60480005176 NAD binding site [chemical binding]; other site 60480005177 Phe binding site; other site 60480005178 Cupin superfamily protein; Region: Cupin_4; pfam08007 60480005179 Cupin-like domain; Region: Cupin_8; pfam13621 60480005180 adenylosuccinate lyase; Provisional; Region: PRK09285 60480005181 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 60480005182 tetramer interface [polypeptide binding]; other site 60480005183 active site 60480005184 putative lysogenization regulator; Reviewed; Region: PRK00218 60480005185 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 60480005186 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 60480005187 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 60480005188 nudix motif; other site 60480005189 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 60480005190 pseudouridine synthase; Region: TIGR00093 60480005191 probable active site [active] 60480005192 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 60480005193 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 60480005194 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 60480005195 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 60480005196 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 60480005197 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 60480005198 Peptidase S8 family domain in Protein convertases; Region: Peptidases_S8_Protein_convertases_Kexins_Furin-lik; cd04059 60480005199 calcium binding site 1 [ion binding]; other site 60480005200 active site 60480005201 catalytic triad [active] 60480005202 calcium binding site 2 [ion binding]; other site 60480005203 calcium binding site 3 [ion binding]; other site 60480005204 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 60480005205 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480005206 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480005207 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 60480005208 dimerization interface [polypeptide binding]; other site 60480005209 DoxX-like family; Region: DoxX_2; pfam13564 60480005210 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 60480005211 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 60480005212 putative active site [active] 60480005213 metal binding site [ion binding]; metal-binding site 60480005214 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 60480005215 UbiA prenyltransferase family; Region: UbiA; pfam01040 60480005216 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 60480005217 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480005218 NAD(P) binding site [chemical binding]; other site 60480005219 active site 60480005220 acyl-CoA thioesterase II; Provisional; Region: PRK10526 60480005221 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 60480005222 active site 60480005223 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 60480005224 catalytic triad [active] 60480005225 dimer interface [polypeptide binding]; other site 60480005226 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 60480005227 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480005228 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480005229 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 60480005230 dimerization interface [polypeptide binding]; other site 60480005231 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 60480005232 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480005233 putative substrate translocation pore; other site 60480005234 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 60480005235 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 60480005236 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 60480005237 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480005238 Protein export membrane protein; Region: SecD_SecF; cl14618 60480005239 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480005240 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480005241 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480005242 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480005243 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 60480005244 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 60480005245 dimer interface [polypeptide binding]; other site 60480005246 active site 60480005247 citrylCoA binding site [chemical binding]; other site 60480005248 NADH binding [chemical binding]; other site 60480005249 cationic pore residues; other site 60480005250 oxalacetate/citrate binding site [chemical binding]; other site 60480005251 coenzyme A binding site [chemical binding]; other site 60480005252 catalytic triad [active] 60480005253 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 60480005254 Iron-sulfur protein interface; other site 60480005255 proximal quinone binding site [chemical binding]; other site 60480005256 SdhD (CybS) interface [polypeptide binding]; other site 60480005257 proximal heme binding site [chemical binding]; other site 60480005258 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 60480005259 SdhC subunit interface [polypeptide binding]; other site 60480005260 proximal heme binding site [chemical binding]; other site 60480005261 cardiolipin binding site; other site 60480005262 Iron-sulfur protein interface; other site 60480005263 proximal quinone binding site [chemical binding]; other site 60480005264 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 60480005265 L-aspartate oxidase; Provisional; Region: PRK06175 60480005266 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 60480005267 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 60480005268 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 60480005269 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 60480005270 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 60480005271 TPP-binding site [chemical binding]; other site 60480005272 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 60480005273 PYR/PP interface [polypeptide binding]; other site 60480005274 dimer interface [polypeptide binding]; other site 60480005275 TPP binding site [chemical binding]; other site 60480005276 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 60480005277 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 60480005278 E3 interaction surface; other site 60480005279 lipoyl attachment site [posttranslational modification]; other site 60480005280 e3 binding domain; Region: E3_binding; pfam02817 60480005281 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 60480005282 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 60480005283 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 60480005284 CoA-ligase; Region: Ligase_CoA; pfam00549 60480005285 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 60480005286 CoA binding domain; Region: CoA_binding; pfam02629 60480005287 CoA-ligase; Region: Ligase_CoA; pfam00549 60480005288 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 60480005289 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 60480005290 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 60480005291 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 60480005292 ferric uptake regulator; Provisional; Region: fur; PRK09462 60480005293 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 60480005294 metal binding site 2 [ion binding]; metal-binding site 60480005295 putative DNA binding helix; other site 60480005296 metal binding site 1 [ion binding]; metal-binding site 60480005297 dimer interface [polypeptide binding]; other site 60480005298 structural Zn2+ binding site [ion binding]; other site 60480005299 NAD-dependent deacetylase; Provisional; Region: PRK00481 60480005300 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 60480005301 NAD+ binding site [chemical binding]; other site 60480005302 substrate binding site [chemical binding]; other site 60480005303 Zn binding site [ion binding]; other site 60480005304 AAA domain; Region: AAA_33; pfam13671 60480005305 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 60480005306 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 60480005307 Cl binding site [ion binding]; other site 60480005308 oligomer interface [polypeptide binding]; other site 60480005309 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 60480005310 DNA-binding site [nucleotide binding]; DNA binding site 60480005311 RNA-binding motif; other site 60480005312 Uncharacterized conserved protein [Function unknown]; Region: COG2127 60480005313 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 60480005314 Clp amino terminal domain; Region: Clp_N; pfam02861 60480005315 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 60480005316 Walker A motif; other site 60480005317 ATP binding site [chemical binding]; other site 60480005318 Walker B motif; other site 60480005319 arginine finger; other site 60480005320 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 60480005321 Walker A motif; other site 60480005322 ATP binding site [chemical binding]; other site 60480005323 Walker B motif; other site 60480005324 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 60480005325 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 60480005326 rRNA binding site [nucleotide binding]; other site 60480005327 predicted 30S ribosome binding site; other site 60480005328 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 60480005329 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 60480005330 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 60480005331 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 60480005332 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 60480005333 Uncharacterized conserved protein [Function unknown]; Region: COG0327 60480005334 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 60480005335 Predicted permeases [General function prediction only]; Region: COG0679 60480005336 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 60480005337 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 60480005338 active site 60480005339 HIGH motif; other site 60480005340 KMSKS motif; other site 60480005341 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 60480005342 tRNA binding surface [nucleotide binding]; other site 60480005343 anticodon binding site; other site 60480005344 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 60480005345 dimer interface [polypeptide binding]; other site 60480005346 putative tRNA-binding site [nucleotide binding]; other site 60480005347 antiporter inner membrane protein; Provisional; Region: PRK11670 60480005348 Domain of unknown function DUF59; Region: DUF59; cl00941 60480005349 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 60480005350 Walker A motif; other site 60480005351 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 60480005352 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 60480005353 Sugar specificity; other site 60480005354 Pyrimidine base specificity; other site 60480005355 ATP-binding site [chemical binding]; other site 60480005356 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 60480005357 trimer interface [polypeptide binding]; other site 60480005358 active site 60480005359 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 60480005360 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 60480005361 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480005362 catalytic residue [active] 60480005363 YceG-like family; Region: YceG; pfam02618 60480005364 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 60480005365 dimerization interface [polypeptide binding]; other site 60480005366 thymidylate kinase; Validated; Region: tmk; PRK00698 60480005367 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 60480005368 TMP-binding site; other site 60480005369 ATP-binding site [chemical binding]; other site 60480005370 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 60480005371 DNA polymerase III subunit delta'; Validated; Region: PRK08485 60480005372 PilZ domain; Region: PilZ; cl01260 60480005373 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 60480005374 active site 60480005375 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 60480005376 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 60480005377 S-adenosylmethionine binding site [chemical binding]; other site 60480005378 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 60480005379 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 60480005380 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 60480005381 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 60480005382 mce related protein; Region: MCE; pfam02470 60480005383 mce related protein; Region: MCE; pfam02470 60480005384 mce related protein; Region: MCE; pfam02470 60480005385 mce related protein; Region: MCE; pfam02470 60480005386 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 60480005387 mce related protein; Region: MCE; pfam02470 60480005388 Paraquat-inducible protein A; Region: PqiA; pfam04403 60480005389 Paraquat-inducible protein A; Region: PqiA; pfam04403 60480005390 YebG protein; Region: YebG; pfam07130 60480005391 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 60480005392 GAF domain; Region: GAF_2; pfam13185 60480005393 ProP expression regulator; Provisional; Region: PRK04950 60480005394 ProQ/FINO family; Region: ProQ; smart00945 60480005395 carboxy-terminal protease; Provisional; Region: PRK11186 60480005396 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 60480005397 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 60480005398 protein binding site [polypeptide binding]; other site 60480005399 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 60480005400 Catalytic dyad [active] 60480005401 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 60480005402 aminopeptidase N; Provisional; Region: pepN; PRK14015 60480005403 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 60480005404 active site 60480005405 Zn binding site [ion binding]; other site 60480005406 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 60480005407 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 60480005408 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 60480005409 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 60480005410 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 60480005411 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 60480005412 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 60480005413 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 60480005414 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 60480005415 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 60480005416 quinone interaction residues [chemical binding]; other site 60480005417 active site 60480005418 catalytic residues [active] 60480005419 FMN binding site [chemical binding]; other site 60480005420 substrate binding site [chemical binding]; other site 60480005421 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 60480005422 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 60480005423 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 60480005424 putative catalytic cysteine [active] 60480005425 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 60480005426 putative active site [active] 60480005427 metal binding site [ion binding]; metal-binding site 60480005428 hypothetical protein; Provisional; Region: PRK11111 60480005429 Nitrate and nitrite sensing; Region: NIT; pfam08376 60480005430 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480005431 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 60480005432 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480005433 dimer interface [polypeptide binding]; other site 60480005434 putative CheW interface [polypeptide binding]; other site 60480005435 integrase; Provisional; Region: PRK09692 60480005436 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 60480005437 active site 60480005438 Int/Topo IB signature motif; other site 60480005439 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 60480005440 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 60480005441 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 60480005442 Predicted transcriptional regulator [Transcription]; Region: COG3905 60480005443 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 60480005444 INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available; Region: INT_SG3_C; cd01186 60480005445 Int/Topo IB signature motif; other site 60480005446 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 60480005447 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 60480005448 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 60480005449 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 60480005450 MPN+ (JAMM) motif; other site 60480005451 Zinc-binding site [ion binding]; other site 60480005452 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 60480005453 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 60480005454 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 60480005455 Walker A motif; other site 60480005456 ATP binding site [chemical binding]; other site 60480005457 Walker B motif; other site 60480005458 arginine finger; other site 60480005459 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 60480005460 Walker A motif; other site 60480005461 ATP binding site [chemical binding]; other site 60480005462 Walker B motif; other site 60480005463 arginine finger; other site 60480005464 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2425 60480005465 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 60480005466 metal ion-dependent adhesion site (MIDAS); other site 60480005467 Methyltransferase domain; Region: Methyltransf_26; pfam13659 60480005468 Protein of unknown function DUF262; Region: DUF262; pfam03235 60480005469 Uncharacterized conserved protein [Function unknown]; Region: COG1479 60480005470 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 60480005471 Zeta toxin; Region: Zeta_toxin; pfam06414 60480005472 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 60480005473 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480005474 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 60480005475 ATP binding site [chemical binding]; other site 60480005476 putative Mg++ binding site [ion binding]; other site 60480005477 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480005478 AAA-like domain; Region: AAA_10; pfam12846 60480005479 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 60480005480 nucleotide binding site [chemical binding]; other site 60480005481 Methyltransferase domain; Region: Methyltransf_23; pfam13489 60480005482 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 60480005483 S-adenosylmethionine binding site [chemical binding]; other site 60480005484 HNH endonuclease; Region: HNH_4; pfam13395 60480005485 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 60480005486 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 60480005487 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 60480005488 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 60480005489 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 60480005490 beta-hexosaminidase; Provisional; Region: PRK05337 60480005491 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 60480005492 hypothetical protein; Provisional; Region: PRK04940 60480005493 acylphosphatase; Provisional; Region: PRK14429 60480005494 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 60480005495 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 60480005496 transcription-repair coupling factor; Provisional; Region: PRK10689 60480005497 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 60480005498 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 60480005499 ATP binding site [chemical binding]; other site 60480005500 putative Mg++ binding site [ion binding]; other site 60480005501 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 60480005502 nucleotide binding region [chemical binding]; other site 60480005503 ATP-binding site [chemical binding]; other site 60480005504 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 60480005505 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 60480005506 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 60480005507 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 60480005508 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 60480005509 Walker A/P-loop; other site 60480005510 ATP binding site [chemical binding]; other site 60480005511 Q-loop/lid; other site 60480005512 ABC transporter signature motif; other site 60480005513 Walker B; other site 60480005514 D-loop; other site 60480005515 H-loop/switch region; other site 60480005516 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 60480005517 FtsX-like permease family; Region: FtsX; pfam02687 60480005518 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 60480005519 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 60480005520 active site 60480005521 dimerization interface [polypeptide binding]; other site 60480005522 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 60480005523 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 60480005524 serine O-acetyltransferase; Region: cysE; TIGR01172 60480005525 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 60480005526 trimer interface [polypeptide binding]; other site 60480005527 active site 60480005528 substrate binding site [chemical binding]; other site 60480005529 CoA binding site [chemical binding]; other site 60480005530 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 60480005531 Rrf2 family protein; Region: rrf2_super; TIGR00738 60480005532 cysteine desulfurase; Provisional; Region: PRK14012 60480005533 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 60480005534 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480005535 catalytic residue [active] 60480005536 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 60480005537 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 60480005538 trimerization site [polypeptide binding]; other site 60480005539 active site 60480005540 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 60480005541 co-chaperone HscB; Provisional; Region: hscB; PRK05014 60480005542 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 60480005543 HSP70 interaction site [polypeptide binding]; other site 60480005544 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 60480005545 chaperone protein HscA; Provisional; Region: hscA; PRK05183 60480005546 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 60480005547 nucleotide binding site [chemical binding]; other site 60480005548 putative NEF/HSP70 interaction site [polypeptide binding]; other site 60480005549 SBD interface [polypeptide binding]; other site 60480005550 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 60480005551 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 60480005552 catalytic loop [active] 60480005553 iron binding site [ion binding]; other site 60480005554 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 60480005555 ATP-grasp domain; Region: ATP-grasp_4; cl17255 60480005556 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 60480005557 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 60480005558 active site 60480005559 multimer interface [polypeptide binding]; other site 60480005560 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 60480005561 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 60480005562 putative dimer interface [polypeptide binding]; other site 60480005563 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 60480005564 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 60480005565 putative valine binding site [chemical binding]; other site 60480005566 dimer interface [polypeptide binding]; other site 60480005567 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 60480005568 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08979 60480005569 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 60480005570 PYR/PP interface [polypeptide binding]; other site 60480005571 dimer interface [polypeptide binding]; other site 60480005572 TPP binding site [chemical binding]; other site 60480005573 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 60480005574 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 60480005575 TPP-binding site [chemical binding]; other site 60480005576 dimer interface [polypeptide binding]; other site 60480005577 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 60480005578 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 60480005579 putative substrate translocation pore; other site 60480005580 Uncharacterized conserved protein [Function unknown]; Region: COG3391 60480005581 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 60480005582 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480005583 DNA-binding site [nucleotide binding]; DNA binding site 60480005584 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 60480005585 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480005586 homodimer interface [polypeptide binding]; other site 60480005587 catalytic residue [active] 60480005588 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 60480005589 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 60480005590 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 60480005591 Sulfate transporter family; Region: Sulfate_transp; pfam00916 60480005592 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 60480005593 Integrase core domain; Region: rve; pfam00665 60480005594 Integrase core domain; Region: rve_3; pfam13683 60480005595 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 60480005596 Glutaredoxin, GrxB family; Region: GRXB; TIGR02182 60480005597 putative GSH binding site (G-site) [chemical binding]; other site 60480005598 active site cysteine [active] 60480005599 putative C-terminal domain interface [polypeptide binding]; other site 60480005600 putative dimer interface [polypeptide binding]; other site 60480005601 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 60480005602 putative N-terminal domain interface [polypeptide binding]; other site 60480005603 putative dimer interface [polypeptide binding]; other site 60480005604 putative substrate binding pocket (H-site) [chemical binding]; other site 60480005605 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 60480005606 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 60480005607 active site residue [active] 60480005608 PTS system glucose-specific transporter subunit; Provisional; Region: PRK09439 60480005609 HPr interaction site; other site 60480005610 glycerol kinase (GK) interaction site [polypeptide binding]; other site 60480005611 active site 60480005612 phosphorylation site [posttranslational modification] 60480005613 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 60480005614 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 60480005615 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 60480005616 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 60480005617 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 60480005618 dimerization domain swap beta strand [polypeptide binding]; other site 60480005619 regulatory protein interface [polypeptide binding]; other site 60480005620 active site 60480005621 regulatory phosphorylation site [posttranslational modification]; other site 60480005622 Uncharacterized conserved protein [Function unknown]; Region: COG3603 60480005623 Family description; Region: ACT_7; pfam13840 60480005624 Cache domain; Region: Cache_2; pfam08269 60480005625 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480005626 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 60480005627 dimerization interface [polypeptide binding]; other site 60480005628 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480005629 dimer interface [polypeptide binding]; other site 60480005630 putative CheW interface [polypeptide binding]; other site 60480005631 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 60480005632 Transcriptional regulators [Transcription]; Region: PurR; COG1609 60480005633 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 60480005634 DNA binding site [nucleotide binding] 60480005635 domain linker motif; other site 60480005636 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 60480005637 putative dimerization interface [polypeptide binding]; other site 60480005638 putative ligand binding site [chemical binding]; other site 60480005639 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 60480005640 active site 60480005641 catalytic site [active] 60480005642 substrate binding site [chemical binding]; other site 60480005643 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 60480005644 S-adenosylmethionine binding site [chemical binding]; other site 60480005645 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 60480005646 AAA domain; Region: AAA_30; pfam13604 60480005647 Family description; Region: UvrD_C_2; pfam13538 60480005648 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 60480005649 Family description; Region: UvrD_C_2; pfam13538 60480005650 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 60480005651 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 60480005652 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 60480005653 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 60480005654 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 60480005655 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 60480005656 Protein of unknown function DUF58; Region: DUF58; pfam01882 60480005657 MoxR-like ATPases [General function prediction only]; Region: COG0714 60480005658 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 60480005659 Walker A motif; other site 60480005660 ATP binding site [chemical binding]; other site 60480005661 Walker B motif; other site 60480005662 arginine finger; other site 60480005663 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 60480005664 Transposase; Region: DEDD_Tnp_IS110; pfam01548 60480005665 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 60480005666 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 60480005667 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 60480005668 Y-family of DNA polymerases; Region: PolY; cl12025 60480005669 active site 60480005670 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 60480005671 putative active site [active] 60480005672 catalytic site [active] 60480005673 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 60480005674 Catalytic site [active] 60480005675 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 60480005676 Catalytic site [active] 60480005677 Protein of unknown function (DUF938); Region: DUF938; pfam06080 60480005678 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 60480005679 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 60480005680 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480005681 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480005682 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 60480005683 putative effector binding pocket; other site 60480005684 putative dimerization interface [polypeptide binding]; other site 60480005685 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 60480005686 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 60480005687 substrate binding site [chemical binding]; other site 60480005688 catalytic Zn binding site [ion binding]; other site 60480005689 NAD binding site [chemical binding]; other site 60480005690 structural Zn binding site [ion binding]; other site 60480005691 dimer interface [polypeptide binding]; other site 60480005692 S-formylglutathione hydrolase; Region: PLN02442 60480005693 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 60480005694 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 60480005695 active site 60480005696 substrate binding sites [chemical binding]; other site 60480005697 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 60480005698 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 60480005699 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 60480005700 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 60480005701 aromatic amino acid transport protein; Region: araaP; TIGR00837 60480005702 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 60480005703 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 60480005704 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 60480005705 metal binding site [ion binding]; metal-binding site 60480005706 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 60480005707 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 60480005708 substrate binding site [chemical binding]; other site 60480005709 glutamase interaction surface [polypeptide binding]; other site 60480005710 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 60480005711 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 60480005712 catalytic residues [active] 60480005713 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 60480005714 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 60480005715 putative active site [active] 60480005716 oxyanion strand; other site 60480005717 catalytic triad [active] 60480005718 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 60480005719 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 60480005720 active site 60480005721 motif I; other site 60480005722 motif II; other site 60480005723 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 60480005724 putative active site pocket [active] 60480005725 4-fold oligomerization interface [polypeptide binding]; other site 60480005726 metal binding residues [ion binding]; metal-binding site 60480005727 3-fold/trimer interface [polypeptide binding]; other site 60480005728 histidinol-phosphate aminotransferase; Provisional; Region: PRK04635 60480005729 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 60480005730 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480005731 homodimer interface [polypeptide binding]; other site 60480005732 catalytic residue [active] 60480005733 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 60480005734 histidinol dehydrogenase; Region: hisD; TIGR00069 60480005735 NAD binding site [chemical binding]; other site 60480005736 dimerization interface [polypeptide binding]; other site 60480005737 product binding site; other site 60480005738 substrate binding site [chemical binding]; other site 60480005739 zinc binding site [ion binding]; other site 60480005740 catalytic residues [active] 60480005741 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 60480005742 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 60480005743 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 60480005744 Membrane bound O-acyl transferase family; Region: MBOAT_2; pfam13813 60480005745 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 60480005746 DEAD/DEAH box helicase; Region: DEAD; pfam00270 60480005747 DEAD_2; Region: DEAD_2; pfam06733 60480005748 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 60480005749 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 60480005750 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 60480005751 N-terminal plug; other site 60480005752 ligand-binding site [chemical binding]; other site 60480005753 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480005754 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480005755 dimer interface [polypeptide binding]; other site 60480005756 putative CheW interface [polypeptide binding]; other site 60480005757 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 60480005758 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 60480005759 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 60480005760 dimer interface [polypeptide binding]; other site 60480005761 motif 1; other site 60480005762 active site 60480005763 motif 2; other site 60480005764 motif 3; other site 60480005765 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 60480005766 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 60480005767 putative tRNA-binding site [nucleotide binding]; other site 60480005768 B3/4 domain; Region: B3_4; pfam03483 60480005769 tRNA synthetase B5 domain; Region: B5; smart00874 60480005770 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 60480005771 dimer interface [polypeptide binding]; other site 60480005772 motif 1; other site 60480005773 motif 3; other site 60480005774 motif 2; other site 60480005775 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 60480005776 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 60480005777 IHF dimer interface [polypeptide binding]; other site 60480005778 IHF - DNA interface [nucleotide binding]; other site 60480005779 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 60480005780 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 60480005781 putative acyl-acceptor binding pocket; other site 60480005782 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 60480005783 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 60480005784 dimerization interface [polypeptide binding]; other site 60480005785 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 60480005786 ATP binding site [chemical binding]; other site 60480005787 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 60480005788 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 60480005789 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 60480005790 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 60480005791 Acylphosphatase; Region: Acylphosphatase; pfam00708 60480005792 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 60480005793 HypF finger; Region: zf-HYPF; pfam07503 60480005794 HypF finger; Region: zf-HYPF; pfam07503 60480005795 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 60480005796 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 60480005797 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 60480005798 putative substrate-binding site; other site 60480005799 nickel binding site [ion binding]; other site 60480005800 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 60480005801 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 60480005802 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 60480005803 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 60480005804 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 60480005805 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 60480005806 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480005807 catalytic residues [active] 60480005808 Domain of unknown function (DUF4266); Region: DUF4266; pfam14086 60480005809 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 60480005810 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 60480005811 ApbE family; Region: ApbE; pfam02424 60480005812 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480005813 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480005814 active site 60480005815 phosphorylation site [posttranslational modification] 60480005816 intermolecular recognition site; other site 60480005817 dimerization interface [polypeptide binding]; other site 60480005818 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 60480005819 DNA binding site [nucleotide binding] 60480005820 sensor protein QseC; Provisional; Region: PRK10337 60480005821 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 60480005822 dimer interface [polypeptide binding]; other site 60480005823 phosphorylation site [posttranslational modification] 60480005824 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 60480005825 ATP binding site [chemical binding]; other site 60480005826 Mg2+ binding site [ion binding]; other site 60480005827 G-X-G motif; other site 60480005828 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 60480005829 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 60480005830 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 60480005831 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 60480005832 Ligand binding site; other site 60480005833 DXD motif; other site 60480005834 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 60480005835 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 60480005836 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 60480005837 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 60480005838 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 60480005839 Bacterial protein of unknown function (DUF882); Region: Peptidase_M15_2; pfam05951 60480005840 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 60480005841 5S rRNA interface [nucleotide binding]; other site 60480005842 CTC domain interface [polypeptide binding]; other site 60480005843 L16 interface [polypeptide binding]; other site 60480005844 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 60480005845 Family of unknown function (DUF490); Region: DUF490; pfam04357 60480005846 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 60480005847 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480005848 Surface antigen; Region: Bac_surface_Ag; pfam01103 60480005849 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 60480005850 catalytic nucleophile [active] 60480005851 FOG: CBS domain [General function prediction only]; Region: COG0517 60480005852 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 60480005853 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 60480005854 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 60480005855 ATP binding site [chemical binding]; other site 60480005856 putative Mg++ binding site [ion binding]; other site 60480005857 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 60480005858 nucleotide binding region [chemical binding]; other site 60480005859 ATP-binding site [chemical binding]; other site 60480005860 Helicase associated domain (HA2); Region: HA2; pfam04408 60480005861 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 60480005862 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 60480005863 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 60480005864 NapD protein; Region: NapD; pfam03927 60480005865 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 60480005866 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 60480005867 [4Fe-4S] binding site [ion binding]; other site 60480005868 molybdopterin cofactor binding site; other site 60480005869 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 60480005870 molybdopterin cofactor binding site; other site 60480005871 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 60480005872 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 60480005873 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 60480005874 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480005875 Walker A/P-loop; other site 60480005876 ATP binding site [chemical binding]; other site 60480005877 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 60480005878 putative active site [active] 60480005879 putative metal-binding site [ion binding]; other site 60480005880 Isochorismatase family; Region: Isochorismatase; pfam00857 60480005881 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 60480005882 catalytic triad [active] 60480005883 conserved cis-peptide bond; other site 60480005884 Protein of unknown function (DUF2185); Region: DUF2185; cl02019 60480005885 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480005886 Coenzyme A binding pocket [chemical binding]; other site 60480005887 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 60480005888 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 60480005889 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 60480005890 Ligand binding site; other site 60480005891 oligomer interface; other site 60480005892 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH3; cd08184 60480005893 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 60480005894 putative active site [active] 60480005895 metal binding site [ion binding]; metal-binding site 60480005896 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 60480005897 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 60480005898 inhibitor-cofactor binding pocket; inhibition site 60480005899 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480005900 catalytic residue [active] 60480005901 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 60480005902 active site clefts [active] 60480005903 zinc binding site [ion binding]; other site 60480005904 dimer interface [polypeptide binding]; other site 60480005905 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 60480005906 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 60480005907 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 60480005908 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 60480005909 metal binding site [ion binding]; metal-binding site 60480005910 dimer interface [polypeptide binding]; other site 60480005911 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 60480005912 ArsC family; Region: ArsC; pfam03960 60480005913 putative catalytic residues [active] 60480005914 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 60480005915 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 60480005916 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480005917 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480005918 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 60480005919 dimerization interface [polypeptide binding]; other site 60480005920 putative effector binding pocket; other site 60480005921 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480005922 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480005923 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480005924 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480005925 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 60480005926 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 60480005927 RNHCP domain; Region: RNHCP; pfam12647 60480005928 Paraquat-inducible protein A; Region: PqiA; pfam04403 60480005929 Paraquat-inducible protein A; Region: PqiA; pfam04403 60480005930 paraquat-inducible protein B; Provisional; Region: PRK10807 60480005931 mce related protein; Region: MCE; pfam02470 60480005932 mce related protein; Region: MCE; pfam02470 60480005933 mce related protein; Region: MCE; pfam02470 60480005934 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 60480005935 Protein of unknown function (DUF330); Region: DUF330; pfam03886 60480005936 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 60480005937 Citrate transporter; Region: CitMHS; pfam03600 60480005938 transmembrane helices; other site 60480005939 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480005940 Helix-turn-helix domain; Region: HTH_18; pfam12833 60480005941 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480005942 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 60480005943 Domain interface; other site 60480005944 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 60480005945 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 60480005946 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 60480005947 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 60480005948 YCII-related domain; Region: YCII; cl00999 60480005949 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 60480005950 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 60480005951 catalytic site [active] 60480005952 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 60480005953 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 60480005954 putative RNA binding site [nucleotide binding]; other site 60480005955 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 60480005956 S-adenosylmethionine binding site [chemical binding]; other site 60480005957 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 60480005958 Uncharacterized conserved protein [Function unknown]; Region: COG2128 60480005959 Helix-turn-helix domain; Region: HTH_18; pfam12833 60480005960 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480005961 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 60480005962 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 60480005963 Family of unknown function (DUF633); Region: DUF633; pfam04816 60480005964 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 60480005965 nudix motif; other site 60480005966 Haemolysin-III related; Region: HlyIII; cl03831 60480005967 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 60480005968 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 60480005969 ThiC-associated domain; Region: ThiC-associated; pfam13667 60480005970 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 60480005971 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 60480005972 dimer interface [polypeptide binding]; other site 60480005973 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 60480005974 substrate binding site [chemical binding]; other site 60480005975 ATP binding site [chemical binding]; other site 60480005976 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 60480005977 active site 60480005978 thiamine phosphate binding site [chemical binding]; other site 60480005979 pyrophosphate binding site [ion binding]; other site 60480005980 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 60480005981 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 60480005982 ATP binding site [chemical binding]; other site 60480005983 substrate interface [chemical binding]; other site 60480005984 MoeZ/MoeB domain; Region: MoeZ_MoeB; pfam05237 60480005985 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 60480005986 thiS-thiF/thiG interaction site; other site 60480005987 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 60480005988 ThiS interaction site; other site 60480005989 putative active site [active] 60480005990 tetramer interface [polypeptide binding]; other site 60480005991 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 60480005992 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 60480005993 FeS/SAM binding site; other site 60480005994 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 60480005995 SprA-related family; Region: SprA-related; pfam12118 60480005996 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480005997 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480005998 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 60480005999 dimerization interface [polypeptide binding]; other site 60480006000 Domain of unknown function (DUF3541); Region: DUF3541; pfam12060 60480006001 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 60480006002 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 60480006003 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 60480006004 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 60480006005 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 60480006006 Methyltransferase domain; Region: Methyltransf_23; pfam13489 60480006007 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 60480006008 S-adenosylmethionine binding site [chemical binding]; other site 60480006009 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 60480006010 S-adenosylmethionine binding site [chemical binding]; other site 60480006011 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480006012 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 60480006013 substrate binding pocket [chemical binding]; other site 60480006014 membrane-bound complex binding site; other site 60480006015 hinge residues; other site 60480006016 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480006017 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 60480006018 substrate binding pocket [chemical binding]; other site 60480006019 membrane-bound complex binding site; other site 60480006020 hinge residues; other site 60480006021 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480006022 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 60480006023 substrate binding pocket [chemical binding]; other site 60480006024 membrane-bound complex binding site; other site 60480006025 hinge residues; other site 60480006026 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006027 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006028 metal binding site [ion binding]; metal-binding site 60480006029 active site 60480006030 I-site; other site 60480006031 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 60480006032 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 60480006033 dimer interface [polypeptide binding]; other site 60480006034 anticodon binding site; other site 60480006035 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 60480006036 homodimer interface [polypeptide binding]; other site 60480006037 motif 1; other site 60480006038 active site 60480006039 motif 2; other site 60480006040 GAD domain; Region: GAD; pfam02938 60480006041 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 60480006042 active site 60480006043 motif 3; other site 60480006044 hypothetical protein; Validated; Region: PRK00110 60480006045 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 60480006046 active site 60480006047 putative DNA-binding cleft [nucleotide binding]; other site 60480006048 dimer interface [polypeptide binding]; other site 60480006049 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 60480006050 RuvA N terminal domain; Region: RuvA_N; pfam01330 60480006051 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 60480006052 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 60480006053 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 60480006054 Walker A motif; other site 60480006055 ATP binding site [chemical binding]; other site 60480006056 Walker B motif; other site 60480006057 arginine finger; other site 60480006058 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 60480006059 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480006060 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 60480006061 N-terminal plug; other site 60480006062 ligand-binding site [chemical binding]; other site 60480006063 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480006064 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480006065 active site 60480006066 phosphorylation site [posttranslational modification] 60480006067 intermolecular recognition site; other site 60480006068 dimerization interface [polypeptide binding]; other site 60480006069 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 60480006070 DNA binding site [nucleotide binding] 60480006071 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 60480006072 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 60480006073 putative active site [active] 60480006074 Zn binding site [ion binding]; other site 60480006075 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 60480006076 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 60480006077 active site 60480006078 homodimer interface [polypeptide binding]; other site 60480006079 protease 4; Provisional; Region: PRK10949 60480006080 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 60480006081 tandem repeat interface [polypeptide binding]; other site 60480006082 oligomer interface [polypeptide binding]; other site 60480006083 active site residues [active] 60480006084 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 60480006085 tandem repeat interface [polypeptide binding]; other site 60480006086 oligomer interface [polypeptide binding]; other site 60480006087 active site residues [active] 60480006088 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 60480006089 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 60480006090 active site 60480006091 FMN binding site [chemical binding]; other site 60480006092 2,4-decadienoyl-CoA binding site; other site 60480006093 catalytic residue [active] 60480006094 4Fe-4S cluster binding site [ion binding]; other site 60480006095 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 60480006096 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480006097 putative transposase OrfB; Reviewed; Region: PHA02517 60480006098 Integrase core domain; Region: rve; pfam00665 60480006099 Integrase core domain; Region: rve_3; pfam13683 60480006100 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 60480006101 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 60480006102 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 60480006103 catalytic loop [active] 60480006104 iron binding site [ion binding]; other site 60480006105 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 60480006106 dimer interface [polypeptide binding]; other site 60480006107 putative radical transfer pathway; other site 60480006108 diiron center [ion binding]; other site 60480006109 tyrosyl radical; other site 60480006110 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 60480006111 ATP cone domain; Region: ATP-cone; pfam03477 60480006112 Class I ribonucleotide reductase; Region: RNR_I; cd01679 60480006113 active site 60480006114 dimer interface [polypeptide binding]; other site 60480006115 catalytic residues [active] 60480006116 effector binding site; other site 60480006117 R2 peptide binding site; other site 60480006118 2-phosphoglycolate phosphatase, prokaryotic; Region: PGP_bact; TIGR01449 60480006119 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 60480006120 active site 60480006121 motif I; other site 60480006122 motif II; other site 60480006123 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 60480006124 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 60480006125 S-adenosylmethionine binding site [chemical binding]; other site 60480006126 DNA gyrase subunit A; Validated; Region: PRK05560 60480006127 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 60480006128 CAP-like domain; other site 60480006129 active site 60480006130 primary dimer interface [polypeptide binding]; other site 60480006131 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 60480006132 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 60480006133 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 60480006134 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 60480006135 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 60480006136 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 60480006137 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 60480006138 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480006139 catalytic residue [active] 60480006140 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 60480006141 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 60480006142 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480006143 homodimer interface [polypeptide binding]; other site 60480006144 catalytic residue [active] 60480006145 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 60480006146 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 60480006147 hinge; other site 60480006148 active site 60480006149 cytidylate kinase; Provisional; Region: cmk; PRK00023 60480006150 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 60480006151 CMP-binding site; other site 60480006152 The sites determining sugar specificity; other site 60480006153 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 60480006154 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 60480006155 RNA binding site [nucleotide binding]; other site 60480006156 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 60480006157 RNA binding site [nucleotide binding]; other site 60480006158 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 60480006159 RNA binding site [nucleotide binding]; other site 60480006160 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 60480006161 RNA binding site [nucleotide binding]; other site 60480006162 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 60480006163 RNA binding site [nucleotide binding]; other site 60480006164 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 60480006165 RNA binding site [nucleotide binding]; other site 60480006166 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 60480006167 IHF dimer interface [polypeptide binding]; other site 60480006168 IHF - DNA interface [nucleotide binding]; other site 60480006169 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 60480006170 tetratricopeptide repeat protein; Provisional; Region: PRK11788 60480006171 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 60480006172 binding surface 60480006173 TPR motif; other site 60480006174 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 60480006175 active site 60480006176 dimer interface [polypeptide binding]; other site 60480006177 short chain dehydrogenase; Provisional; Region: PRK07576 60480006178 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480006179 NAD(P) binding site [chemical binding]; other site 60480006180 active site 60480006181 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 60480006182 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 60480006183 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 60480006184 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 60480006185 active site 60480006186 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 60480006187 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 60480006188 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 60480006189 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 60480006190 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 60480006191 domain interface [polypeptide binding]; other site 60480006192 putative active site [active] 60480006193 catalytic site [active] 60480006194 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 60480006195 domain interface [polypeptide binding]; other site 60480006196 putative active site [active] 60480006197 catalytic site [active] 60480006198 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 60480006199 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 60480006200 putative substrate translocation pore; other site 60480006201 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 60480006202 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 60480006203 Uncharacterized conserved protein [Function unknown]; Region: COG3148 60480006204 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480006205 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480006206 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480006207 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 60480006208 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 60480006209 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 60480006210 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 60480006211 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 60480006212 active site 60480006213 DNA binding site [nucleotide binding] 60480006214 Int/Topo IB signature motif; other site 60480006215 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480006216 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 60480006217 ATP binding site [chemical binding]; other site 60480006218 putative Mg++ binding site [ion binding]; other site 60480006219 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 60480006220 nucleotide binding region [chemical binding]; other site 60480006221 ATP-binding site [chemical binding]; other site 60480006222 ecotin; Provisional; Region: PRK03719 60480006223 secondary substrate binding site; other site 60480006224 primary substrate binding site; other site 60480006225 inhibition loop; other site 60480006226 dimerization interface [polypeptide binding]; other site 60480006227 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 60480006228 multidrug efflux protein; Reviewed; Region: PRK01766 60480006229 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 60480006230 cation binding site [ion binding]; other site 60480006231 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 60480006232 Lumazine binding domain; Region: Lum_binding; pfam00677 60480006233 Lumazine binding domain; Region: Lum_binding; pfam00677 60480006234 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 60480006235 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 60480006236 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 60480006237 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 60480006238 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 60480006239 active site 60480006240 dimer interface [polypeptide binding]; other site 60480006241 motif 1; other site 60480006242 motif 2; other site 60480006243 motif 3; other site 60480006244 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 60480006245 anticodon binding site; other site 60480006246 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 60480006247 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 60480006248 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 60480006249 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 60480006250 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 60480006251 23S rRNA binding site [nucleotide binding]; other site 60480006252 L21 binding site [polypeptide binding]; other site 60480006253 L13 binding site [polypeptide binding]; other site 60480006254 thioredoxin reductase; Provisional; Region: PRK10262 60480006255 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480006256 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 60480006257 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 60480006258 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 60480006259 hexamer interface [polypeptide binding]; other site 60480006260 ligand binding site [chemical binding]; other site 60480006261 putative active site [active] 60480006262 NAD(P) binding site [chemical binding]; other site 60480006263 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 60480006264 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 60480006265 putative DNA binding site [nucleotide binding]; other site 60480006266 putative Zn2+ binding site [ion binding]; other site 60480006267 AsnC family; Region: AsnC_trans_reg; pfam01037 60480006268 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 60480006269 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 60480006270 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 60480006271 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 60480006272 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 60480006273 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 60480006274 recombination factor protein RarA; Reviewed; Region: PRK13342 60480006275 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 60480006276 Walker A motif; other site 60480006277 ATP binding site [chemical binding]; other site 60480006278 Walker B motif; other site 60480006279 arginine finger; other site 60480006280 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 60480006281 camphor resistance protein CrcB; Provisional; Region: PRK14197 60480006282 seryl-tRNA synthetase; Provisional; Region: PRK05431 60480006283 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 60480006284 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 60480006285 dimer interface [polypeptide binding]; other site 60480006286 active site 60480006287 motif 1; other site 60480006288 motif 2; other site 60480006289 motif 3; other site 60480006290 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 60480006291 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 60480006292 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 60480006293 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 60480006294 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 60480006295 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 60480006296 YccA-like proteins; Region: YccA_like; cd10433 60480006297 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 60480006298 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480006299 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 60480006300 dimerization interface [polypeptide binding]; other site 60480006301 putative transporter; Provisional; Region: PRK11043 60480006302 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 60480006303 putative substrate translocation pore; other site 60480006304 ribulokinase; Provisional; Region: PRK04123 60480006305 Ribulokinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_RBK; cd07781 60480006306 N- and C-terminal domain interface [polypeptide binding]; other site 60480006307 active site 60480006308 MgATP binding site [chemical binding]; other site 60480006309 catalytic site [active] 60480006310 metal binding site [ion binding]; metal-binding site 60480006311 carbohydrate binding site [chemical binding]; other site 60480006312 homodimer interface [polypeptide binding]; other site 60480006313 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 60480006314 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 60480006315 intersubunit interface [polypeptide binding]; other site 60480006316 active site 60480006317 Zn2+ binding site [ion binding]; other site 60480006318 L-arabinose isomerase; Provisional; Region: PRK02929 60480006319 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 60480006320 hexamer (dimer of trimers) interface [polypeptide binding]; other site 60480006321 trimer interface [polypeptide binding]; other site 60480006322 substrate binding site [chemical binding]; other site 60480006323 Mn binding site [ion binding]; other site 60480006324 fructose-1-P/6-phosphogluconate phosphatase; Provisional; Region: PRK10725 60480006325 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 60480006326 active site 60480006327 motif I; other site 60480006328 motif II; other site 60480006329 Transcriptional regulators [Transcription]; Region: FadR; COG2186 60480006330 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480006331 DNA-binding site [nucleotide binding]; DNA binding site 60480006332 FCD domain; Region: FCD; pfam07729 60480006333 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 60480006334 substrate binding site [chemical binding]; other site 60480006335 active site 60480006336 dihydroxy-acid dehydratase; Validated; Region: PRK06131 60480006337 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 60480006338 classical (c) SDRs; Region: SDR_c; cd05233 60480006339 NAD(P) binding site [chemical binding]; other site 60480006340 active site 60480006341 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 60480006342 active site 60480006343 catalytic residues [active] 60480006344 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 60480006345 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 60480006346 putative ligand binding site [chemical binding]; other site 60480006347 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 60480006348 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 60480006349 Walker A/P-loop; other site 60480006350 ATP binding site [chemical binding]; other site 60480006351 Q-loop/lid; other site 60480006352 ABC transporter signature motif; other site 60480006353 Walker B; other site 60480006354 D-loop; other site 60480006355 H-loop/switch region; other site 60480006356 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 60480006357 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 60480006358 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 60480006359 TM-ABC transporter signature motif; other site 60480006360 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 60480006361 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 60480006362 TM-ABC transporter signature motif; other site 60480006363 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 60480006364 active site 60480006365 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 60480006366 active site 60480006367 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 60480006368 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 60480006369 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 60480006370 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 60480006371 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 60480006372 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 60480006373 substrate binding site [chemical binding]; other site 60480006374 active site 60480006375 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 60480006376 active site 60480006377 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 60480006378 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 60480006379 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 60480006380 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 60480006381 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 60480006382 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 60480006383 substrate binding site [chemical binding]; other site 60480006384 active site 60480006385 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 60480006386 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 60480006387 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 60480006388 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 60480006389 Int/Topo IB signature motif; other site 60480006390 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480006391 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 60480006392 active site 60480006393 phosphorylation site [posttranslational modification] 60480006394 intermolecular recognition site; other site 60480006395 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 60480006396 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480006397 Zn2+ binding site [ion binding]; other site 60480006398 Mg2+ binding site [ion binding]; other site 60480006399 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 60480006400 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 60480006401 Low-spin heme binding site [chemical binding]; other site 60480006402 Putative water exit pathway; other site 60480006403 Binuclear center (active site) [active] 60480006404 Putative proton exit pathway; other site 60480006405 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 60480006406 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 60480006407 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 60480006408 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 60480006409 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 60480006410 Cytochrome c; Region: Cytochrom_C; pfam00034 60480006411 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 60480006412 FixH; Region: FixH; pfam05751 60480006413 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 60480006414 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 60480006415 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 60480006416 metal-binding site [ion binding] 60480006417 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 60480006418 Soluble P-type ATPase [General function prediction only]; Region: COG4087 60480006419 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 60480006420 Family description; Region: DsbD_2; pfam13386 60480006421 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 60480006422 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 60480006423 ligand binding site [chemical binding]; other site 60480006424 flexible hinge region; other site 60480006425 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 60480006426 putative switch regulator; other site 60480006427 non-specific DNA interactions [nucleotide binding]; other site 60480006428 DNA binding site [nucleotide binding] 60480006429 sequence specific DNA binding site [nucleotide binding]; other site 60480006430 putative cAMP binding site [chemical binding]; other site 60480006431 universal stress protein UspE; Provisional; Region: PRK11175 60480006432 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 60480006433 Ligand Binding Site [chemical binding]; other site 60480006434 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 60480006435 Ligand Binding Site [chemical binding]; other site 60480006436 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 60480006437 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 60480006438 Ligand Binding Site [chemical binding]; other site 60480006439 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 60480006440 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 60480006441 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 60480006442 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 60480006443 phosphate binding site [ion binding]; other site 60480006444 putative substrate binding pocket [chemical binding]; other site 60480006445 dimer interface [polypeptide binding]; other site 60480006446 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 60480006447 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 60480006448 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480006449 homodimer interface [polypeptide binding]; other site 60480006450 catalytic residue [active] 60480006451 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 60480006452 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 60480006453 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 60480006454 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 60480006455 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 60480006456 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 60480006457 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 60480006458 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 60480006459 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 60480006460 E-class dimer interface [polypeptide binding]; other site 60480006461 P-class dimer interface [polypeptide binding]; other site 60480006462 active site 60480006463 Cu2+ binding site [ion binding]; other site 60480006464 Zn2+ binding site [ion binding]; other site 60480006465 quinolinate synthetase; Provisional; Region: PRK09375 60480006466 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 60480006467 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 60480006468 E3 interaction surface; other site 60480006469 lipoyl attachment site [posttranslational modification]; other site 60480006470 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 60480006471 E3 interaction surface; other site 60480006472 lipoyl attachment site [posttranslational modification]; other site 60480006473 e3 binding domain; Region: E3_binding; pfam02817 60480006474 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 60480006475 3-methyl-2-oxobutanate dehydrogenase; Provisional; Region: PTZ00182 60480006476 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 60480006477 alpha subunit interface [polypeptide binding]; other site 60480006478 TPP binding site [chemical binding]; other site 60480006479 heterodimer interface [polypeptide binding]; other site 60480006480 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 60480006481 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 60480006482 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 60480006483 tetramer interface [polypeptide binding]; other site 60480006484 TPP-binding site [chemical binding]; other site 60480006485 heterodimer interface [polypeptide binding]; other site 60480006486 phosphorylation loop region [posttranslational modification] 60480006487 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 60480006488 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 60480006489 putative active site [active] 60480006490 Zn binding site [ion binding]; other site 60480006491 methionine sulfoxide reductase A; Provisional; Region: PRK14054 60480006492 phosphoglucomutase; Validated; Region: PRK07564 60480006493 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 60480006494 active site 60480006495 substrate binding site [chemical binding]; other site 60480006496 metal binding site [ion binding]; metal-binding site 60480006497 replication initiation regulator SeqA; Provisional; Region: PRK11187 60480006498 PGAP1-like protein; Region: PGAP1; pfam07819 60480006499 acyl-CoA esterase; Provisional; Region: PRK10673 60480006500 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 60480006501 LexA regulated protein; Provisional; Region: PRK11675 60480006502 flavodoxin FldA; Validated; Region: PRK09267 60480006503 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 60480006504 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 60480006505 elongation factor P; Validated; Region: PRK00529 60480006506 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 60480006507 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 60480006508 RNA binding site [nucleotide binding]; other site 60480006509 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 60480006510 RNA binding site [nucleotide binding]; other site 60480006511 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 60480006512 Short chain fatty acid transporter; Region: SCFA_trans; cl17380 60480006513 aminotransferase AlaT; Validated; Region: PRK09265 60480006514 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 60480006515 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480006516 homodimer interface [polypeptide binding]; other site 60480006517 catalytic residue [active] 60480006518 5'-nucleotidase; Provisional; Region: PRK03826 60480006519 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 60480006520 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480006521 Zn2+ binding site [ion binding]; other site 60480006522 Mg2+ binding site [ion binding]; other site 60480006523 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 60480006524 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 60480006525 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 60480006526 active site 60480006527 intersubunit interface [polypeptide binding]; other site 60480006528 catalytic residue [active] 60480006529 phosphogluconate dehydratase; Validated; Region: PRK09054 60480006530 6-phosphogluconate dehydratase; Region: edd; TIGR01196 60480006531 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 60480006532 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 60480006533 putative active site [active] 60480006534 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 60480006535 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 60480006536 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 60480006537 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 60480006538 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 60480006539 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 60480006540 putative active site [active] 60480006541 pyruvate kinase; Provisional; Region: PRK05826 60480006542 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 60480006543 domain interfaces; other site 60480006544 active site 60480006545 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 60480006546 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 60480006547 active site 60480006548 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 60480006549 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480006550 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480006551 Peptidase family M2 Angiotensin converting enzyme (ACE); Region: M2_ACE; cd06461 60480006552 active site 60480006553 Zn binding site [ion binding]; other site 60480006554 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 60480006555 Smr domain; Region: Smr; pfam01713 60480006556 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 60480006557 SEC-C motif; Region: SEC-C; pfam02810 60480006558 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480006559 GAF domain; Region: GAF; pfam01590 60480006560 PAS domain S-box; Region: sensory_box; TIGR00229 60480006561 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 60480006562 putative active site [active] 60480006563 heme pocket [chemical binding]; other site 60480006564 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006565 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006566 metal binding site [ion binding]; metal-binding site 60480006567 active site 60480006568 I-site; other site 60480006569 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 60480006570 Protein of unknown function (DUF406); Region: DUF406; pfam04175 60480006571 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 60480006572 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 60480006573 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 60480006574 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 60480006575 Ligand Binding Site [chemical binding]; other site 60480006576 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 60480006577 excinuclease ABC subunit B; Provisional; Region: PRK05298 60480006578 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 60480006579 ATP binding site [chemical binding]; other site 60480006580 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 60480006581 nucleotide binding region [chemical binding]; other site 60480006582 ATP-binding site [chemical binding]; other site 60480006583 Ultra-violet resistance protein B; Region: UvrB; pfam12344 60480006584 UvrB/uvrC motif; Region: UVR; pfam02151 60480006585 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006586 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006587 active site 60480006588 I-site; other site 60480006589 metal binding site [ion binding]; metal-binding site 60480006590 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 60480006591 electron transport complex protein RsxA; Provisional; Region: PRK05151 60480006592 ferredoxin; Provisional; Region: PRK08764 60480006593 Putative Fe-S cluster; Region: FeS; pfam04060 60480006594 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 60480006595 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 60480006596 SLBB domain; Region: SLBB; pfam10531 60480006597 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 60480006598 electron transport complex protein RnfD; Reviewed; Region: rnfD; PRK00816 60480006599 electron transport complex protein RnfG; Validated; Region: PRK01908 60480006600 electron transport complex RsxE subunit; Provisional; Region: PRK12405 60480006601 endonuclease III; Provisional; Region: PRK10702 60480006602 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 60480006603 minor groove reading motif; other site 60480006604 helix-hairpin-helix signature motif; other site 60480006605 substrate binding pocket [chemical binding]; other site 60480006606 active site 60480006607 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 60480006608 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480006609 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480006610 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 60480006611 substrate binding pocket [chemical binding]; other site 60480006612 dimerization interface [polypeptide binding]; other site 60480006613 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 60480006614 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 60480006615 FeS/SAM binding site; other site 60480006616 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 60480006617 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 60480006618 Sulfatase; Region: Sulfatase; pfam00884 60480006619 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 60480006620 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 60480006621 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 60480006622 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 60480006623 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 60480006624 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 60480006625 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006626 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006627 metal binding site [ion binding]; metal-binding site 60480006628 active site 60480006629 I-site; other site 60480006630 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 60480006631 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 60480006632 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 60480006633 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 60480006634 Phytase; Region: Phytase; cl17685 60480006635 Phytase; Region: Phytase; cl17685 60480006636 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 60480006637 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480006638 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480006639 Walker A/P-loop; other site 60480006640 ATP binding site [chemical binding]; other site 60480006641 ABC transporter signature motif; other site 60480006642 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480006643 Walker B; other site 60480006644 ABC transporter; Region: ABC_tran_2; pfam12848 60480006645 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480006646 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 60480006647 putative hydrophobic ligand binding site [chemical binding]; other site 60480006648 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 60480006649 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 60480006650 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480006651 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480006652 active site 60480006653 phosphorylation site [posttranslational modification] 60480006654 intermolecular recognition site; other site 60480006655 dimerization interface [polypeptide binding]; other site 60480006656 Response regulator receiver domain; Region: Response_reg; pfam00072 60480006657 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480006658 active site 60480006659 phosphorylation site [posttranslational modification] 60480006660 intermolecular recognition site; other site 60480006661 dimerization interface [polypeptide binding]; other site 60480006662 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006663 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006664 metal binding site [ion binding]; metal-binding site 60480006665 active site 60480006666 I-site; other site 60480006667 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 60480006668 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480006669 active site 60480006670 phosphorylation site [posttranslational modification] 60480006671 intermolecular recognition site; other site 60480006672 dimerization interface [polypeptide binding]; other site 60480006673 CheB methylesterase; Region: CheB_methylest; pfam01339 60480006674 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 60480006675 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 60480006676 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 60480006677 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 60480006678 PAS fold; Region: PAS; pfam00989 60480006679 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480006680 dimer interface [polypeptide binding]; other site 60480006681 putative CheW interface [polypeptide binding]; other site 60480006682 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 60480006683 putative CheA interaction surface; other site 60480006684 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 60480006685 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 60480006686 putative binding surface; other site 60480006687 active site 60480006688 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 60480006689 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 60480006690 ATP binding site [chemical binding]; other site 60480006691 Mg2+ binding site [ion binding]; other site 60480006692 G-X-G motif; other site 60480006693 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 60480006694 Response regulator receiver domain; Region: Response_reg; pfam00072 60480006695 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480006696 active site 60480006697 phosphorylation site [posttranslational modification] 60480006698 intermolecular recognition site; other site 60480006699 dimerization interface [polypeptide binding]; other site 60480006700 Response regulator receiver domain; Region: Response_reg; pfam00072 60480006701 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480006702 active site 60480006703 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 60480006704 phosphorylation site [posttranslational modification] 60480006705 intermolecular recognition site; other site 60480006706 dimerization interface [polypeptide binding]; other site 60480006707 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 60480006708 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 60480006709 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 60480006710 ATP binding site [chemical binding]; other site 60480006711 Mg2+ binding site [ion binding]; other site 60480006712 G-X-G motif; other site 60480006713 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 60480006714 anti sigma factor interaction site; other site 60480006715 regulatory phosphorylation site [posttranslational modification]; other site 60480006716 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 60480006717 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480006718 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480006719 dimer interface [polypeptide binding]; other site 60480006720 putative CheW interface [polypeptide binding]; other site 60480006721 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 60480006722 CoA binding domain; Region: CoA_binding_2; pfam13380 60480006723 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 60480006724 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 60480006725 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 60480006726 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 60480006727 putative substrate translocation pore; other site 60480006728 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 60480006729 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 60480006730 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480006731 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480006732 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 60480006733 MarR family; Region: MarR_2; pfam12802 60480006734 RTX N-terminal domain; Region: RTX; pfam02382 60480006735 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006736 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006737 metal binding site [ion binding]; metal-binding site 60480006738 active site 60480006739 I-site; other site 60480006740 putative metal dependent hydrolase; Provisional; Region: PRK11598 60480006741 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 60480006742 Sulfatase; Region: Sulfatase; pfam00884 60480006743 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 60480006744 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480006745 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 60480006746 MarR family; Region: MarR; pfam01047 60480006747 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 60480006748 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 60480006749 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480006750 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 60480006751 dimer interface [polypeptide binding]; other site 60480006752 active site 60480006753 metal binding site [ion binding]; metal-binding site 60480006754 glutathione binding site [chemical binding]; other site 60480006755 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 60480006756 TMAO/DMSO reductase; Reviewed; Region: PRK05363 60480006757 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 60480006758 Moco binding site; other site 60480006759 metal coordination site [ion binding]; other site 60480006760 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 60480006761 RmuC family; Region: RmuC; pfam02646 60480006762 lytic murein transglycosylase; Provisional; Region: PRK11619 60480006763 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 60480006764 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480006765 catalytic residue [active] 60480006766 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 60480006767 FimV N-terminal domain; Region: FimV_core; TIGR03505 60480006768 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 60480006769 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 60480006770 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 60480006771 putative transposase OrfB; Reviewed; Region: PHA02517 60480006772 Integrase core domain; Region: rve; pfam00665 60480006773 Integrase core domain; Region: rve_3; pfam13683 60480006774 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 60480006775 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 60480006776 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 60480006777 putative active site [active] 60480006778 putative NTP binding site [chemical binding]; other site 60480006779 putative nucleic acid binding site [nucleotide binding]; other site 60480006780 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 60480006781 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 60480006782 DNA binding site [nucleotide binding] 60480006783 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 60480006784 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 60480006785 putative active site [active] 60480006786 Zn binding site [ion binding]; other site 60480006787 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 60480006788 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 60480006789 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480006790 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480006791 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 60480006792 Fumarase C-terminus; Region: Fumerase_C; pfam05683 60480006793 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 60480006794 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 60480006795 chorismate binding enzyme; Region: Chorismate_bind; cl10555 60480006796 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 60480006797 putative active site [active] 60480006798 putative CoA binding site [chemical binding]; other site 60480006799 nudix motif; other site 60480006800 metal binding site [ion binding]; metal-binding site 60480006801 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 60480006802 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 60480006803 putative anticodon binding site; other site 60480006804 putative dimer interface [polypeptide binding]; other site 60480006805 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 60480006806 homodimer interface [polypeptide binding]; other site 60480006807 motif 1; other site 60480006808 motif 2; other site 60480006809 active site 60480006810 motif 3; other site 60480006811 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 60480006812 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 60480006813 ATP-grasp domain; Region: ATP-grasp_4; cl17255 60480006814 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480006815 GAF domain; Region: GAF; pfam01590 60480006816 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 60480006817 PAS domain; Region: PAS_9; pfam13426 60480006818 putative active site [active] 60480006819 heme pocket [chemical binding]; other site 60480006820 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006821 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006822 metal binding site [ion binding]; metal-binding site 60480006823 active site 60480006824 I-site; other site 60480006825 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 60480006826 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 60480006827 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 60480006828 S-adenosylmethionine binding site [chemical binding]; other site 60480006829 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 60480006830 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480006831 putative substrate translocation pore; other site 60480006832 glucose/galactose transporter; Region: gluP; TIGR01272 60480006833 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 60480006834 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 60480006835 active site 60480006836 catalytic site [active] 60480006837 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 60480006838 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 60480006839 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 60480006840 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 60480006841 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 60480006842 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 60480006843 Ca binding site [ion binding]; other site 60480006844 active site 60480006845 homodimer interface [polypeptide binding]; other site 60480006846 catalytic site [active] 60480006847 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 60480006848 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 60480006849 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 60480006850 active site 60480006851 catalytic site [active] 60480006852 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 60480006853 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480006854 putative metal binding site [ion binding]; other site 60480006855 Part of AAA domain; Region: AAA_19; pfam13245 60480006856 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 60480006857 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 60480006858 active site 60480006859 catalytic residues [active] 60480006860 metal binding site [ion binding]; metal-binding site 60480006861 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 60480006862 active site 60480006863 DNA binding site [nucleotide binding] 60480006864 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 60480006865 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 60480006866 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 60480006867 putative active site [active] 60480006868 putative dimer interface [polypeptide binding]; other site 60480006869 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 60480006870 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 60480006871 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 60480006872 active site 60480006873 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 60480006874 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 60480006875 TrkA-N domain; Region: TrkA_N; pfam02254 60480006876 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480006877 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480006878 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480006879 LysR substrate binding domain; Region: LysR_substrate; pfam03466 60480006880 dimerization interface [polypeptide binding]; other site 60480006881 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 60480006882 heme-binding residues [chemical binding]; other site 60480006883 L-aspartate oxidase; Provisional; Region: PRK06175 60480006884 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 60480006885 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 60480006886 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 60480006887 NADP binding site [chemical binding]; other site 60480006888 dimer interface [polypeptide binding]; other site 60480006889 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480006890 PAS domain; Region: PAS; smart00091 60480006891 putative active site [active] 60480006892 heme pocket [chemical binding]; other site 60480006893 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480006894 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480006895 metal binding site [ion binding]; metal-binding site 60480006896 active site 60480006897 I-site; other site 60480006898 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 60480006899 TIGR03503 family protein; Region: TIGR03503 60480006900 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 60480006901 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 60480006902 active site 60480006903 catalytic site [active] 60480006904 substrate binding site [chemical binding]; other site 60480006905 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 60480006906 RNA/DNA hybrid binding site [nucleotide binding]; other site 60480006907 active site 60480006908 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 60480006909 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480006910 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 60480006911 putative dimerization interface [polypeptide binding]; other site 60480006912 Methyltransferase domain; Region: Methyltransf_11; pfam08241 60480006913 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 60480006914 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 60480006915 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 60480006916 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480006917 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480006918 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480006919 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 60480006920 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480006921 Intracellular proteinase inhibitor; Region: BsuPI; pfam12690 60480006922 AsmA family; Region: AsmA; pfam05170 60480006923 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 60480006924 ribonuclease activity regulator protein RraA; Reviewed; Region: PRK12487 60480006925 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 60480006926 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 60480006927 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480006928 ATP binding site [chemical binding]; other site 60480006929 Mg++ binding site [ion binding]; other site 60480006930 motif III; other site 60480006931 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 60480006932 nucleotide binding region [chemical binding]; other site 60480006933 ATP-binding site [chemical binding]; other site 60480006934 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 60480006935 substrate binding site [chemical binding]; other site 60480006936 hypothetical protein; Provisional; Region: PRK05170 60480006937 Transglycosylase SLT domain; Region: SLT_2; pfam13406 60480006938 murein hydrolase B; Provisional; Region: PRK10760; cl17906 60480006939 YcgL domain; Region: YcgL; pfam05166 60480006940 septum formation inhibitor; Reviewed; Region: minC; PRK04804 60480006941 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 60480006942 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 60480006943 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 60480006944 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 60480006945 Switch I; other site 60480006946 Switch II; other site 60480006947 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 60480006948 ribonuclease D; Region: rnd; TIGR01388 60480006949 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 60480006950 catalytic site [active] 60480006951 putative active site [active] 60480006952 putative substrate binding site [chemical binding]; other site 60480006953 HRDC domain; Region: HRDC; pfam00570 60480006954 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 60480006955 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 60480006956 acyl-activating enzyme (AAE) consensus motif; other site 60480006957 putative AMP binding site [chemical binding]; other site 60480006958 putative active site [active] 60480006959 putative CoA binding site [chemical binding]; other site 60480006960 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 60480006961 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 60480006962 Predicted methyltransferase [General function prediction only]; Region: COG4798 60480006963 Methyltransferase domain; Region: Methyltransf_23; pfam13489 60480006964 Peptidase M50B-like; Region: Peptidase_M50B; pfam13398 60480006965 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 60480006966 Glycoprotease family; Region: Peptidase_M22; pfam00814 60480006967 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 60480006968 dimer interface [polypeptide binding]; other site 60480006969 active site 60480006970 Schiff base residues; other site 60480006971 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 60480006972 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 60480006973 methionine sulfoxide reductase A; Provisional; Region: PRK14054 60480006974 aminocyclopropanecarboxylate oxidase; Region: PLN02403 60480006975 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 60480006976 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 60480006977 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 60480006978 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 60480006979 GTP/Mg2+ binding site [chemical binding]; other site 60480006980 G4 box; other site 60480006981 G5 box; other site 60480006982 G1 box; other site 60480006983 Switch I region; other site 60480006984 G2 box; other site 60480006985 G3 box; other site 60480006986 Switch II region; other site 60480006987 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 60480006988 Low molecular weight phosphatase family; Region: LMWPc; cd00115 60480006989 active site 60480006990 DNA ligase; Provisional; Region: PRK09125 60480006991 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 60480006992 DNA binding site [nucleotide binding] 60480006993 active site 60480006994 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 60480006995 DNA binding site [nucleotide binding] 60480006996 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 60480006997 transcriptional regulator HdfR; Provisional; Region: PRK03601 60480006998 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480006999 LysR substrate binding domain; Region: LysR_substrate; pfam03466 60480007000 hypothetical protein; Provisional; Region: PRK11027 60480007001 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 60480007002 ATP-grasp domain; Region: ATP-grasp_4; cl17255 60480007003 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 60480007004 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 60480007005 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480007006 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 60480007007 Peptidase family M28; Region: Peptidase_M28; pfam04389 60480007008 metal binding site [ion binding]; metal-binding site 60480007009 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480007010 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480007011 metal binding site [ion binding]; metal-binding site 60480007012 active site 60480007013 I-site; other site 60480007014 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 60480007015 active site 60480007016 catalytic site [active] 60480007017 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 60480007018 marine proteobacterial sortase target protein; Region: marine_srt_targ; TIGR03788 60480007019 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 60480007020 metal ion-dependent adhesion site (MIDAS); other site 60480007021 proteobacterial sortase system OmpA family protein; Region: pdsO; TIGR03789 60480007022 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480007023 ligand binding site [chemical binding]; other site 60480007024 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 60480007025 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480007026 active site 60480007027 phosphorylation site [posttranslational modification] 60480007028 intermolecular recognition site; other site 60480007029 dimerization interface [polypeptide binding]; other site 60480007030 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 60480007031 DNA binding site [nucleotide binding] 60480007032 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 60480007033 DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases; Region: CBM9_like_HisKa; cd09622 60480007034 putative ligand binding site [chemical binding]; other site 60480007035 HAMP domain; Region: HAMP; pfam00672 60480007036 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 60480007037 dimer interface [polypeptide binding]; other site 60480007038 phosphorylation site [posttranslational modification] 60480007039 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 60480007040 ATP binding site [chemical binding]; other site 60480007041 Mg2+ binding site [ion binding]; other site 60480007042 G-X-G motif; other site 60480007043 cystathionine beta-lyase; Provisional; Region: PRK09028 60480007044 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 60480007045 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480007046 catalytic residue [active] 60480007047 CreA protein; Region: CreA; pfam05981 60480007048 putative chaperone; Provisional; Region: PRK11678 60480007049 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 60480007050 nucleotide binding site [chemical binding]; other site 60480007051 putative NEF/HSP70 interaction site [polypeptide binding]; other site 60480007052 SBD interface [polypeptide binding]; other site 60480007053 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 60480007054 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 60480007055 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 60480007056 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 60480007057 putative active site [active] 60480007058 catalytic site [active] 60480007059 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 60480007060 domain interface [polypeptide binding]; other site 60480007061 active site 60480007062 catalytic site [active] 60480007063 exopolyphosphatase; Region: exo_poly_only; TIGR03706 60480007064 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 60480007065 Ion transport protein; Region: Ion_trans; pfam00520 60480007066 Ion channel; Region: Ion_trans_2; pfam07885 60480007067 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 60480007068 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 60480007069 putative metal binding site [ion binding]; other site 60480007070 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 60480007071 Peptidase family M23; Region: Peptidase_M23; pfam01551 60480007072 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 60480007073 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 60480007074 Nucleoid-associated protein [General function prediction only]; Region: COG3081 60480007075 nucleoid-associated protein NdpA; Validated; Region: PRK00378 60480007076 hypothetical protein; Provisional; Region: PRK13689 60480007077 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 60480007078 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 60480007079 Sulfatase; Region: Sulfatase; cl17466 60480007080 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 60480007081 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 60480007082 active site 60480007083 FMN binding site [chemical binding]; other site 60480007084 substrate binding site [chemical binding]; other site 60480007085 homotetramer interface [polypeptide binding]; other site 60480007086 catalytic residue [active] 60480007087 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480007088 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480007089 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 60480007090 dimerization interface [polypeptide binding]; other site 60480007091 PAS domain; Region: PAS_9; pfam13426 60480007092 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480007093 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480007094 metal binding site [ion binding]; metal-binding site 60480007095 active site 60480007096 I-site; other site 60480007097 transcriptional regulator NarL; Provisional; Region: PRK10651 60480007098 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480007099 active site 60480007100 phosphorylation site [posttranslational modification] 60480007101 intermolecular recognition site; other site 60480007102 dimerization interface [polypeptide binding]; other site 60480007103 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 60480007104 DNA binding residues [nucleotide binding] 60480007105 dimerization interface [polypeptide binding]; other site 60480007106 nitrate/nitrite sensor protein NarX; Provisional; Region: PRK10600 60480007107 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 60480007108 HAMP domain; Region: HAMP; pfam00672 60480007109 dimerization interface [polypeptide binding]; other site 60480007110 Histidine kinase; Region: HisKA_3; pfam07730 60480007111 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 60480007112 ATP binding site [chemical binding]; other site 60480007113 Mg2+ binding site [ion binding]; other site 60480007114 G-X-G motif; other site 60480007115 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 60480007116 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 60480007117 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 60480007118 [4Fe-4S] binding site [ion binding]; other site 60480007119 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 60480007120 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 60480007121 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 60480007122 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 60480007123 molybdopterin cofactor binding site; other site 60480007124 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 60480007125 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 60480007126 respiratory nitrate reductase, gamma subunit; Region: narI; TIGR00351 60480007127 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480007128 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480007129 active site 60480007130 I-site; other site 60480007131 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 60480007132 non-specific DNA binding site [nucleotide binding]; other site 60480007133 salt bridge; other site 60480007134 sequence-specific DNA binding site [nucleotide binding]; other site 60480007135 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 60480007136 Transposase; Region: HTH_Tnp_1; pfam01527 60480007137 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 60480007138 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 60480007139 PapC N-terminal domain; Region: PapC_N; pfam13954 60480007140 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 60480007141 PapC C-terminal domain; Region: PapC_C; pfam13953 60480007142 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 60480007143 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 60480007144 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 60480007145 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 60480007146 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 60480007147 Fimbrial protein; Region: Fimbrial; pfam00419 60480007148 EAL domain; Region: EAL; pfam00563 60480007149 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480007150 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480007151 metal binding site [ion binding]; metal-binding site 60480007152 active site 60480007153 I-site; other site 60480007154 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480007155 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 60480007156 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 60480007157 homodimer interface [polypeptide binding]; other site 60480007158 NAD binding pocket [chemical binding]; other site 60480007159 ATP binding pocket [chemical binding]; other site 60480007160 Mg binding site [ion binding]; other site 60480007161 active-site loop [active] 60480007162 inosine/guanosine kinase; Provisional; Region: PRK15074 60480007163 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 60480007164 substrate binding site [chemical binding]; other site 60480007165 ATP binding site [chemical binding]; other site 60480007166 ferrochelatase; Reviewed; Region: hemH; PRK00035 60480007167 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 60480007168 C-terminal domain interface [polypeptide binding]; other site 60480007169 active site 60480007170 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 60480007171 active site 60480007172 N-terminal domain interface [polypeptide binding]; other site 60480007173 adenylate kinase; Reviewed; Region: adk; PRK00279 60480007174 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 60480007175 AMP-binding site [chemical binding]; other site 60480007176 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 60480007177 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 60480007178 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 60480007179 heat shock protein 90; Provisional; Region: PRK05218 60480007180 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 60480007181 ATP binding site [chemical binding]; other site 60480007182 Mg2+ binding site [ion binding]; other site 60480007183 G-X-G motif; other site 60480007184 recombination protein RecR; Reviewed; Region: recR; PRK00076 60480007185 RecR protein; Region: RecR; pfam02132 60480007186 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 60480007187 putative active site [active] 60480007188 putative metal-binding site [ion binding]; other site 60480007189 tetramer interface [polypeptide binding]; other site 60480007190 hypothetical protein; Validated; Region: PRK00153 60480007191 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14949 60480007192 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 60480007193 Walker A motif; other site 60480007194 ATP binding site [chemical binding]; other site 60480007195 Walker B motif; other site 60480007196 DNA polymerase III subunit delta'; Validated; Region: PRK08485 60480007197 arginine finger; other site 60480007198 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 60480007199 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 60480007200 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480007201 active site 60480007202 hypothetical protein; Provisional; Region: PRK10527 60480007203 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 60480007204 hypothetical protein; Provisional; Region: PRK05409 60480007205 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 60480007206 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 60480007207 FMN binding site [chemical binding]; other site 60480007208 active site 60480007209 catalytic residues [active] 60480007210 substrate binding site [chemical binding]; other site 60480007211 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; pfam01258 60480007212 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 60480007213 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480007214 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 60480007215 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 60480007216 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 60480007217 active site 60480007218 metal binding site [ion binding]; metal-binding site 60480007219 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 60480007220 putative hydrolase; Provisional; Region: PRK11460 60480007221 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 60480007222 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 60480007223 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 60480007224 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 60480007225 active site 60480007226 Zn binding site [ion binding]; other site 60480007227 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 60480007228 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 60480007229 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480007230 Transglycosylase SLT domain; Region: SLT_2; pfam13406 60480007231 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 60480007232 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480007233 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 60480007234 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 60480007235 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 60480007236 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480007237 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480007238 active site 60480007239 phosphorylation site [posttranslational modification] 60480007240 intermolecular recognition site; other site 60480007241 dimerization interface [polypeptide binding]; other site 60480007242 Methyltransferase domain; Region: Methyltransf_31; pfam13847 60480007243 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 60480007244 S-adenosylmethionine binding site [chemical binding]; other site 60480007245 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 60480007246 RNA polymerase sigma factor; Provisional; Region: PRK11924 60480007247 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480007248 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 60480007249 DNA binding residues [nucleotide binding] 60480007250 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 60480007251 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 60480007252 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 60480007253 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 60480007254 hypothetical protein; Provisional; Region: PRK11770 60480007255 Domain of unknown function (DUF307); Region: DUF307; pfam03733 60480007256 Domain of unknown function (DUF307); Region: DUF307; pfam03733 60480007257 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480007258 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 60480007259 active site 60480007260 Zn binding site [ion binding]; other site 60480007261 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 60480007262 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 60480007263 membrane-bound complex binding site; other site 60480007264 hinge residues; other site 60480007265 Putative transmembrane protein (PGPGW); Region: PGPGW; pfam09656 60480007266 AMP-binding domain protein; Validated; Region: PRK08315 60480007267 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 60480007268 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 60480007269 acyl-activating enzyme (AAE) consensus motif; other site 60480007270 putative AMP binding site [chemical binding]; other site 60480007271 putative active site [active] 60480007272 putative CoA binding site [chemical binding]; other site 60480007273 Uncharacterized conserved protein [Function unknown]; Region: COG2947 60480007274 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 60480007275 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480007276 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480007277 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 60480007278 dimerization interface [polypeptide binding]; other site 60480007279 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 60480007280 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 60480007281 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 60480007282 dimer interface [polypeptide binding]; other site 60480007283 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 60480007284 active site 60480007285 Fe binding site [ion binding]; other site 60480007286 MASE1; Region: MASE1; cl17823 60480007287 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480007288 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480007289 metal binding site [ion binding]; metal-binding site 60480007290 active site 60480007291 I-site; other site 60480007292 maltose O-acetyltransferase; Provisional; Region: PRK10092 60480007293 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 60480007294 active site 60480007295 substrate binding site [chemical binding]; other site 60480007296 trimer interface [polypeptide binding]; other site 60480007297 CoA binding site [chemical binding]; other site 60480007298 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 60480007299 Protein of unknown function, DUF482; Region: DUF482; pfam04339 60480007300 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 60480007301 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 60480007302 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 60480007303 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 60480007304 hypothetical protein; Provisional; Region: PRK06156 60480007305 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 60480007306 active site 60480007307 metal binding site [ion binding]; metal-binding site 60480007308 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 60480007309 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 60480007310 active site 60480007311 Zn binding site [ion binding]; other site 60480007312 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 60480007313 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 60480007314 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 60480007315 putative FMN binding site [chemical binding]; other site 60480007316 DoxX; Region: DoxX; cl17842 60480007317 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 60480007318 active site 60480007319 ATP binding site [chemical binding]; other site 60480007320 Phosphotransferase enzyme family; Region: APH; pfam01636 60480007321 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 60480007322 substrate binding site [chemical binding]; other site 60480007323 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 60480007324 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480007325 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 60480007326 N-terminal plug; other site 60480007327 ligand-binding site [chemical binding]; other site 60480007328 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 60480007329 putative dimer interface [polypeptide binding]; other site 60480007330 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 60480007331 CoenzymeA binding site [chemical binding]; other site 60480007332 subunit interaction site [polypeptide binding]; other site 60480007333 PHB binding site; other site 60480007334 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 60480007335 CoenzymeA binding site [chemical binding]; other site 60480007336 subunit interaction site [polypeptide binding]; other site 60480007337 PHB binding site; other site 60480007338 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 60480007339 nucleotide binding site/active site [active] 60480007340 HIT family signature motif; other site 60480007341 catalytic residue [active] 60480007342 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 60480007343 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 60480007344 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 60480007345 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 60480007346 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 60480007347 DNA binding residues [nucleotide binding] 60480007348 dimerization interface [polypeptide binding]; other site 60480007349 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 60480007350 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 60480007351 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 60480007352 acyl-activating enzyme (AAE) consensus motif; other site 60480007353 AMP binding site [chemical binding]; other site 60480007354 active site 60480007355 CoA binding site [chemical binding]; other site 60480007356 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 60480007357 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 60480007358 Shikimate / quinate 5-dehydrogenase; Region: Shikimate_DH; pfam01488 60480007359 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 60480007360 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 60480007361 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 60480007362 DNA binding residues [nucleotide binding] 60480007363 putative dimer interface [polypeptide binding]; other site 60480007364 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 60480007365 isovaleryl-CoA dehydrogenase; Region: PLN02519 60480007366 substrate binding site [chemical binding]; other site 60480007367 FAD binding site [chemical binding]; other site 60480007368 catalytic base [active] 60480007369 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 60480007370 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 60480007371 enoyl-CoA hydratase; Provisional; Region: PRK05995 60480007372 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 60480007373 substrate binding site [chemical binding]; other site 60480007374 oxyanion hole (OAH) forming residues; other site 60480007375 trimer interface [polypeptide binding]; other site 60480007376 Pleckstrin homology-like domain; Region: PH-like; cl17171 60480007377 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 60480007378 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 60480007379 ATP-grasp domain; Region: ATP-grasp_4; cl17255 60480007380 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 60480007381 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 60480007382 carboxyltransferase (CT) interaction site; other site 60480007383 biotinylation site [posttranslational modification]; other site 60480007384 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 60480007385 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 60480007386 active site 60480007387 catalytic residues [active] 60480007388 metal binding site [ion binding]; metal-binding site 60480007389 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 60480007390 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 60480007391 Putative amidotransferase; Region: DUF4066; pfam13278 60480007392 conserved cys residue [active] 60480007393 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480007394 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 60480007395 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 60480007396 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480007397 Coenzyme A binding pocket [chemical binding]; other site 60480007398 Transposase IS200 like; Region: Y1_Tnp; pfam01797 60480007399 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480007400 Protein export membrane protein; Region: SecD_SecF; cl14618 60480007401 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480007402 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480007403 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480007404 lipoprotein; Provisional; Region: PRK11679 60480007405 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 60480007406 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 60480007407 dihydrodipicolinate synthase; Region: dapA; TIGR00674 60480007408 dimer interface [polypeptide binding]; other site 60480007409 active site 60480007410 catalytic residue [active] 60480007411 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 60480007412 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 60480007413 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 60480007414 catalytic triad [active] 60480007415 Lysine efflux permease [General function prediction only]; Region: COG1279 60480007416 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 60480007417 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480007418 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 60480007419 putative dimerization interface [polypeptide binding]; other site 60480007420 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 60480007421 Domain of unknown function DUF20; Region: UPF0118; pfam01594 60480007422 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 60480007423 CPxP motif; other site 60480007424 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 60480007425 Peptidase family M48; Region: Peptidase_M48; cl12018 60480007426 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 60480007427 binding surface 60480007428 TPR motif; other site 60480007429 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 60480007430 ArsC family; Region: ArsC; pfam03960 60480007431 catalytic residues [active] 60480007432 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 60480007433 heat shock protein HtpX; Provisional; Region: PRK05457 60480007434 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 60480007435 active site pocket [active] 60480007436 oxyanion hole [active] 60480007437 catalytic triad [active] 60480007438 active site nucleophile [active] 60480007439 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 60480007440 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 60480007441 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 60480007442 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 60480007443 AAA domain; Region: AAA_26; pfam13500 60480007444 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 60480007445 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 60480007446 S-adenosylmethionine binding site [chemical binding]; other site 60480007447 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 60480007448 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 60480007449 substrate-cofactor binding pocket; other site 60480007450 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480007451 catalytic residue [active] 60480007452 biotin synthase; Provisional; Region: PRK15108 60480007453 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 60480007454 FeS/SAM binding site; other site 60480007455 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 60480007456 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 60480007457 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 60480007458 inhibitor-cofactor binding pocket; inhibition site 60480007459 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480007460 catalytic residue [active] 60480007461 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 60480007462 Na binding site [ion binding]; other site 60480007463 PAS domain; Region: PAS; smart00091 60480007464 PAS fold; Region: PAS_7; pfam12860 60480007465 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480007466 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 60480007467 dimer interface [polypeptide binding]; other site 60480007468 phosphorylation site [posttranslational modification] 60480007469 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 60480007470 ATP binding site [chemical binding]; other site 60480007471 Mg2+ binding site [ion binding]; other site 60480007472 G-X-G motif; other site 60480007473 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 60480007474 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480007475 active site 60480007476 phosphorylation site [posttranslational modification] 60480007477 intermolecular recognition site; other site 60480007478 dimerization interface [polypeptide binding]; other site 60480007479 acetyl-CoA synthetase; Provisional; Region: PRK00174 60480007480 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 60480007481 active site 60480007482 CoA binding site [chemical binding]; other site 60480007483 acyl-activating enzyme (AAE) consensus motif; other site 60480007484 AMP binding site [chemical binding]; other site 60480007485 acetate binding site [chemical binding]; other site 60480007486 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 60480007487 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 60480007488 ATP binding site [chemical binding]; other site 60480007489 putative Mg++ binding site [ion binding]; other site 60480007490 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 60480007491 nucleotide binding region [chemical binding]; other site 60480007492 ATP-binding site [chemical binding]; other site 60480007493 Double zinc ribbon; Region: DZR; pfam12773 60480007494 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 60480007495 GSH binding site [chemical binding]; other site 60480007496 catalytic residues [active] 60480007497 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 60480007498 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 60480007499 binding surface 60480007500 TPR motif; other site 60480007501 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 60480007502 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480007503 ligand binding site [chemical binding]; other site 60480007504 translocation protein TolB; Provisional; Region: tolB; PRK04792 60480007505 TolB amino-terminal domain; Region: TolB_N; pfam04052 60480007506 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480007507 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480007508 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480007509 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480007510 TolA protein; Region: tolA_full; TIGR02794 60480007511 TolA C-terminal; Region: TolA; pfam06519 60480007512 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 60480007513 TolR protein; Region: tolR; TIGR02801 60480007514 TolQ protein; Region: tolQ; TIGR02796 60480007515 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 60480007516 active site 60480007517 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 60480007518 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480007519 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 60480007520 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480007521 ligand binding site [chemical binding]; other site 60480007522 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 60480007523 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 60480007524 dimer interface [polypeptide binding]; other site 60480007525 catalytic site [active] 60480007526 putative active site [active] 60480007527 putative substrate binding site [chemical binding]; other site 60480007528 peroxidase; Provisional; Region: PRK15000 60480007529 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 60480007530 dimer interface [polypeptide binding]; other site 60480007531 decamer (pentamer of dimers) interface [polypeptide binding]; other site 60480007532 catalytic triad [active] 60480007533 peroxidatic and resolving cysteines [active] 60480007534 Predicted permease [General function prediction only]; Region: COG2056 60480007535 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 60480007536 RDD family; Region: RDD; pfam06271 60480007537 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480007538 active site 60480007539 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 60480007540 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 60480007541 dimerization interface [polypeptide binding]; other site 60480007542 putative ATP binding site [chemical binding]; other site 60480007543 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 60480007544 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 60480007545 active site 60480007546 substrate binding site [chemical binding]; other site 60480007547 cosubstrate binding site; other site 60480007548 catalytic site [active] 60480007549 UMP phosphatase; Provisional; Region: PRK10444 60480007550 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 60480007551 active site 60480007552 motif I; other site 60480007553 motif II; other site 60480007554 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 60480007555 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 60480007556 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 60480007557 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480007558 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 60480007559 Peptidase family M28; Region: Peptidase_M28; pfam04389 60480007560 metal binding site [ion binding]; metal-binding site 60480007561 asparagine synthetase B; Provisional; Region: asnB; PRK09431 60480007562 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 60480007563 active site 60480007564 dimer interface [polypeptide binding]; other site 60480007565 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 60480007566 Ligand Binding Site [chemical binding]; other site 60480007567 Molecular Tunnel; other site 60480007568 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 60480007569 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 60480007570 active site 60480007571 nucleophile elbow; other site 60480007572 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480007573 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 60480007574 N-terminal plug; other site 60480007575 ligand-binding site [chemical binding]; other site 60480007576 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 60480007577 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 60480007578 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 60480007579 active site 60480007580 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 60480007581 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 60480007582 active site 60480007583 phosphate binding residues; other site 60480007584 catalytic residues [active] 60480007585 Integrase core domain; Region: rve; pfam00665 60480007586 Integrase core domain; Region: rve_3; pfam13683 60480007587 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 60480007588 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 60480007589 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 60480007590 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 60480007591 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 60480007592 dimer interface [polypeptide binding]; other site 60480007593 active site 60480007594 acyl carrier protein; Provisional; Region: acpP; PRK00982 60480007595 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 60480007596 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 60480007597 NAD(P) binding site [chemical binding]; other site 60480007598 homotetramer interface [polypeptide binding]; other site 60480007599 homodimer interface [polypeptide binding]; other site 60480007600 active site 60480007601 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 60480007602 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 60480007603 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 60480007604 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 60480007605 dimer interface [polypeptide binding]; other site 60480007606 active site 60480007607 CoA binding pocket [chemical binding]; other site 60480007608 putative phosphate acyltransferase; Provisional; Region: PRK05331 60480007609 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 60480007610 hypothetical protein; Provisional; Region: PRK11193 60480007611 Maf-like protein; Region: Maf; pfam02545 60480007612 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 60480007613 active site 60480007614 dimer interface [polypeptide binding]; other site 60480007615 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 60480007616 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 60480007617 motif II; other site 60480007618 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 60480007619 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 60480007620 RNA binding surface [nucleotide binding]; other site 60480007621 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 60480007622 active site 60480007623 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 60480007624 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 60480007625 homodimer interface [polypeptide binding]; other site 60480007626 oligonucleotide binding site [chemical binding]; other site 60480007627 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 60480007628 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 60480007629 Sulfate transporter family; Region: Sulfate_transp; pfam00916 60480007630 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 60480007631 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 60480007632 DNA-binding site [nucleotide binding]; DNA binding site 60480007633 RNA-binding motif; other site 60480007634 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 60480007635 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 60480007636 S-adenosylmethionine binding site [chemical binding]; other site 60480007637 exonuclease I; Provisional; Region: sbcB; PRK11779 60480007638 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 60480007639 active site 60480007640 catalytic site [active] 60480007641 substrate binding site [chemical binding]; other site 60480007642 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 60480007643 cytidine deaminase; Provisional; Region: PRK09027 60480007644 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 60480007645 active site 60480007646 catalytic motif [active] 60480007647 Zn binding site [ion binding]; other site 60480007648 Cytidine and deoxycytidylate deaminase zinc-binding region; Region: dCMP_cyt_deam_2; pfam08211 60480007649 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 60480007650 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 60480007651 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480007652 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 60480007653 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 60480007654 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 60480007655 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 60480007656 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 60480007657 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 60480007658 Predicted membrane protein [Function unknown]; Region: COG3235 60480007659 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 60480007660 Uncharacterized conserved protein [Function unknown]; Region: COG2835 60480007661 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 60480007662 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 60480007663 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 60480007664 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 60480007665 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 60480007666 Walker A/P-loop; other site 60480007667 ATP binding site [chemical binding]; other site 60480007668 Q-loop/lid; other site 60480007669 ABC transporter signature motif; other site 60480007670 Walker B; other site 60480007671 D-loop; other site 60480007672 H-loop/switch region; other site 60480007673 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 60480007674 ComEC family competence protein; Provisional; Region: PRK11539 60480007675 Competence protein; Region: Competence; pfam03772 60480007676 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 60480007677 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 60480007678 NnrS protein; Region: NnrS; pfam05940 60480007679 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 60480007680 PilZ domain; Region: PilZ; pfam07238 60480007681 ParA-like protein; Provisional; Region: PHA02518 60480007682 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 60480007683 P-loop; other site 60480007684 Magnesium ion binding site [ion binding]; other site 60480007685 Protein of unknown function (DUF2492); Region: DUF2492; pfam10678 60480007686 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 60480007687 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 60480007688 GAF domain; Region: GAF; pfam01590 60480007689 Histidine kinase; Region: His_kinase; pfam06580 60480007690 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 60480007691 ATP binding site [chemical binding]; other site 60480007692 Mg2+ binding site [ion binding]; other site 60480007693 G-X-G motif; other site 60480007694 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 60480007695 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480007696 active site 60480007697 phosphorylation site [posttranslational modification] 60480007698 intermolecular recognition site; other site 60480007699 dimerization interface [polypeptide binding]; other site 60480007700 LytTr DNA-binding domain; Region: LytTR; pfam04397 60480007701 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 60480007702 Carbon starvation protein CstA; Region: CstA; pfam02554 60480007703 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 60480007704 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 60480007705 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 60480007706 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 60480007707 dimerization interface [polypeptide binding]; other site 60480007708 active site 60480007709 hypothetical protein; Provisional; Region: PRK11020 60480007710 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; PRK11121 60480007711 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 60480007712 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 60480007713 ATP cone domain; Region: ATP-cone; pfam03477 60480007714 Class III ribonucleotide reductase; Region: RNR_III; cd01675 60480007715 effector binding site; other site 60480007716 active site 60480007717 Zn binding site [ion binding]; other site 60480007718 glycine loop; other site 60480007719 hypothetical protein; Provisional; Region: PRK10279 60480007720 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 60480007721 active site 60480007722 nucleophile elbow; other site 60480007723 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 60480007724 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480007725 ATP binding site [chemical binding]; other site 60480007726 Mg++ binding site [ion binding]; other site 60480007727 motif III; other site 60480007728 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 60480007729 nucleotide binding region [chemical binding]; other site 60480007730 ATP-binding site [chemical binding]; other site 60480007731 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 60480007732 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 60480007733 putative peptidase; Provisional; Region: PRK11649 60480007734 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 60480007735 Peptidase family M23; Region: Peptidase_M23; pfam01551 60480007736 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 60480007737 AAA domain; Region: AAA_23; pfam13476 60480007738 Walker A/P-loop; other site 60480007739 ATP binding site [chemical binding]; other site 60480007740 Q-loop/lid; other site 60480007741 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 60480007742 ABC transporter signature motif; other site 60480007743 Walker B; other site 60480007744 D-loop; other site 60480007745 H-loop/switch region; other site 60480007746 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 60480007747 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 60480007748 active site 60480007749 metal binding site [ion binding]; metal-binding site 60480007750 DNA binding site [nucleotide binding] 60480007751 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 60480007752 hypothetical protein; Provisional; Region: PRK10621 60480007753 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480007754 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 60480007755 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480007756 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 60480007757 dimerization interface [polypeptide binding]; other site 60480007758 substrate binding pocket [chemical binding]; other site 60480007759 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 60480007760 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 60480007761 RNA binding surface [nucleotide binding]; other site 60480007762 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 60480007763 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 60480007764 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 60480007765 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 60480007766 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480007767 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480007768 metal binding site [ion binding]; metal-binding site 60480007769 active site 60480007770 I-site; other site 60480007771 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 60480007772 TPR motif; other site 60480007773 binding surface 60480007774 TPR repeat; Region: TPR_11; pfam13414 60480007775 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 60480007776 TPR motif; other site 60480007777 binding surface 60480007778 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 60480007779 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 60480007780 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 60480007781 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 60480007782 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 60480007783 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 60480007784 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 60480007785 Transposase IS200 like; Region: Y1_Tnp; pfam01797 60480007786 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480007787 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 60480007788 N-terminal plug; other site 60480007789 ligand-binding site [chemical binding]; other site 60480007790 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480007791 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 60480007792 trimer interface [polypeptide binding]; other site 60480007793 eyelet of channel; other site 60480007794 DNA polymerase II; Reviewed; Region: PRK05762 60480007795 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 60480007796 active site 60480007797 catalytic site [active] 60480007798 substrate binding site [chemical binding]; other site 60480007799 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 60480007800 active site 60480007801 metal-binding site 60480007802 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 60480007803 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 60480007804 hypothetical protein; Provisional; Region: PRK10621 60480007805 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480007806 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 60480007807 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 60480007808 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 60480007809 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 60480007810 putative active site [active] 60480007811 Zn binding site [ion binding]; other site 60480007812 Late competence development protein ComFB; Region: ComFB; pfam10719 60480007813 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 60480007814 methionine gamma-lyase; Provisional; Region: PRK06234 60480007815 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 60480007816 homodimer interface [polypeptide binding]; other site 60480007817 substrate-cofactor binding pocket; other site 60480007818 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480007819 catalytic residue [active] 60480007820 hypothetical protein; Provisional; Region: PRK05415 60480007821 Domain of unknown function (DUF697); Region: DUF697; pfam05128 60480007822 YcjX-like family, DUF463; Region: DUF463; pfam04317 60480007823 PspC domain; Region: PspC; cl00864 60480007824 phage shock protein C; Region: phageshock_pspC; TIGR02978 60480007825 phage shock protein B; Provisional; Region: pspB; PRK09458 60480007826 phage shock protein A; Region: phageshock_pspA; TIGR02977 60480007827 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 60480007828 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 60480007829 Walker A motif; other site 60480007830 ATP binding site [chemical binding]; other site 60480007831 Walker B motif; other site 60480007832 arginine finger; other site 60480007833 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480007834 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 60480007835 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 60480007836 peptide binding site [polypeptide binding]; other site 60480007837 nickel ABC transporter, permease subunit NikB; Region: nickel_nikB; TIGR02789 60480007838 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 60480007839 dimer interface [polypeptide binding]; other site 60480007840 conserved gate region; other site 60480007841 putative PBP binding loops; other site 60480007842 ABC-ATPase subunit interface; other site 60480007843 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 60480007844 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 60480007845 dimer interface [polypeptide binding]; other site 60480007846 conserved gate region; other site 60480007847 putative PBP binding loops; other site 60480007848 ABC-ATPase subunit interface; other site 60480007849 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 60480007850 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 60480007851 Walker A/P-loop; other site 60480007852 ATP binding site [chemical binding]; other site 60480007853 Q-loop/lid; other site 60480007854 ABC transporter signature motif; other site 60480007855 Walker B; other site 60480007856 D-loop; other site 60480007857 H-loop/switch region; other site 60480007858 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 60480007859 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 60480007860 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 60480007861 Walker A/P-loop; other site 60480007862 ATP binding site [chemical binding]; other site 60480007863 Q-loop/lid; other site 60480007864 ABC transporter signature motif; other site 60480007865 Walker B; other site 60480007866 D-loop; other site 60480007867 H-loop/switch region; other site 60480007868 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 60480007869 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 60480007870 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 60480007871 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 60480007872 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 60480007873 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 60480007874 periplasmic folding chaperone; Provisional; Region: PRK10788 60480007875 SurA N-terminal domain; Region: SurA_N_3; cl07813 60480007876 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 60480007877 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 60480007878 IHF dimer interface [polypeptide binding]; other site 60480007879 IHF - DNA interface [nucleotide binding]; other site 60480007880 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 60480007881 Found in ATP-dependent protease La (LON); Region: LON; smart00464 60480007882 Found in ATP-dependent protease La (LON); Region: LON; smart00464 60480007883 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 60480007884 Walker A motif; other site 60480007885 ATP binding site [chemical binding]; other site 60480007886 Walker B motif; other site 60480007887 arginine finger; other site 60480007888 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 60480007889 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 60480007890 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 60480007891 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 60480007892 Walker A motif; other site 60480007893 ATP binding site [chemical binding]; other site 60480007894 Walker B motif; other site 60480007895 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 60480007896 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 60480007897 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 60480007898 oligomer interface [polypeptide binding]; other site 60480007899 active site residues [active] 60480007900 trigger factor; Provisional; Region: tig; PRK01490 60480007901 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480007902 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 60480007903 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 60480007904 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 60480007905 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 60480007906 homodimer interface [polypeptide binding]; other site 60480007907 NADP binding site [chemical binding]; other site 60480007908 substrate binding site [chemical binding]; other site 60480007909 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 60480007910 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 60480007911 active site 60480007912 HIGH motif; other site 60480007913 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 60480007914 KMSKS motif; other site 60480007915 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 60480007916 tRNA binding surface [nucleotide binding]; other site 60480007917 anticodon binding site; other site 60480007918 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 60480007919 substrate binding site [chemical binding]; other site 60480007920 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 60480007921 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 60480007922 putative active site [active] 60480007923 putative metal binding site [ion binding]; other site 60480007924 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 60480007925 active site 60480007926 dinuclear metal binding site [ion binding]; other site 60480007927 dimerization interface [polypeptide binding]; other site 60480007928 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 60480007929 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 60480007930 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 60480007931 active site 60480007932 HIGH motif; other site 60480007933 nucleotide binding site [chemical binding]; other site 60480007934 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 60480007935 KMSKS motif; other site 60480007936 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 60480007937 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 60480007938 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 60480007939 G1 box; other site 60480007940 GTP/Mg2+ binding site [chemical binding]; other site 60480007941 Switch I region; other site 60480007942 G2 box; other site 60480007943 G3 box; other site 60480007944 Switch II region; other site 60480007945 G4 box; other site 60480007946 G5 box; other site 60480007947 Nucleoside recognition; Region: Gate; pfam07670 60480007948 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 60480007949 Nucleoside recognition; Region: Gate; pfam07670 60480007950 FeoA domain; Region: FeoA; pfam04023 60480007951 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 60480007952 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 60480007953 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 60480007954 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 60480007955 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 60480007956 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 60480007957 heme-binding residues [chemical binding]; other site 60480007958 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 60480007959 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 60480007960 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 60480007961 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 60480007962 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 60480007963 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 60480007964 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 60480007965 putative uracil binding site [chemical binding]; other site 60480007966 putative active site [active] 60480007967 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 60480007968 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 60480007969 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 60480007970 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 60480007971 active site 60480007972 Zn binding site [ion binding]; other site 60480007973 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 60480007974 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 60480007975 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 60480007976 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 60480007977 putative heme binding pocket [chemical binding]; other site 60480007978 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 60480007979 fructuronate transporter; Provisional; Region: PRK10034; cl15264 60480007980 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 60480007981 putative pyridoxal-dependent aspartate 1-decarboxylase; Region: NOD_PanD_pyr; TIGR03799 60480007982 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480007983 catalytic residue [active] 60480007984 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 60480007985 active site 60480007986 catalytic triad [active] 60480007987 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 60480007988 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 60480007989 Walker A motif; other site 60480007990 ATP binding site [chemical binding]; other site 60480007991 Walker B motif; other site 60480007992 arginine finger; other site 60480007993 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 60480007994 trimer interface [polypeptide binding]; other site 60480007995 active site 60480007996 substrate binding site [chemical binding]; other site 60480007997 CoA binding site [chemical binding]; other site 60480007998 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 60480007999 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 60480008000 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480008001 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480008002 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 60480008003 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 60480008004 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 60480008005 L-fucose transporter; Provisional; Region: PRK10133; cl17665 60480008006 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 60480008007 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 60480008008 active site 60480008009 dimer interface [polypeptide binding]; other site 60480008010 fructokinase; Reviewed; Region: PRK09557 60480008011 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 60480008012 nucleotide binding site [chemical binding]; other site 60480008013 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 60480008014 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 60480008015 dimer interface [polypeptide binding]; other site 60480008016 active site 60480008017 AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases; Region: SIS_AgaS_like; cd05010 60480008018 putative active site [active] 60480008019 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; pfam08013 60480008020 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 60480008021 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 60480008022 DNA-binding transcriptional regulator AgaR; Provisional; Region: PRK09802 60480008023 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 60480008024 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 60480008025 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 60480008026 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 60480008027 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 60480008028 ligand-binding site [chemical binding]; other site 60480008029 Predicted transcriptional regulator [Transcription]; Region: COG2378 60480008030 HTH domain; Region: HTH_11; pfam08279 60480008031 WYL domain; Region: WYL; pfam13280 60480008032 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 60480008033 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 60480008034 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480008035 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 60480008036 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 60480008037 active site 60480008038 substrate binding site [chemical binding]; other site 60480008039 metal binding site [ion binding]; metal-binding site 60480008040 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 60480008041 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 60480008042 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480008043 3-beta hydroxysteroid dehydrogenase/isomerase family; Region: 3Beta_HSD; pfam01073 60480008044 NAD(P) binding site [chemical binding]; other site 60480008045 active site 60480008046 peptide synthase; Provisional; Region: PRK09274 60480008047 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 60480008048 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_1; cd05910 60480008049 acyl-activating enzyme (AAE) consensus motif; other site 60480008050 putative AMP binding site [chemical binding]; other site 60480008051 putative active site [active] 60480008052 putative CoA binding site [chemical binding]; other site 60480008053 haloalkane dehalogenase; Provisional; Region: PRK03592 60480008054 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 60480008055 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 60480008056 dimer interface [polypeptide binding]; other site 60480008057 active site 60480008058 CoA binding pocket [chemical binding]; other site 60480008059 Methyltransferase domain; Region: Methyltransf_32; pfam13679 60480008060 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 60480008061 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 60480008062 active site 60480008063 BCCT family transporter; Region: BCCT; pfam02028 60480008064 Protein of unknown function (DUF502); Region: DUF502; pfam04367 60480008065 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 60480008066 dimer interface [polypeptide binding]; other site 60480008067 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480008068 metal binding site [ion binding]; metal-binding site 60480008069 Domain of unknown function DUF1829; Region: DUF1829; pfam08862 60480008070 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 60480008071 transcriptional regulator PhoU; Provisional; Region: PRK11115 60480008072 PhoU domain; Region: PhoU; pfam01895 60480008073 PhoU domain; Region: PhoU; pfam01895 60480008074 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 60480008075 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 60480008076 Walker A/P-loop; other site 60480008077 ATP binding site [chemical binding]; other site 60480008078 Q-loop/lid; other site 60480008079 ABC transporter signature motif; other site 60480008080 Walker B; other site 60480008081 D-loop; other site 60480008082 H-loop/switch region; other site 60480008083 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 60480008084 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 60480008085 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 60480008086 dimer interface [polypeptide binding]; other site 60480008087 conserved gate region; other site 60480008088 putative PBP binding loops; other site 60480008089 ABC-ATPase subunit interface; other site 60480008090 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 60480008091 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 60480008092 conserved gate region; other site 60480008093 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 60480008094 ABC-ATPase subunit interface; other site 60480008095 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 60480008096 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 60480008097 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 60480008098 EamA-like transporter family; Region: EamA; pfam00892 60480008099 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 60480008100 EamA-like transporter family; Region: EamA; pfam00892 60480008101 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 60480008102 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 60480008103 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 60480008104 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480008105 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 60480008106 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 60480008107 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 60480008108 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 60480008109 active site 60480008110 catalytic residues [active] 60480008111 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 60480008112 PA/subtilisin-like domain interface [polypeptide binding]; other site 60480008113 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 60480008114 catalytic residues [active] 60480008115 SseB protein; Region: SseB; cl06279 60480008116 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 60480008117 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 60480008118 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 60480008119 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 60480008120 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 60480008121 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 60480008122 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 60480008123 Walker A/P-loop; other site 60480008124 ATP binding site [chemical binding]; other site 60480008125 Q-loop/lid; other site 60480008126 ABC transporter signature motif; other site 60480008127 Walker B; other site 60480008128 D-loop; other site 60480008129 H-loop/switch region; other site 60480008130 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 60480008131 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480008132 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480008133 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480008134 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 60480008135 DNA binding site [nucleotide binding] 60480008136 AAA ATPase domain; Region: AAA_16; pfam13191 60480008137 Tetratricopeptide repeat; Region: TPR_12; pfam13424 60480008138 Tetratricopeptide repeat; Region: TPR_12; pfam13424 60480008139 Domain of unknown function (DUF1888); Region: DUF1888; pfam08985 60480008140 PAS domain S-box; Region: sensory_box; TIGR00229 60480008141 PAS domain; Region: PAS; smart00091 60480008142 putative active site [active] 60480008143 heme pocket [chemical binding]; other site 60480008144 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480008145 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480008146 metal binding site [ion binding]; metal-binding site 60480008147 active site 60480008148 I-site; other site 60480008149 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 60480008150 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 60480008151 FAD binding domain; Region: FAD_binding_4; pfam01565 60480008152 Berberine and berberine like; Region: BBE; pfam08031 60480008153 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 60480008154 EamA-like transporter family; Region: EamA; pfam00892 60480008155 EamA-like transporter family; Region: EamA; pfam00892 60480008156 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 60480008157 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 60480008158 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480008159 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480008160 Walker A/P-loop; other site 60480008161 ATP binding site [chemical binding]; other site 60480008162 Q-loop/lid; other site 60480008163 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480008164 Walker B; other site 60480008165 ABC transporter; Region: ABC_tran_2; pfam12848 60480008166 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 60480008167 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 60480008168 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 60480008169 metal-binding site [ion binding] 60480008170 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 60480008171 Soluble P-type ATPase [General function prediction only]; Region: COG4087 60480008172 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 60480008173 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 60480008174 DNA binding residues [nucleotide binding] 60480008175 dimer interface [polypeptide binding]; other site 60480008176 copper binding site [ion binding]; other site 60480008177 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 60480008178 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480008179 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 60480008180 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480008181 NAD(P) binding site [chemical binding]; other site 60480008182 active site 60480008183 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 60480008184 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 60480008185 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 60480008186 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 60480008187 substrate binding site [chemical binding]; other site 60480008188 oxyanion hole (OAH) forming residues; other site 60480008189 trimer interface [polypeptide binding]; other site 60480008190 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 60480008191 enoyl-CoA hydratase; Provisional; Region: PRK09076 60480008192 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 60480008193 substrate binding site [chemical binding]; other site 60480008194 oxyanion hole (OAH) forming residues; other site 60480008195 trimer interface [polypeptide binding]; other site 60480008196 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 60480008197 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 60480008198 active site 60480008199 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 60480008200 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 60480008201 tetrameric interface [polypeptide binding]; other site 60480008202 NAD binding site [chemical binding]; other site 60480008203 catalytic residues [active] 60480008204 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 60480008205 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 60480008206 dimer interface [polypeptide binding]; other site 60480008207 active site 60480008208 homoserine O-succinyltransferase; Provisional; Region: PRK05368 60480008209 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 60480008210 proposed active site lysine [active] 60480008211 conserved cys residue [active] 60480008212 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 60480008213 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 60480008214 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480008215 NAD(P) binding site [chemical binding]; other site 60480008216 active site 60480008217 outer membrane protein W; Provisional; Region: PRK10959 60480008218 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 60480008219 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 60480008220 maleylacetoacetate isomerase; Region: maiA; TIGR01262 60480008221 C-terminal domain interface [polypeptide binding]; other site 60480008222 GSH binding site (G-site) [chemical binding]; other site 60480008223 putative dimer interface [polypeptide binding]; other site 60480008224 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 60480008225 dimer interface [polypeptide binding]; other site 60480008226 N-terminal domain interface [polypeptide binding]; other site 60480008227 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 60480008228 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 60480008229 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 60480008230 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 60480008231 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 60480008232 putative aromatic amino acid binding site; other site 60480008233 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 60480008234 Walker A motif; other site 60480008235 ATP binding site [chemical binding]; other site 60480008236 Walker B motif; other site 60480008237 arginine finger; other site 60480008238 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 60480008239 aromatic arch; other site 60480008240 DCoH dimer interaction site [polypeptide binding]; other site 60480008241 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 60480008242 DCoH tetramer interaction site [polypeptide binding]; other site 60480008243 substrate binding site [chemical binding]; other site 60480008244 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 60480008245 cofactor binding site; other site 60480008246 metal binding site [ion binding]; metal-binding site 60480008247 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 60480008248 active site 60480008249 tetramer interface; other site 60480008250 UDP-glucose 4-epimerase; Region: PLN02240 60480008251 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 60480008252 NAD binding site [chemical binding]; other site 60480008253 homodimer interface [polypeptide binding]; other site 60480008254 active site 60480008255 substrate binding site [chemical binding]; other site 60480008256 ferredoxin-type protein; Provisional; Region: PRK10194 60480008257 4Fe-4S binding domain; Region: Fer4; cl02805 60480008258 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 60480008259 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 60480008260 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480008261 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 60480008262 dimerization interface [polypeptide binding]; other site 60480008263 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 60480008264 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 60480008265 Uncharacterized conserved protein [Function unknown]; Region: COG1434 60480008266 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 60480008267 putative active site [active] 60480008268 fructokinase; Reviewed; Region: PRK09557 60480008269 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 60480008270 nucleotide binding site [chemical binding]; other site 60480008271 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 60480008272 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 60480008273 active site 60480008274 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 60480008275 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 60480008276 NADP binding site [chemical binding]; other site 60480008277 active site 60480008278 putative substrate binding site [chemical binding]; other site 60480008279 putative hydrolase; Validated; Region: PRK09248 60480008280 Polymerase and Histidinol Phosphatase domain of Ycdx like; Region: PHP_HisPPase_Ycdx_like; cd07437 60480008281 active site 60480008282 SWIM zinc finger; Region: SWIM; pfam04434 60480008283 Bacterial SNF2 helicase associated; Region: SNF2_assoc; pfam08455 60480008284 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 60480008285 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 60480008286 ATP binding site [chemical binding]; other site 60480008287 putative Mg++ binding site [ion binding]; other site 60480008288 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 60480008289 nucleotide binding region [chemical binding]; other site 60480008290 ATP-binding site [chemical binding]; other site 60480008291 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 60480008292 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 60480008293 DNA-binding site [nucleotide binding]; DNA binding site 60480008294 RNA-binding motif; other site 60480008295 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 60480008296 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 60480008297 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 60480008298 TrkA-N domain; Region: TrkA_N; pfam02254 60480008299 TrkA-C domain; Region: TrkA_C; pfam02080 60480008300 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480008301 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480008302 metal binding site [ion binding]; metal-binding site 60480008303 active site 60480008304 I-site; other site 60480008305 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 60480008306 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 60480008307 Ligand Binding Site [chemical binding]; other site 60480008308 TilS substrate binding domain; Region: TilS; pfam09179 60480008309 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 60480008310 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 60480008311 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 60480008312 putative active site [active] 60480008313 putative PHP Thumb interface [polypeptide binding]; other site 60480008314 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 60480008315 generic binding surface II; other site 60480008316 generic binding surface I; other site 60480008317 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 60480008318 RNA/DNA hybrid binding site [nucleotide binding]; other site 60480008319 active site 60480008320 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 60480008321 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 60480008322 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 60480008323 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 60480008324 active site 60480008325 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 60480008326 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 60480008327 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 60480008328 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 60480008329 trimer interface [polypeptide binding]; other site 60480008330 active site 60480008331 UDP-GlcNAc binding site [chemical binding]; other site 60480008332 lipid binding site [chemical binding]; lipid-binding site 60480008333 periplasmic chaperone; Provisional; Region: PRK10780 60480008334 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 60480008335 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 60480008336 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480008337 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480008338 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480008339 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480008340 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 60480008341 Surface antigen; Region: Bac_surface_Ag; pfam01103 60480008342 zinc metallopeptidase RseP; Provisional; Region: PRK10779 60480008343 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 60480008344 active site 60480008345 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 60480008346 protein binding site [polypeptide binding]; other site 60480008347 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 60480008348 protein binding site [polypeptide binding]; other site 60480008349 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 60480008350 putative substrate binding region [chemical binding]; other site 60480008351 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 60480008352 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 60480008353 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 60480008354 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 60480008355 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 60480008356 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 60480008357 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 60480008358 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 60480008359 catalytic residue [active] 60480008360 putative FPP diphosphate binding site; other site 60480008361 putative FPP binding hydrophobic cleft; other site 60480008362 dimer interface [polypeptide binding]; other site 60480008363 putative IPP diphosphate binding site; other site 60480008364 ribosome recycling factor; Reviewed; Region: frr; PRK00083 60480008365 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 60480008366 hinge region; other site 60480008367 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 60480008368 putative nucleotide binding site [chemical binding]; other site 60480008369 uridine monophosphate binding site [chemical binding]; other site 60480008370 homohexameric interface [polypeptide binding]; other site 60480008371 elongation factor Ts; Provisional; Region: tsf; PRK09377 60480008372 UBA/TS-N domain; Region: UBA; pfam00627 60480008373 Elongation factor TS; Region: EF_TS; pfam00889 60480008374 Elongation factor TS; Region: EF_TS; pfam00889 60480008375 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 60480008376 rRNA interaction site [nucleotide binding]; other site 60480008377 S8 interaction site; other site 60480008378 putative laminin-1 binding site; other site 60480008379 methionine aminopeptidase; Provisional; Region: PRK12318 60480008380 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 60480008381 active site 60480008382 PII uridylyl-transferase; Provisional; Region: PRK05007 60480008383 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 60480008384 metal binding triad; other site 60480008385 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 60480008386 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 60480008387 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 60480008388 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 60480008389 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 60480008390 trimer interface [polypeptide binding]; other site 60480008391 active site 60480008392 substrate binding site [chemical binding]; other site 60480008393 CoA binding site [chemical binding]; other site 60480008394 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 60480008395 GAF domain; Region: GAF; pfam01590 60480008396 GAF domain; Region: GAF_2; pfam13185 60480008397 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 60480008398 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480008399 Zn2+ binding site [ion binding]; other site 60480008400 Mg2+ binding site [ion binding]; other site 60480008401 FOG: CBS domain [General function prediction only]; Region: COG0517 60480008402 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 60480008403 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 60480008404 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 60480008405 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 60480008406 putative active site [active] 60480008407 putative substrate binding site [chemical binding]; other site 60480008408 putative cosubstrate binding site; other site 60480008409 catalytic site [active] 60480008410 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 60480008411 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 60480008412 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 60480008413 active site turn [active] 60480008414 phosphorylation site [posttranslational modification] 60480008415 flavodoxin; Provisional; Region: PRK08105 60480008416 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 60480008417 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 60480008418 probable active site [active] 60480008419 tRNA pseudouridine synthase C; Region: DUF446; pfam04287 60480008420 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 60480008421 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 60480008422 Protein of unknown function (DUF962); Region: DUF962; pfam06127 60480008423 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480008424 Coenzyme A binding pocket [chemical binding]; other site 60480008425 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 60480008426 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 60480008427 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 60480008428 SecY interacting protein Syd; Provisional; Region: PRK04968 60480008429 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 60480008430 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 60480008431 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 60480008432 Sporulation control protein [General function prediction only]; Region: Spo0M; COG4326 60480008433 SpoOM protein; Region: Spo0M; pfam07070 60480008434 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 60480008435 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 60480008436 Homeodomain-like domain; Region: HTH_23; pfam13384 60480008437 Winged helix-turn helix; Region: HTH_29; pfam13551 60480008438 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 60480008439 3-oxoacyl-acyl carrier protein synthase; Provisional; Region: PTZ00050 60480008440 active site 60480008441 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 60480008442 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 60480008443 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 60480008444 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 60480008445 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 60480008446 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 60480008447 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 60480008448 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 60480008449 This enzymatic domain is part of bacterial polyketide synthases; Region: PKS_KR; smart00822 60480008450 putative NADP binding site [chemical binding]; other site 60480008451 active site 60480008452 Acyl transferase domain; Region: Acyl_transf_1; cl08282 60480008453 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 60480008454 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 60480008455 active site 60480008456 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 60480008457 active site 60480008458 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 60480008459 active site 2 [active] 60480008460 dimer interface [polypeptide binding]; other site 60480008461 active site 1 [active] 60480008462 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 60480008463 active site 1 [active] 60480008464 dimer interface [polypeptide binding]; other site 60480008465 active site 2 [active] 60480008466 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 60480008467 FMN binding site [chemical binding]; other site 60480008468 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 60480008469 substrate binding site [chemical binding]; other site 60480008470 putative catalytic residue [active] 60480008471 hypothetical protein; Provisional; Region: PRK12361 60480008472 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 60480008473 active site 60480008474 catalytic residues [active] 60480008475 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 60480008476 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 60480008477 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 60480008478 Walker A motif; other site 60480008479 ATP binding site [chemical binding]; other site 60480008480 Walker B motif; other site 60480008481 arginine finger; other site 60480008482 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480008483 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 60480008484 BON domain; Region: BON; pfam04972 60480008485 BON domain; Region: BON; pfam04972 60480008486 Protein of unknown function (DUF3224); Region: DUF3224; pfam11528 60480008487 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 60480008488 catalytic core [active] 60480008489 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 60480008490 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480008491 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 60480008492 trimer interface [polypeptide binding]; other site 60480008493 eyelet of channel; other site 60480008494 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 60480008495 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 60480008496 putative substrate translocation pore; other site 60480008497 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 60480008498 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 60480008499 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 60480008500 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 60480008501 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 60480008502 dimer interface [polypeptide binding]; other site 60480008503 phosphorylation site [posttranslational modification] 60480008504 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 60480008505 ATP binding site [chemical binding]; other site 60480008506 Mg2+ binding site [ion binding]; other site 60480008507 G-X-G motif; other site 60480008508 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 60480008509 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480008510 active site 60480008511 phosphorylation site [posttranslational modification] 60480008512 intermolecular recognition site; other site 60480008513 dimerization interface [polypeptide binding]; other site 60480008514 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 60480008515 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480008516 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 60480008517 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 60480008518 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 60480008519 ligand binding site [chemical binding]; other site 60480008520 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 60480008521 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 60480008522 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 60480008523 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 60480008524 putative active site [active] 60480008525 Zn binding site [ion binding]; other site 60480008526 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 60480008527 MarR family; Region: MarR; pfam01047 60480008528 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 60480008529 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 60480008530 PhnA protein; Region: PhnA; pfam03831 60480008531 TIGR02453 family protein; Region: TIGR02453 60480008532 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480008533 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480008534 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 60480008535 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 60480008536 putative C-terminal domain interface [polypeptide binding]; other site 60480008537 putative GSH binding site (G-site) [chemical binding]; other site 60480008538 putative dimer interface [polypeptide binding]; other site 60480008539 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 60480008540 putative N-terminal domain interface [polypeptide binding]; other site 60480008541 putative dimer interface [polypeptide binding]; other site 60480008542 putative substrate binding pocket (H-site) [chemical binding]; other site 60480008543 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 60480008544 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 60480008545 C-terminal domain interface [polypeptide binding]; other site 60480008546 GSH binding site (G-site) [chemical binding]; other site 60480008547 dimer interface [polypeptide binding]; other site 60480008548 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 60480008549 N-terminal domain interface [polypeptide binding]; other site 60480008550 putative dimer interface [polypeptide binding]; other site 60480008551 active site 60480008552 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 60480008553 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 60480008554 S-adenosylmethionine binding site [chemical binding]; other site 60480008555 Acetoacetate decarboxylase (ADC); Region: ADC; cl01919 60480008556 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 60480008557 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 60480008558 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 60480008559 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480008560 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480008561 metal binding site [ion binding]; metal-binding site 60480008562 active site 60480008563 I-site; other site 60480008564 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 60480008565 EamA-like transporter family; Region: EamA; pfam00892 60480008566 EamA-like transporter family; Region: EamA; cl17759 60480008567 YfaZ precursor; Region: YfaZ; pfam07437 60480008568 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 60480008569 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 60480008570 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480008571 Coenzyme A binding pocket [chemical binding]; other site 60480008572 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 60480008573 MgtE intracellular N domain; Region: MgtE_N; smart00924 60480008574 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 60480008575 Divalent cation transporter; Region: MgtE; cl00786 60480008576 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 60480008577 catalytic residues [active] 60480008578 dimer interface [polypeptide binding]; other site 60480008579 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 60480008580 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 60480008581 active site 60480008582 Zn binding site [ion binding]; other site 60480008583 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 60480008584 PBP superfamily domain; Region: PBP_like_2; cl17296 60480008585 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 60480008586 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 60480008587 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 60480008588 putative active site [active] 60480008589 heme pocket [chemical binding]; other site 60480008590 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 60480008591 dimer interface [polypeptide binding]; other site 60480008592 phosphorylation site [posttranslational modification] 60480008593 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 60480008594 ATP binding site [chemical binding]; other site 60480008595 Mg2+ binding site [ion binding]; other site 60480008596 G-X-G motif; other site 60480008597 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 60480008598 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480008599 active site 60480008600 phosphorylation site [posttranslational modification] 60480008601 intermolecular recognition site; other site 60480008602 dimerization interface [polypeptide binding]; other site 60480008603 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 60480008604 DNA binding site [nucleotide binding] 60480008605 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 60480008606 trimer interface [polypeptide binding]; other site 60480008607 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480008608 eyelet of channel; other site 60480008609 recombination associated protein; Reviewed; Region: rdgC; PRK00321 60480008610 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 60480008611 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 60480008612 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 60480008613 protein binding site [polypeptide binding]; other site 60480008614 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 60480008615 binding surface 60480008616 TPR motif; other site 60480008617 Tetratricopeptide repeat; Region: TPR_12; pfam13424 60480008618 Tetratricopeptide repeat; Region: TPR_12; pfam13424 60480008619 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480008620 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480008621 metal binding site [ion binding]; metal-binding site 60480008622 active site 60480008623 I-site; other site 60480008624 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 60480008625 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 60480008626 flap endonuclease-like protein; Provisional; Region: PRK09482 60480008627 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 60480008628 active site 60480008629 metal binding site 1 [ion binding]; metal-binding site 60480008630 putative 5' ssDNA interaction site; other site 60480008631 metal binding site 3; metal-binding site 60480008632 metal binding site 2 [ion binding]; metal-binding site 60480008633 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 60480008634 putative DNA binding site [nucleotide binding]; other site 60480008635 putative metal binding site [ion binding]; other site 60480008636 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 60480008637 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 60480008638 Catalytic domain of Protein Kinases; Region: PKc; cd00180 60480008639 active site 60480008640 ATP binding site [chemical binding]; other site 60480008641 substrate binding site [chemical binding]; other site 60480008642 activation loop (A-loop); other site 60480008643 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480008644 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480008645 isocitrate dehydrogenase; Provisional; Region: PRK08997 60480008646 tartrate dehydrogenase; Region: TTC; TIGR02089 60480008647 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 60480008648 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 60480008649 Protein of unknown function (DUF423); Region: DUF423; pfam04241 60480008650 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 60480008651 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 60480008652 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480008653 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 60480008654 dimerization interface [polypeptide binding]; other site 60480008655 substrate binding pocket [chemical binding]; other site 60480008656 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 60480008657 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 60480008658 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 60480008659 Ligand Binding Site [chemical binding]; other site 60480008660 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 60480008661 active site residue [active] 60480008662 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 60480008663 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 60480008664 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480008665 ligand binding site [chemical binding]; other site 60480008666 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 60480008667 flagellar motor protein PomA; Reviewed; Region: PRK08990 60480008668 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 60480008669 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 60480008670 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 60480008671 substrate binding pocket [chemical binding]; other site 60480008672 chain length determination region; other site 60480008673 substrate-Mg2+ binding site; other site 60480008674 catalytic residues [active] 60480008675 aspartate-rich region 1; other site 60480008676 active site lid residues [active] 60480008677 aspartate-rich region 2; other site 60480008678 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 60480008679 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 60480008680 TPP-binding site; other site 60480008681 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 60480008682 PYR/PP interface [polypeptide binding]; other site 60480008683 dimer interface [polypeptide binding]; other site 60480008684 TPP binding site [chemical binding]; other site 60480008685 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 60480008686 GrpE; Region: GrpE; pfam01025 60480008687 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 60480008688 dimer interface [polypeptide binding]; other site 60480008689 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 60480008690 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03378 60480008691 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 60480008692 L-lactate permease; Region: Lactate_perm; cl00701 60480008693 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 60480008694 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 60480008695 FAD binding domain; Region: FAD_binding_4; pfam01565 60480008696 4Fe-4S binding domain; Region: Fer4; pfam00037 60480008697 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 60480008698 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 60480008699 Cysteine-rich domain; Region: CCG; pfam02754 60480008700 Cysteine-rich domain; Region: CCG; pfam02754 60480008701 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 60480008702 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 60480008703 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 60480008704 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 60480008705 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 60480008706 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 60480008707 Domain of unknown function DUF20; Region: UPF0118; pfam01594 60480008708 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 60480008709 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 60480008710 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480008711 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480008712 voltage-gated potassium channel; Provisional; Region: PRK10537 60480008713 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 60480008714 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 60480008715 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 60480008716 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480008717 putative substrate translocation pore; other site 60480008718 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 60480008719 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 60480008720 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 60480008721 substrate binding pocket [chemical binding]; other site 60480008722 membrane-bound complex binding site; other site 60480008723 hinge residues; other site 60480008724 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 60480008725 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 60480008726 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 60480008727 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 60480008728 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480008729 ATP binding site [chemical binding]; other site 60480008730 Mg++ binding site [ion binding]; other site 60480008731 motif III; other site 60480008732 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 60480008733 nucleotide binding region [chemical binding]; other site 60480008734 ATP-binding site [chemical binding]; other site 60480008735 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 60480008736 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 60480008737 PAS domain; Region: PAS_9; pfam13426 60480008738 putative active site [active] 60480008739 heme pocket [chemical binding]; other site 60480008740 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 60480008741 PAS fold; Region: PAS_3; pfam08447 60480008742 putative active site [active] 60480008743 heme pocket [chemical binding]; other site 60480008744 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 60480008745 PAS domain; Region: PAS_9; pfam13426 60480008746 putative active site [active] 60480008747 heme pocket [chemical binding]; other site 60480008748 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480008749 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480008750 metal binding site [ion binding]; metal-binding site 60480008751 active site 60480008752 I-site; other site 60480008753 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 60480008754 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 60480008755 glycogen/starch synthase, ADP-glucose type; Region: glgA; TIGR02095 60480008756 ADP-binding pocket [chemical binding]; other site 60480008757 homodimer interface [polypeptide binding]; other site 60480008758 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 60480008759 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 60480008760 ligand binding site; other site 60480008761 oligomer interface; other site 60480008762 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 60480008763 dimer interface [polypeptide binding]; other site 60480008764 N-terminal domain interface [polypeptide binding]; other site 60480008765 sulfate 1 binding site; other site 60480008766 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 60480008767 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 60480008768 homodimer interface [polypeptide binding]; other site 60480008769 active site pocket [active] 60480008770 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 60480008771 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 60480008772 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 60480008773 active site 60480008774 catalytic site [active] 60480008775 glycogen branching enzyme; Provisional; Region: PRK05402 60480008776 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 60480008777 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 60480008778 active site 60480008779 catalytic site [active] 60480008780 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 60480008781 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 60480008782 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 60480008783 active site 60480008784 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 60480008785 MarR family; Region: MarR; pfam01047 60480008786 MarR family; Region: MarR_2; cl17246 60480008787 putative alcohol dehydrogenase; Provisional; Region: PRK09860 60480008788 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 60480008789 dimer interface [polypeptide binding]; other site 60480008790 active site 60480008791 metal binding site [ion binding]; metal-binding site 60480008792 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 60480008793 isocitrate lyase; Provisional; Region: PRK15063 60480008794 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 60480008795 tetramer interface [polypeptide binding]; other site 60480008796 active site 60480008797 Mg2+/Mn2+ binding site [ion binding]; other site 60480008798 malate synthase A; Region: malate_syn_A; TIGR01344 60480008799 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 60480008800 active site 60480008801 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 60480008802 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480008803 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 60480008804 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 60480008805 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 60480008806 TrkA-N domain; Region: TrkA_N; pfam02254 60480008807 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480008808 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480008809 metal binding site [ion binding]; metal-binding site 60480008810 active site 60480008811 I-site; other site 60480008812 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cl06673 60480008813 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 60480008814 active site 60480008815 SAM binding site [chemical binding]; other site 60480008816 homodimer interface [polypeptide binding]; other site 60480008817 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 60480008818 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 60480008819 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 60480008820 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 60480008821 putative coenzyme Q binding site [chemical binding]; other site 60480008822 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 60480008823 SmpB-tmRNA interface; other site 60480008824 integrase; Provisional; Region: PRK09692 60480008825 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 60480008826 active site 60480008827 Int/Topo IB signature motif; other site 60480008828 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 60480008829 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 60480008830 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 60480008831 DNA methylase; Region: N6_N4_Mtase; cl17433 60480008832 DNA methylase; Region: N6_N4_Mtase; pfam01555 60480008833 DNA methylase; Region: N6_N4_Mtase; cl17433 60480008834 Helix-turn-helix domain; Region: HTH_17; pfam12728 60480008835 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 60480008836 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 60480008837 catalytic residues [active] 60480008838 catalytic nucleophile [active] 60480008839 Presynaptic Site I dimer interface [polypeptide binding]; other site 60480008840 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 60480008841 Synaptic Flat tetramer interface [polypeptide binding]; other site 60480008842 Synaptic Site I dimer interface [polypeptide binding]; other site 60480008843 DNA binding site [nucleotide binding] 60480008844 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 60480008845 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 60480008846 active site 60480008847 Int/Topo IB signature motif; other site 60480008848 catalytic residues [active] 60480008849 DNA binding site [nucleotide binding] 60480008850 Helix-turn-helix domain; Region: HTH_17; pfam12728 60480008851 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 60480008852 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480008853 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480008854 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480008855 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 60480008856 metal-binding site [ion binding] 60480008857 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 60480008858 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 60480008859 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 60480008860 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 60480008861 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 60480008862 homotrimer interaction site [polypeptide binding]; other site 60480008863 putative active site [active] 60480008864 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 60480008865 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 60480008866 YheO-like PAS domain; Region: PAS_6; pfam08348 60480008867 HTH domain; Region: HTH_22; pfam13309 60480008868 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 60480008869 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 60480008870 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 60480008871 Domain of unknown function (DUF368); Region: DUF368; pfam04018 60480008872 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 60480008873 CoenzymeA binding site [chemical binding]; other site 60480008874 subunit interaction site [polypeptide binding]; other site 60480008875 PHB binding site; other site 60480008876 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 60480008877 nucleoside/Zn binding site; other site 60480008878 dimer interface [polypeptide binding]; other site 60480008879 catalytic motif [active] 60480008880 Predicted membrane protein [Function unknown]; Region: COG2311 60480008881 Protein of unknown function (DUF418); Region: DUF418; cl12135 60480008882 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 60480008883 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480008884 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480008885 HPP family; Region: HPP; pfam04982 60480008886 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 60480008887 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 60480008888 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 60480008889 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480008890 N-terminal Early set domain associated with the catalytic domain of chitinase; Region: E_set_Chitinase_N; cd02848 60480008891 Glyco_18 domain; Region: Glyco_18; smart00636 60480008892 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 60480008893 active site 60480008894 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 60480008895 aromatic chitin/cellulose binding site residues [chemical binding]; other site 60480008896 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 60480008897 aromatic chitin/cellulose binding site residues [chemical binding]; other site 60480008898 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 60480008899 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 60480008900 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 60480008901 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 60480008902 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 60480008903 active site 60480008904 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 60480008905 PAS domain; Region: PAS_9; pfam13426 60480008906 putative active site [active] 60480008907 heme pocket [chemical binding]; other site 60480008908 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480008909 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480008910 dimer interface [polypeptide binding]; other site 60480008911 putative CheW interface [polypeptide binding]; other site 60480008912 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 60480008913 DEAD-like helicases superfamily; Region: DEXDc; smart00487 60480008914 ATP binding site [chemical binding]; other site 60480008915 Mg++ binding site [ion binding]; other site 60480008916 motif III; other site 60480008917 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 60480008918 nucleotide binding region [chemical binding]; other site 60480008919 ATP-binding site [chemical binding]; other site 60480008920 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 60480008921 putative catalytic residues [active] 60480008922 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 60480008923 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 60480008924 membrane-bound complex binding site; other site 60480008925 hinge residues; other site 60480008926 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 60480008927 intracellular protease, PfpI family; Region: PfpI; TIGR01382 60480008928 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 60480008929 conserved cys residue [active] 60480008930 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 60480008931 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 60480008932 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 60480008933 DsrE/DsrF-like family; Region: DrsE; pfam02635 60480008934 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 60480008935 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 60480008936 active site 60480008937 Zn binding site [ion binding]; other site 60480008938 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 60480008939 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480008940 Coenzyme A binding pocket [chemical binding]; other site 60480008941 Protein of unknown function, DUF486; Region: DUF486; pfam04342 60480008942 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 60480008943 RDD family; Region: RDD; pfam06271 60480008944 lipopolysaccharide ABC transporter permease; Provisional; Region: PRK15071 60480008945 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 60480008946 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 60480008947 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 60480008948 multifunctional aminopeptidase A; Provisional; Region: PRK00913 60480008949 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 60480008950 interface (dimer of trimers) [polypeptide binding]; other site 60480008951 Substrate-binding/catalytic site; other site 60480008952 Zn-binding sites [ion binding]; other site 60480008953 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 60480008954 chorismate mutase domain of proteobacterial P-protein, clade 1; Region: CM_P_1; TIGR01797 60480008955 Prephenate dehydratase; Region: PDT; pfam00800 60480008956 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 60480008957 putative L-Phe binding site [chemical binding]; other site 60480008958 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 60480008959 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 60480008960 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 60480008961 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 60480008962 FAD binding pocket [chemical binding]; other site 60480008963 FAD binding motif [chemical binding]; other site 60480008964 phosphate binding motif [ion binding]; other site 60480008965 beta-alpha-beta structure motif; other site 60480008966 NAD binding pocket [chemical binding]; other site 60480008967 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 60480008968 catalytic loop [active] 60480008969 iron binding site [ion binding]; other site 60480008970 hybrid cluster protein; Provisional; Region: PRK05290 60480008971 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 60480008972 ACS interaction site; other site 60480008973 CODH interaction site; other site 60480008974 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 60480008975 ACS interaction site; other site 60480008976 CODH interaction site; other site 60480008977 metal cluster binding site [ion binding]; other site 60480008978 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 60480008979 chorismate mutase domain of T-protein; Region: CM_T; TIGR01799 60480008980 prephenate dehydrogenase; Validated; Region: PRK08507 60480008981 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 60480008982 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 60480008983 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 60480008984 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 60480008985 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 60480008986 RimM N-terminal domain; Region: RimM; pfam01782 60480008987 PRC-barrel domain; Region: PRC; pfam05239 60480008988 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 60480008989 signal recognition particle protein; Provisional; Region: PRK10867 60480008990 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 60480008991 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 60480008992 P loop; other site 60480008993 GTP binding site [chemical binding]; other site 60480008994 Signal peptide binding domain; Region: SRP_SPB; pfam02978 60480008995 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 60480008996 Domain of unknown function DUF21; Region: DUF21; pfam01595 60480008997 hypothetical protein; Provisional; Region: PRK11573 60480008998 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 60480008999 Transporter associated domain; Region: CorC_HlyC; smart01091 60480009000 Protein of unknown function (DUF962); Region: DUF962; cl01879 60480009001 Transposase IS200 like; Region: Y1_Tnp; pfam01797 60480009002 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 60480009003 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 60480009004 active site 60480009005 hydrophilic channel; other site 60480009006 dimerization interface [polypeptide binding]; other site 60480009007 catalytic residues [active] 60480009008 active site lid [active] 60480009009 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 60480009010 Recombination protein O N terminal; Region: RecO_N; pfam11967 60480009011 Recombination protein O C terminal; Region: RecO_C; pfam02565 60480009012 GTPase Era; Reviewed; Region: era; PRK00089 60480009013 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 60480009014 G1 box; other site 60480009015 GTP/Mg2+ binding site [chemical binding]; other site 60480009016 Switch I region; other site 60480009017 G2 box; other site 60480009018 Switch II region; other site 60480009019 G3 box; other site 60480009020 G4 box; other site 60480009021 G5 box; other site 60480009022 KH domain; Region: KH_2; pfam07650 60480009023 ribonuclease III; Reviewed; Region: rnc; PRK00102 60480009024 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 60480009025 dimerization interface [polypeptide binding]; other site 60480009026 active site 60480009027 metal binding site [ion binding]; metal-binding site 60480009028 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 60480009029 dsRNA binding site [nucleotide binding]; other site 60480009030 signal peptidase I; Provisional; Region: PRK10861 60480009031 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 60480009032 Catalytic site [active] 60480009033 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 60480009034 GTP-binding protein LepA; Provisional; Region: PRK05433 60480009035 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 60480009036 G1 box; other site 60480009037 putative GEF interaction site [polypeptide binding]; other site 60480009038 GTP/Mg2+ binding site [chemical binding]; other site 60480009039 Switch I region; other site 60480009040 G2 box; other site 60480009041 G3 box; other site 60480009042 Switch II region; other site 60480009043 G4 box; other site 60480009044 G5 box; other site 60480009045 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 60480009046 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 60480009047 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 60480009048 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 60480009049 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 60480009050 anti-sigma E factor; Provisional; Region: rseB; PRK09455 60480009051 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 60480009052 anti-RNA polymerase sigma factor SigE; Provisional; Region: PRK10863 60480009053 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 60480009054 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 60480009055 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480009056 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 60480009057 DNA binding residues [nucleotide binding] 60480009058 L-aspartate oxidase; Provisional; Region: PRK09077 60480009059 L-aspartate oxidase; Provisional; Region: PRK06175 60480009060 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 60480009061 Uncharacterized conserved protein [Function unknown]; Region: COG2938 60480009062 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 60480009063 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480009064 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 60480009065 dimerization interface [polypeptide binding]; other site 60480009066 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09561 60480009067 thymidylate synthase; Reviewed; Region: thyA; PRK01827 60480009068 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 60480009069 dimerization interface [polypeptide binding]; other site 60480009070 active site 60480009071 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 60480009072 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480009073 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 60480009074 GAF domain; Region: GAF; pfam01590 60480009075 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 60480009076 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 60480009077 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 60480009078 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 60480009079 putative active site [active] 60480009080 Ap4A binding site [chemical binding]; other site 60480009081 nudix motif; other site 60480009082 putative metal binding site [ion binding]; other site 60480009083 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 60480009084 putative DNA-binding cleft [nucleotide binding]; other site 60480009085 putative DNA clevage site; other site 60480009086 molecular lever; other site 60480009087 cyclase homology domain; Region: CHD; cd07302 60480009088 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 60480009089 nucleotidyl binding site; other site 60480009090 metal binding site [ion binding]; metal-binding site 60480009091 dimer interface [polypeptide binding]; other site 60480009092 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480009093 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480009094 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 60480009095 dimerization interface [polypeptide binding]; other site 60480009096 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 60480009097 putative binding surface; other site 60480009098 active site 60480009099 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 60480009100 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 60480009101 FeS/SAM binding site; other site 60480009102 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 60480009103 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 60480009104 active site 60480009105 dimer interface [polypeptide binding]; other site 60480009106 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 60480009107 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 60480009108 active site 60480009109 FMN binding site [chemical binding]; other site 60480009110 substrate binding site [chemical binding]; other site 60480009111 3Fe-4S cluster binding site [ion binding]; other site 60480009112 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 60480009113 domain interface; other site 60480009114 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 60480009115 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 60480009116 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480009117 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 60480009118 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 60480009119 Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]; Region: CbiB; COG1270 60480009120 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 60480009121 hypothetical protein; Provisional; Region: PRK10578 60480009122 UPF0126 domain; Region: UPF0126; pfam03458 60480009123 UPF0126 domain; Region: UPF0126; pfam03458 60480009124 SnoaL-like domain; Region: SnoaL_2; pfam12680 60480009125 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 60480009126 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 60480009127 active site 60480009128 HIGH motif; other site 60480009129 dimer interface [polypeptide binding]; other site 60480009130 KMSKS motif; other site 60480009131 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 60480009132 RNA binding surface [nucleotide binding]; other site 60480009133 putative peptidase; Provisional; Region: PRK11649 60480009134 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 60480009135 Peptidase family M23; Region: Peptidase_M23; pfam01551 60480009136 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 60480009137 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 60480009138 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480009139 DNA binding site [nucleotide binding] 60480009140 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 60480009141 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 60480009142 X-Pro dipeptidyl-peptidase (S15 family); Region: Peptidase_S15; pfam02129 60480009143 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480009144 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 60480009145 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 60480009146 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 60480009147 amphipathic channel; other site 60480009148 Asn-Pro-Ala signature motifs; other site 60480009149 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 60480009150 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 60480009151 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 60480009152 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 60480009153 Cl- selectivity filter; other site 60480009154 Cl- binding residues [ion binding]; other site 60480009155 pore gating glutamate residue; other site 60480009156 dimer interface [polypeptide binding]; other site 60480009157 aspartate carbamoyltransferase; Provisional; Region: PRK08192 60480009158 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 60480009159 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 60480009160 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 60480009161 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 60480009162 inhibitor-cofactor binding pocket; inhibition site 60480009163 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480009164 catalytic residue [active] 60480009165 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 60480009166 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 60480009167 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 60480009168 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 60480009169 Walker A motif; other site 60480009170 ATP binding site [chemical binding]; other site 60480009171 Walker B motif; other site 60480009172 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 60480009173 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 60480009174 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 60480009175 active site 60480009176 NTP binding site [chemical binding]; other site 60480009177 metal binding triad [ion binding]; metal-binding site 60480009178 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 60480009179 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480009180 Zn2+ binding site [ion binding]; other site 60480009181 Mg2+ binding site [ion binding]; other site 60480009182 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 60480009183 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 60480009184 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 60480009185 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 60480009186 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 60480009187 catalytic center binding site [active] 60480009188 ATP binding site [chemical binding]; other site 60480009189 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 60480009190 homooctamer interface [polypeptide binding]; other site 60480009191 active site 60480009192 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 60480009193 UGMP family protein; Validated; Region: PRK09604 60480009194 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 60480009195 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 60480009196 Yqey-like protein; Region: YqeY; pfam09424 60480009197 DNA primase; Validated; Region: dnaG; PRK05667 60480009198 CHC2 zinc finger; Region: zf-CHC2; pfam01807 60480009199 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 60480009200 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 60480009201 active site 60480009202 metal binding site [ion binding]; metal-binding site 60480009203 interdomain interaction site; other site 60480009204 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 60480009205 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 60480009206 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 60480009207 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 60480009208 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 60480009209 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 60480009210 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480009211 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 60480009212 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 60480009213 DNA binding residues [nucleotide binding] 60480009214 Cache domain; Region: Cache_1; pfam02743 60480009215 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 60480009216 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480009217 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480009218 dimer interface [polypeptide binding]; other site 60480009219 putative CheW interface [polypeptide binding]; other site 60480009220 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 60480009221 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 60480009222 putative substrate translocation pore; other site 60480009223 POT family; Region: PTR2; cl17359 60480009224 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 60480009225 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 60480009226 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 60480009227 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 60480009228 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 60480009229 inhibitor-cofactor binding pocket; inhibition site 60480009230 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480009231 catalytic residue [active] 60480009232 succinate-semialdehyde dehydrogenase I; Provisional; Region: gabD; PRK11241 60480009233 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 60480009234 tetramerization interface [polypeptide binding]; other site 60480009235 NAD(P) binding site [chemical binding]; other site 60480009236 catalytic residues [active] 60480009237 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 60480009238 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 60480009239 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 60480009240 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 60480009241 dimer interface [polypeptide binding]; other site 60480009242 conserved gate region; other site 60480009243 putative PBP binding loops; other site 60480009244 ABC-ATPase subunit interface; other site 60480009245 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 60480009246 dimer interface [polypeptide binding]; other site 60480009247 conserved gate region; other site 60480009248 putative PBP binding loops; other site 60480009249 ABC-ATPase subunit interface; other site 60480009250 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 60480009251 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480009252 Walker A/P-loop; other site 60480009253 ATP binding site [chemical binding]; other site 60480009254 Q-loop/lid; other site 60480009255 ABC transporter signature motif; other site 60480009256 Walker B; other site 60480009257 D-loop; other site 60480009258 H-loop/switch region; other site 60480009259 TOBE domain; Region: TOBE_2; pfam08402 60480009260 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 60480009261 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 60480009262 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 60480009263 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 60480009264 Peptidase C26; Region: Peptidase_C26; pfam07722 60480009265 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 60480009266 catalytic triad [active] 60480009267 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 60480009268 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 60480009269 non-specific DNA binding site [nucleotide binding]; other site 60480009270 salt bridge; other site 60480009271 sequence-specific DNA binding site [nucleotide binding]; other site 60480009272 Cupin domain; Region: Cupin_2; pfam07883 60480009273 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 60480009274 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 60480009275 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 60480009276 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 60480009277 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 60480009278 active site residue [active] 60480009279 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 60480009280 active site residue [active] 60480009281 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 60480009282 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 60480009283 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 60480009284 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 60480009285 NAD(P) binding site [chemical binding]; other site 60480009286 catalytic residues [active] 60480009287 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 60480009288 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 60480009289 inhibitor-cofactor binding pocket; inhibition site 60480009290 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480009291 catalytic residue [active] 60480009292 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 60480009293 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 60480009294 tetrameric interface [polypeptide binding]; other site 60480009295 NAD binding site [chemical binding]; other site 60480009296 catalytic residues [active] 60480009297 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 60480009298 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 60480009299 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 60480009300 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 60480009301 putative substrate translocation pore; other site 60480009302 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 60480009303 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 60480009304 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 60480009305 active site 60480009306 dimer interface [polypeptide binding]; other site 60480009307 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 60480009308 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 60480009309 dimer interface [polypeptide binding]; other site 60480009310 active site 60480009311 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 60480009312 dimer interface [polypeptide binding]; other site 60480009313 active site 60480009314 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 60480009315 Putative carbohydrate binding domain; Region: CHB_HEX; smart01081 60480009316 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 60480009317 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 60480009318 active site 60480009319 C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase); Region: E_set_Chitobiase_C; cd02847 60480009320 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 60480009321 dimerization interface [polypeptide binding]; other site 60480009322 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480009323 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480009324 dimer interface [polypeptide binding]; other site 60480009325 putative CheW interface [polypeptide binding]; other site 60480009326 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480009327 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480009328 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 60480009329 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 60480009330 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 60480009331 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 60480009332 Transcriptional regulators [Transcription]; Region: PurR; COG1609 60480009333 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 60480009334 DNA binding site [nucleotide binding] 60480009335 domain linker motif; other site 60480009336 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 60480009337 putative ligand binding site [chemical binding]; other site 60480009338 putative dimerization interface [polypeptide binding]; other site 60480009339 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 60480009340 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 60480009341 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 60480009342 Nitrogen regulatory protein P-II; Region: P-II; smart00938 60480009343 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 60480009344 Type II transport protein GspH; Region: GspH; pfam12019 60480009345 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 60480009346 Type II transport protein GspH; Region: GspH; pfam12019 60480009347 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 60480009348 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 60480009349 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 60480009350 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 60480009351 PilX N-terminal; Region: PilX_N; pfam14341 60480009352 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 60480009353 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 60480009354 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 60480009355 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 60480009356 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 60480009357 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480009358 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 60480009359 lipoprotein signal peptidase; Provisional; Region: PRK14787 60480009360 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 60480009361 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 60480009362 active site 60480009363 HIGH motif; other site 60480009364 nucleotide binding site [chemical binding]; other site 60480009365 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 60480009366 active site 60480009367 KMSKS motif; other site 60480009368 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 60480009369 tRNA binding surface [nucleotide binding]; other site 60480009370 anticodon binding site; other site 60480009371 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 60480009372 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 60480009373 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 60480009374 active site 60480009375 Riboflavin kinase; Region: Flavokinase; smart00904 60480009376 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 60480009377 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 60480009378 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 60480009379 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 60480009380 dimerization interface [polypeptide binding]; other site 60480009381 putative DNA binding site [nucleotide binding]; other site 60480009382 putative Zn2+ binding site [ion binding]; other site 60480009383 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 60480009384 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 60480009385 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480009386 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 60480009387 Peptidase family M28; Region: Peptidase_M28; pfam04389 60480009388 metal binding site [ion binding]; metal-binding site 60480009389 hypothetical protein; Validated; Region: PRK02101 60480009390 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 60480009391 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 60480009392 putative phosphoketolase; Provisional; Region: PRK05261 60480009393 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 60480009394 TPP-binding site; other site 60480009395 XFP C-terminal domain; Region: XFP_C; pfam09363 60480009396 outer membrane protein A; Reviewed; Region: PRK10808 60480009397 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 60480009398 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 60480009399 ligand binding site [chemical binding]; other site 60480009400 transaldolase-like protein; Provisional; Region: PTZ00411 60480009401 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 60480009402 active site 60480009403 dimer interface [polypeptide binding]; other site 60480009404 catalytic residue [active] 60480009405 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 60480009406 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 60480009407 active site 60480009408 dimer interface [polypeptide binding]; other site 60480009409 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 60480009410 dimer interface [polypeptide binding]; other site 60480009411 active site 60480009412 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 60480009413 Hemerythrin-like domain; Region: Hr-like; cd12108 60480009414 Fe binding site [ion binding]; other site 60480009415 RNA polymerase sigma factor; Provisional; Region: PRK12513 60480009416 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480009417 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 60480009418 DNA binding residues [nucleotide binding] 60480009419 von Willebrand factor; Region: vWF_A; pfam12450 60480009420 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 60480009421 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 60480009422 metal ion-dependent adhesion site (MIDAS); other site 60480009423 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 60480009424 putative transporter; Provisional; Region: PRK11660 60480009425 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 60480009426 Sulfate transporter family; Region: Sulfate_transp; pfam00916 60480009427 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 60480009428 AIR carboxylase; Region: AIRC; pfam00731 60480009429 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 60480009430 ATP-grasp domain; Region: ATP-grasp; pfam02222 60480009431 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480009432 GAF domain; Region: GAF; pfam01590 60480009433 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480009434 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480009435 metal binding site [ion binding]; metal-binding site 60480009436 active site 60480009437 I-site; other site 60480009438 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 60480009439 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480009440 catalytic residue [active] 60480009441 glutamate--cysteine ligase; Provisional; Region: PRK02107 60480009442 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 60480009443 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480009444 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480009445 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 60480009446 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480009447 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480009448 Predicted membrane protein [Function unknown]; Region: COG1238 60480009449 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 60480009450 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 60480009451 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 60480009452 oxaloacetate decarboxylase; Provisional; Region: PRK14040 60480009453 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 60480009454 active site 60480009455 catalytic residues [active] 60480009456 metal binding site [ion binding]; metal-binding site 60480009457 homodimer binding site [polypeptide binding]; other site 60480009458 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 60480009459 carboxyltransferase (CT) interaction site; other site 60480009460 biotinylation site [posttranslational modification]; other site 60480009461 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 60480009462 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 60480009463 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 60480009464 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 60480009465 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 60480009466 Clp amino terminal domain; Region: Clp_N; pfam02861 60480009467 Clp amino terminal domain; Region: Clp_N; pfam02861 60480009468 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 60480009469 Walker A motif; other site 60480009470 ATP binding site [chemical binding]; other site 60480009471 Walker B motif; other site 60480009472 arginine finger; other site 60480009473 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 60480009474 Walker A motif; other site 60480009475 ATP binding site [chemical binding]; other site 60480009476 Walker B motif; other site 60480009477 arginine finger; other site 60480009478 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 60480009479 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 60480009480 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 60480009481 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 60480009482 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 60480009483 RNA binding surface [nucleotide binding]; other site 60480009484 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 60480009485 active site 60480009486 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 60480009487 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 60480009488 HAMP domain; Region: HAMP; pfam00672 60480009489 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480009490 dimer interface [polypeptide binding]; other site 60480009491 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 60480009492 putative CheW interface [polypeptide binding]; other site 60480009493 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 60480009494 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 60480009495 heme-binding site [chemical binding]; other site 60480009496 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 60480009497 FAD binding pocket [chemical binding]; other site 60480009498 FAD binding motif [chemical binding]; other site 60480009499 phosphate binding motif [ion binding]; other site 60480009500 beta-alpha-beta structure motif; other site 60480009501 NAD binding pocket [chemical binding]; other site 60480009502 Heme binding pocket [chemical binding]; other site 60480009503 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 60480009504 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 60480009505 RNA binding surface [nucleotide binding]; other site 60480009506 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 60480009507 active site 60480009508 uracil binding [chemical binding]; other site 60480009509 Predicted transcriptional regulator [Transcription]; Region: COG2345 60480009510 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 60480009511 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 60480009512 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480009513 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 60480009514 active site 60480009515 metal binding site [ion binding]; metal-binding site 60480009516 YcxB-like protein; Region: YcxB; pfam14317 60480009517 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 60480009518 MltA-interacting protein MipA; Region: MipA; pfam06629 60480009519 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 60480009520 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 60480009521 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480009522 active site 60480009523 phosphorylation site [posttranslational modification] 60480009524 intermolecular recognition site; other site 60480009525 dimerization interface [polypeptide binding]; other site 60480009526 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 60480009527 DNA binding site [nucleotide binding] 60480009528 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480009529 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 60480009530 dimer interface [polypeptide binding]; other site 60480009531 phosphorylation site [posttranslational modification] 60480009532 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 60480009533 ATP binding site [chemical binding]; other site 60480009534 Mg2+ binding site [ion binding]; other site 60480009535 G-X-G motif; other site 60480009536 Predicted Fe-S protein [General function prediction only]; Region: COG3313 60480009537 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 60480009538 Transposase IS200 like; Region: Y1_Tnp; pfam01797 60480009539 cysteine synthase B; Region: cysM; TIGR01138 60480009540 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 60480009541 dimer interface [polypeptide binding]; other site 60480009542 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480009543 catalytic residue [active] 60480009544 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CysP; COG4150 60480009545 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 60480009546 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 60480009547 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 60480009548 dimer interface [polypeptide binding]; other site 60480009549 conserved gate region; other site 60480009550 putative PBP binding loops; other site 60480009551 ABC-ATPase subunit interface; other site 60480009552 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 60480009553 dimer interface [polypeptide binding]; other site 60480009554 conserved gate region; other site 60480009555 putative PBP binding loops; other site 60480009556 ABC-ATPase subunit interface; other site 60480009557 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 60480009558 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 60480009559 Walker A/P-loop; other site 60480009560 ATP binding site [chemical binding]; other site 60480009561 Q-loop/lid; other site 60480009562 ABC transporter signature motif; other site 60480009563 Walker B; other site 60480009564 D-loop; other site 60480009565 H-loop/switch region; other site 60480009566 TOBE-like domain; Region: TOBE_3; pfam12857 60480009567 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 60480009568 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480009569 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480009570 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 60480009571 Ycf46; Provisional; Region: ycf46; CHL00195 60480009572 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 60480009573 Walker A motif; other site 60480009574 ATP binding site [chemical binding]; other site 60480009575 Walker B motif; other site 60480009576 arginine finger; other site 60480009577 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 60480009578 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; Region: 2-Hacid_dh_C; pfam02826 60480009579 ATP-grasp domain; Region: ATP-grasp; pfam02222 60480009580 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 60480009581 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 60480009582 Transposase; Region: DEDD_Tnp_IS110; pfam01548 60480009583 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 60480009584 Peptidase S46; Region: Peptidase_S46; pfam10459 60480009585 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]; Region: COG3591 60480009586 aromatic amino acid transport protein; Region: araaP; TIGR00837 60480009587 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 60480009588 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 60480009589 Chitin binding domain; Region: Chitin_bind_3; pfam03067 60480009590 Predicted membrane protein [Function unknown]; Region: COG2119 60480009591 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 60480009592 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 60480009593 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 60480009594 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 60480009595 tetramer interface [polypeptide binding]; other site 60480009596 heme binding pocket [chemical binding]; other site 60480009597 NADPH binding site [chemical binding]; other site 60480009598 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 60480009599 CoenzymeA binding site [chemical binding]; other site 60480009600 subunit interaction site [polypeptide binding]; other site 60480009601 PHB binding site; other site 60480009602 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 60480009603 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 60480009604 generic binding surface II; other site 60480009605 generic binding surface I; other site 60480009606 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 60480009607 putative catalytic site [active] 60480009608 putative metal binding site [ion binding]; other site 60480009609 putative phosphate binding site [ion binding]; other site 60480009610 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 60480009611 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 60480009612 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 60480009613 FOG: WD40 repeat [General function prediction only]; Region: COG2319 60480009614 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 60480009615 structural tetrad; other site 60480009616 SlyX; Region: SlyX; pfam04102 60480009617 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 60480009618 active site 60480009619 catalytic residues [active] 60480009620 metal binding site [ion binding]; metal-binding site 60480009621 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 60480009622 uncharacterized proteobacterial lipoprotein; Region: lp_; TIGR02722 60480009623 aminopeptidase N, Streptomyces lividans type; Region: pepN_strep_liv; TIGR02412 60480009624 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_3; cd09602 60480009625 Zn binding site [ion binding]; other site 60480009626 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 60480009627 Cache domain; Region: Cache_1; pfam02743 60480009628 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480009629 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 60480009630 dimerization interface [polypeptide binding]; other site 60480009631 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480009632 dimer interface [polypeptide binding]; other site 60480009633 putative CheW interface [polypeptide binding]; other site 60480009634 PAS domain S-box; Region: sensory_box; TIGR00229 60480009635 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 60480009636 putative active site [active] 60480009637 heme pocket [chemical binding]; other site 60480009638 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480009639 GAF domain; Region: GAF; pfam01590 60480009640 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480009641 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480009642 metal binding site [ion binding]; metal-binding site 60480009643 active site 60480009644 I-site; other site 60480009645 Protein of unknown function DUF72; Region: DUF72; cl00777 60480009646 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 60480009647 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 60480009648 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 60480009649 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 60480009650 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 60480009651 Carbon starvation protein CstA; Region: CstA; pfam02554 60480009652 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 60480009653 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 60480009654 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 60480009655 LrgB-like family; Region: LrgB; pfam04172 60480009656 LrgA family; Region: LrgA; cl00608 60480009657 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480009658 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480009659 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 60480009660 putative dimerization interface [polypeptide binding]; other site 60480009661 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 60480009662 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480009663 substrate binding pocket [chemical binding]; other site 60480009664 membrane-bound complex binding site; other site 60480009665 hinge residues; other site 60480009666 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 60480009667 dimer interface [polypeptide binding]; other site 60480009668 conserved gate region; other site 60480009669 putative PBP binding loops; other site 60480009670 ABC-ATPase subunit interface; other site 60480009671 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 60480009672 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 60480009673 Walker A/P-loop; other site 60480009674 ATP binding site [chemical binding]; other site 60480009675 Q-loop/lid; other site 60480009676 ABC transporter signature motif; other site 60480009677 Walker B; other site 60480009678 D-loop; other site 60480009679 H-loop/switch region; other site 60480009680 Uncharacterized conserved protein [Function unknown]; Region: COG3791 60480009681 Protein of unknown function (DUF3644); Region: DUF3644; pfam12358 60480009682 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; pfam10137 60480009683 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 60480009684 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 60480009685 SCP-2 sterol transfer family; Region: SCP2; pfam02036 60480009686 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 60480009687 dimer interface [polypeptide binding]; other site 60480009688 FMN binding site [chemical binding]; other site 60480009689 DNA-J related protein; Region: DNAJ_related; pfam12339 60480009690 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 60480009691 HSP70 interaction site [polypeptide binding]; other site 60480009692 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 60480009693 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 60480009694 catalytic residues [active] 60480009695 hinge region; other site 60480009696 alpha helical domain; other site 60480009697 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 60480009698 Domain of unknown function (DUF4382); Region: DUF4382; pfam14321 60480009699 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 60480009700 Flavodoxin domain; Region: Flavodoxin_5; cl17428 60480009701 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 60480009702 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480009703 putative substrate translocation pore; other site 60480009704 TIGR03899 family protein; Region: TIGR03899 60480009705 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 60480009706 ligand-binding site [chemical binding]; other site 60480009707 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 60480009708 TrkA-C domain; Region: TrkA_C; pfam02080 60480009709 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 60480009710 TrkA-C domain; Region: TrkA_C; pfam02080 60480009711 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 60480009712 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 60480009713 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 60480009714 CysD dimerization site [polypeptide binding]; other site 60480009715 G1 box; other site 60480009716 putative GEF interaction site [polypeptide binding]; other site 60480009717 GTP/Mg2+ binding site [chemical binding]; other site 60480009718 Switch I region; other site 60480009719 G2 box; other site 60480009720 G3 box; other site 60480009721 Switch II region; other site 60480009722 G4 box; other site 60480009723 G5 box; other site 60480009724 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 60480009725 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 60480009726 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 60480009727 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 60480009728 Active Sites [active] 60480009729 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 60480009730 active site 60480009731 SAM binding site [chemical binding]; other site 60480009732 homodimer interface [polypeptide binding]; other site 60480009733 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 60480009734 dimerization interface [polypeptide binding]; other site 60480009735 substrate binding site [chemical binding]; other site 60480009736 active site 60480009737 calcium binding site [ion binding]; other site 60480009738 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 60480009739 Active site serine [active] 60480009740 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 60480009741 Transglycosylase; Region: Transgly; cl17702 60480009742 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 60480009743 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 60480009744 Active Sites [active] 60480009745 sulfite reductase subunit beta; Provisional; Region: PRK13504 60480009746 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 60480009747 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 60480009748 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 60480009749 Flavodoxin; Region: Flavodoxin_1; pfam00258 60480009750 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 60480009751 FAD binding pocket [chemical binding]; other site 60480009752 FAD binding motif [chemical binding]; other site 60480009753 catalytic residues [active] 60480009754 NAD binding pocket [chemical binding]; other site 60480009755 phosphate binding motif [ion binding]; other site 60480009756 beta-alpha-beta structure motif; other site 60480009757 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 60480009758 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 60480009759 ligand binding site [chemical binding]; other site 60480009760 homodimer interface [polypeptide binding]; other site 60480009761 NAD(P) binding site [chemical binding]; other site 60480009762 trimer interface B [polypeptide binding]; other site 60480009763 trimer interface A [polypeptide binding]; other site 60480009764 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 60480009765 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 60480009766 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 60480009767 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480009768 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 60480009769 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 60480009770 putative ribose interaction site [chemical binding]; other site 60480009771 putative ADP binding site [chemical binding]; other site 60480009772 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 60480009773 active site 60480009774 HIGH motif; other site 60480009775 nucleotide binding site [chemical binding]; other site 60480009776 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 60480009777 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 60480009778 putative acyl-acceptor binding pocket; other site 60480009779 potassium/proton antiporter; Reviewed; Region: PRK05326 60480009780 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 60480009781 TrkA-C domain; Region: TrkA_C; pfam02080 60480009782 Transporter associated domain; Region: CorC_HlyC; smart01091 60480009783 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 60480009784 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 60480009785 GAF domain; Region: GAF; pfam01590 60480009786 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 60480009787 Walker A motif; other site 60480009788 ATP binding site [chemical binding]; other site 60480009789 Walker B motif; other site 60480009790 arginine finger; other site 60480009791 L,D-transpeptidase; Provisional; Region: PRK10190 60480009792 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480009793 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 60480009794 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 60480009795 putative active site [active] 60480009796 Zn binding site [ion binding]; other site 60480009797 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 60480009798 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480009799 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480009800 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480009801 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 60480009802 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480009803 active site 60480009804 phosphorylation site [posttranslational modification] 60480009805 intermolecular recognition site; other site 60480009806 dimerization interface [polypeptide binding]; other site 60480009807 Transcriptional regulator; Region: CitT; pfam12431 60480009808 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 60480009809 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 60480009810 PAS domain; Region: PAS; smart00091 60480009811 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 60480009812 ATP binding site [chemical binding]; other site 60480009813 Mg2+ binding site [ion binding]; other site 60480009814 G-X-G motif; other site 60480009815 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 60480009816 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 60480009817 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 60480009818 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 60480009819 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 60480009820 Predicted ATPase [General function prediction only]; Region: COG1485 60480009821 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480009822 Walker A/P-loop; other site 60480009823 ATP binding site [chemical binding]; other site 60480009824 ABC transporter signature motif; other site 60480009825 Walker B; other site 60480009826 D-loop; other site 60480009827 H-loop/switch region; other site 60480009828 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 60480009829 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 60480009830 DNA binding residues [nucleotide binding] 60480009831 atypical (a) SDRs, subgroup 3; Region: SDR_a3; cd05229 60480009832 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 60480009833 putative NAD(P) binding site [chemical binding]; other site 60480009834 putative active site [active] 60480009835 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 60480009836 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480009837 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 60480009838 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 60480009839 dimerization interface [polypeptide binding]; other site 60480009840 Domain of unknown function (DUF897); Region: DUF897; pfam05982 60480009841 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 60480009842 GAF domain; Region: GAF; pfam01590 60480009843 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480009844 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480009845 metal binding site [ion binding]; metal-binding site 60480009846 active site 60480009847 I-site; other site 60480009848 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 60480009849 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 60480009850 metal binding triad; other site 60480009851 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 60480009852 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 60480009853 metal binding triad; other site 60480009854 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 60480009855 spermidine synthase; Provisional; Region: PRK03612 60480009856 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 60480009857 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; pfam09938 60480009858 PspA/IM30 family; Region: PspA_IM30; pfam04012 60480009859 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 60480009860 Ion transport protein; Region: Ion_trans; pfam00520 60480009861 Ion channel; Region: Ion_trans_2; pfam07885 60480009862 Uncharacterized conserved protein [Function unknown]; Region: COG3025 60480009863 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 60480009864 putative active site [active] 60480009865 putative metal binding residues [ion binding]; other site 60480009866 signature motif; other site 60480009867 putative triphosphate binding site [ion binding]; other site 60480009868 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 60480009869 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 60480009870 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 60480009871 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 60480009872 Bacterial SH3 domain homologues; Region: SH3b; smart00287 60480009873 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 60480009874 Proline dehydrogenase; Region: Pro_dh; pfam01619 60480009875 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 60480009876 Glutamate binding site [chemical binding]; other site 60480009877 NAD binding site [chemical binding]; other site 60480009878 catalytic residues [active] 60480009879 Protein of unknown function, DUF599; Region: DUF599; pfam04654 60480009880 Helix-turn-helix domain; Region: HTH_17; pfam12728 60480009881 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 60480009882 putative active site [active] 60480009883 putative metal binding residues [ion binding]; other site 60480009884 signature motif; other site 60480009885 putative triphosphate binding site [ion binding]; other site 60480009886 dimer interface [polypeptide binding]; other site 60480009887 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 60480009888 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480009889 Walker A/P-loop; other site 60480009890 ATP binding site [chemical binding]; other site 60480009891 Q-loop/lid; other site 60480009892 ABC transporter signature motif; other site 60480009893 Walker B; other site 60480009894 D-loop; other site 60480009895 H-loop/switch region; other site 60480009896 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 60480009897 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 60480009898 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480009899 Walker A/P-loop; other site 60480009900 ATP binding site [chemical binding]; other site 60480009901 Q-loop/lid; other site 60480009902 ABC transporter signature motif; other site 60480009903 Walker B; other site 60480009904 D-loop; other site 60480009905 H-loop/switch region; other site 60480009906 Protein of unknown function (DUF3626); Region: DUF3626; pfam12294 60480009907 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 60480009908 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 60480009909 ATP binding site [chemical binding]; other site 60480009910 Mg++ binding site [ion binding]; other site 60480009911 motif III; other site 60480009912 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 60480009913 nucleotide binding region [chemical binding]; other site 60480009914 ATP-binding site [chemical binding]; other site 60480009915 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480009916 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 60480009917 dimerization interface [polypeptide binding]; other site 60480009918 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480009919 dimer interface [polypeptide binding]; other site 60480009920 putative CheW interface [polypeptide binding]; other site 60480009921 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 60480009922 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 60480009923 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 60480009924 catalytic residue [active] 60480009925 Fe-S metabolism associated domain; Region: SufE; cl00951 60480009926 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 60480009927 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 60480009928 active site 60480009929 Predicted ATPase [General function prediction only]; Region: COG4637 60480009930 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480009931 Walker A/P-loop; other site 60480009932 ATP binding site [chemical binding]; other site 60480009933 Cupin domain; Region: Cupin_2; cl17218 60480009934 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480009935 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 60480009936 Pleckstrin homology (PH)-like domains in bacteria (PHb); Region: PH-like_bacteria; cd13225 60480009937 pentamer interface [polypeptide binding]; other site 60480009938 dodecaamer interface [polypeptide binding]; other site 60480009939 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 60480009940 Peptidase family U32; Region: Peptidase_U32; pfam01136 60480009941 Collagenase; Region: DUF3656; pfam12392 60480009942 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 60480009943 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 60480009944 active site 60480009945 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 60480009946 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 60480009947 putative DNA binding site [nucleotide binding]; other site 60480009948 putative Zn2+ binding site [ion binding]; other site 60480009949 AsnC family; Region: AsnC_trans_reg; pfam01037 60480009950 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 60480009951 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 60480009952 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 60480009953 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480009954 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 60480009955 Zn binding site [ion binding]; other site 60480009956 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 60480009957 inner membrane transport permease; Provisional; Region: PRK15066 60480009958 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 60480009959 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 60480009960 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 60480009961 Walker A/P-loop; other site 60480009962 ATP binding site [chemical binding]; other site 60480009963 Q-loop/lid; other site 60480009964 ABC transporter signature motif; other site 60480009965 Walker B; other site 60480009966 D-loop; other site 60480009967 H-loop/switch region; other site 60480009968 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480009969 active site 60480009970 aromatic acid decarboxylase; Validated; Region: PRK05920 60480009971 Flavoprotein; Region: Flavoprotein; pfam02441 60480009972 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 60480009973 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 60480009974 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 60480009975 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 60480009976 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 60480009977 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 60480009978 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 60480009979 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 60480009980 hypothetical protein; Provisional; Region: PRK11627 60480009981 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 60480009982 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 60480009983 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 60480009984 substrate binding site [chemical binding]; other site 60480009985 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 60480009986 muropeptide transporter; Reviewed; Region: ampG; PRK11902 60480009987 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 60480009988 putative substrate translocation pore; other site 60480009989 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 60480009990 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 60480009991 Predicted integral membrane protein [Function unknown]; Region: COG5652 60480009992 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 60480009993 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 60480009994 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 60480009995 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 60480009996 Nitrogen regulatory protein P-II; Region: P-II; smart00938 60480009997 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 60480009998 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 60480009999 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 60480010000 Protein of unknown function (DUF819); Region: DUF819; cl02317 60480010001 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 60480010002 Tetratricopeptide repeat; Region: TPR_9; pfam13371 60480010003 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 60480010004 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480010005 Coenzyme A binding pocket [chemical binding]; other site 60480010006 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 60480010007 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 60480010008 peptide chain release factor 1; Validated; Region: prfA; PRK00591 60480010009 This domain is found in peptide chain release factors; Region: PCRF; smart00937 60480010010 RF-1 domain; Region: RF-1; pfam00472 60480010011 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 60480010012 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 60480010013 tRNA; other site 60480010014 putative tRNA binding site [nucleotide binding]; other site 60480010015 putative NADP binding site [chemical binding]; other site 60480010016 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 60480010017 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 60480010018 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 60480010019 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 60480010020 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 60480010021 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 60480010022 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 60480010023 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480010024 active site 60480010025 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 60480010026 dimerization interface [polypeptide binding]; other site 60480010027 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480010028 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480010029 dimer interface [polypeptide binding]; other site 60480010030 putative CheW interface [polypeptide binding]; other site 60480010031 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 60480010032 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480010033 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 60480010034 DNA binding residues [nucleotide binding] 60480010035 Domain of unknown function (DUF4097); Region: DUF4097; pfam13349 60480010036 Uncharacterized conserved protein [Function unknown]; Region: COG3595 60480010037 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 60480010038 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 60480010039 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 60480010040 RNA binding surface [nucleotide binding]; other site 60480010041 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 60480010042 active site 60480010043 uracil binding [chemical binding]; other site 60480010044 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 60480010045 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 60480010046 active site 60480010047 Zn binding site [ion binding]; other site 60480010048 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 60480010049 synthetase active site [active] 60480010050 NTP binding site [chemical binding]; other site 60480010051 metal binding site [ion binding]; metal-binding site 60480010052 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 60480010053 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 60480010054 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 60480010055 putative C-terminal domain interface [polypeptide binding]; other site 60480010056 putative GSH binding site (G-site) [chemical binding]; other site 60480010057 putative dimer interface [polypeptide binding]; other site 60480010058 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 60480010059 dimer interface [polypeptide binding]; other site 60480010060 N-terminal domain interface [polypeptide binding]; other site 60480010061 substrate binding pocket (H-site) [chemical binding]; other site 60480010062 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480010063 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 60480010064 N-terminal plug; other site 60480010065 ligand-binding site [chemical binding]; other site 60480010066 Bacterial PH domain; Region: DUF304; pfam03703 60480010067 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 60480010068 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 60480010069 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 60480010070 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 60480010071 malate dehydrogenase; Provisional; Region: PRK13529 60480010072 Malic enzyme, N-terminal domain; Region: malic; pfam00390 60480010073 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 60480010074 NAD(P) binding site [chemical binding]; other site 60480010075 Protein of unknown function (DUF3069); Region: DUF3069; pfam11269 60480010076 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 60480010077 active site 60480010078 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 60480010079 TPR motif; other site 60480010080 binding surface 60480010081 Tetratricopeptide repeat; Region: TPR_12; pfam13424 60480010082 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480010083 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480010084 metal binding site [ion binding]; metal-binding site 60480010085 active site 60480010086 I-site; other site 60480010087 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480010088 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 60480010089 substrate binding pocket [chemical binding]; other site 60480010090 membrane-bound complex binding site; other site 60480010091 hinge residues; other site 60480010092 epoxyqueuosine reductase; Region: TIGR00276 60480010093 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 60480010094 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 60480010095 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 60480010096 TOBE domain; Region: TOBE; cl01440 60480010097 molybdate transporter periplasmic protein; Provisional; Region: modA; PRK10677 60480010098 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 60480010099 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 60480010100 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 60480010101 dimer interface [polypeptide binding]; other site 60480010102 conserved gate region; other site 60480010103 putative PBP binding loops; other site 60480010104 ABC-ATPase subunit interface; other site 60480010105 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 60480010106 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480010107 Walker A/P-loop; other site 60480010108 ATP binding site [chemical binding]; other site 60480010109 Q-loop/lid; other site 60480010110 ABC transporter signature motif; other site 60480010111 Walker B; other site 60480010112 D-loop; other site 60480010113 H-loop/switch region; other site 60480010114 TOBE domain; Region: TOBE; cl01440 60480010115 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 60480010116 active site 60480010117 catalytic residues [active] 60480010118 DNA binding site [nucleotide binding] 60480010119 Int/Topo IB signature motif; other site 60480010120 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 60480010121 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 60480010122 non-specific DNA binding site [nucleotide binding]; other site 60480010123 salt bridge; other site 60480010124 sequence-specific DNA binding site [nucleotide binding]; other site 60480010125 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 60480010126 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 60480010127 cofactor binding site; other site 60480010128 DNA binding site [nucleotide binding] 60480010129 substrate interaction site [chemical binding]; other site 60480010130 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3183 60480010131 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 60480010132 active site 60480010133 putative transposase OrfB; Reviewed; Region: PHA02517 60480010134 HTH-like domain; Region: HTH_21; pfam13276 60480010135 Integrase core domain; Region: rve; pfam00665 60480010136 Integrase core domain; Region: rve_2; pfam13333 60480010137 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 60480010138 SEC-C motif; Region: SEC-C; pfam02810 60480010139 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 60480010140 Divergent AAA domain; Region: AAA_4; pfam04326 60480010141 Caspase domain; Region: Peptidase_C14; pfam00656 60480010142 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 60480010143 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 60480010144 active site 60480010145 DNA binding site [nucleotide binding] 60480010146 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 60480010147 Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members...; Region: MAM; cl02479 60480010148 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 60480010149 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 60480010150 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 60480010151 active site 60480010152 DNA binding site [nucleotide binding] 60480010153 Int/Topo IB signature motif; other site 60480010154 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 60480010155 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 60480010156 Walker A motif; other site 60480010157 ATP binding site [chemical binding]; other site 60480010158 Walker B motif; other site 60480010159 arginine finger; other site 60480010160 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 60480010161 Walker A motif; other site 60480010162 ATP binding site [chemical binding]; other site 60480010163 Walker B motif; other site 60480010164 arginine finger; other site 60480010165 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 60480010166 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 60480010167 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 60480010168 HAMP domain; Region: HAMP; pfam00672 60480010169 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480010170 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480010171 dimer interface [polypeptide binding]; other site 60480010172 putative CheW interface [polypeptide binding]; other site 60480010173 Hemerythrin; Region: Hemerythrin; cd12107 60480010174 Fe binding site [ion binding]; other site 60480010175 Superinfection exclusion protein B; Region: SieB; pfam14163 60480010176 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 60480010177 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 60480010178 dimer interface [polypeptide binding]; other site 60480010179 phosphorylation site [posttranslational modification] 60480010180 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 60480010181 ATP binding site [chemical binding]; other site 60480010182 Mg2+ binding site [ion binding]; other site 60480010183 G-X-G motif; other site 60480010184 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 60480010185 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 60480010186 putative ATP binding site [chemical binding]; other site 60480010187 putative substrate interface [chemical binding]; other site 60480010188 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480010189 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 60480010190 eyelet of channel; other site 60480010191 trimer interface [polypeptide binding]; other site 60480010192 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 60480010193 eyelet of channel; other site 60480010194 trimer interface [polypeptide binding]; other site 60480010195 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480010196 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 60480010197 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 60480010198 CAP-like domain; other site 60480010199 active site 60480010200 primary dimer interface [polypeptide binding]; other site 60480010201 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 60480010202 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 60480010203 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 60480010204 ATP binding site [chemical binding]; other site 60480010205 Mg2+ binding site [ion binding]; other site 60480010206 G-X-G motif; other site 60480010207 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 60480010208 anchoring element; other site 60480010209 dimer interface [polypeptide binding]; other site 60480010210 ATP binding site [chemical binding]; other site 60480010211 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 60480010212 active site 60480010213 metal binding site [ion binding]; metal-binding site 60480010214 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 60480010215 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 60480010216 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480010217 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 60480010218 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 60480010219 active site 60480010220 metal binding site [ion binding]; metal-binding site 60480010221 hexamer interface [polypeptide binding]; other site 60480010222 Protein of unknown function (DUF1249); Region: DUF1249; pfam06853 60480010223 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 60480010224 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 60480010225 dimer interface [polypeptide binding]; other site 60480010226 ADP-ribose binding site [chemical binding]; other site 60480010227 active site 60480010228 nudix motif; other site 60480010229 metal binding site [ion binding]; metal-binding site 60480010230 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 60480010231 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 60480010232 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; pfam10095 60480010233 Protein of unknown function (DUF461); Region: DUF461; pfam04314 60480010234 enoyl-CoA hydratase; Provisional; Region: PRK06688 60480010235 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 60480010236 substrate binding site [chemical binding]; other site 60480010237 oxyanion hole (OAH) forming residues; other site 60480010238 trimer interface [polypeptide binding]; other site 60480010239 PspC domain; Region: PspC; pfam04024 60480010240 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 60480010241 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 60480010242 FMN binding site [chemical binding]; other site 60480010243 active site 60480010244 catalytic residues [active] 60480010245 substrate binding site [chemical binding]; other site 60480010246 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 60480010247 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 60480010248 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 60480010249 N-terminal plug; other site 60480010250 ligand-binding site [chemical binding]; other site 60480010251 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 60480010252 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 60480010253 alanine racemase; Reviewed; Region: alr; PRK00053 60480010254 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 60480010255 active site 60480010256 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 60480010257 substrate binding site [chemical binding]; other site 60480010258 catalytic residues [active] 60480010259 dimer interface [polypeptide binding]; other site 60480010260 replicative DNA helicase; Provisional; Region: PRK08006 60480010261 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 60480010262 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 60480010263 Walker A motif; other site 60480010264 ATP binding site [chemical binding]; other site 60480010265 Walker B motif; other site 60480010266 DNA binding loops [nucleotide binding] 60480010267 Peptidase S46; Region: Peptidase_S46; pfam10459 60480010268 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 60480010269 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 60480010270 4Fe-4S binding domain; Region: Fer4; pfam00037 60480010271 4Fe-4S binding domain; Region: Fer4; pfam00037 60480010272 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 60480010273 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 60480010274 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 60480010275 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 60480010276 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09613 60480010277 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 60480010278 FeS/SAM binding site; other site 60480010279 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 60480010280 biotin synthase; Provisional; Region: PRK07094 60480010281 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 60480010282 FeS/SAM binding site; other site 60480010283 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 60480010284 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 60480010285 G1 box; other site 60480010286 GTP/Mg2+ binding site [chemical binding]; other site 60480010287 Switch I region; other site 60480010288 G2 box; other site 60480010289 Switch II region; other site 60480010290 G3 box; other site 60480010291 G4 box; other site 60480010292 G5 box; other site 60480010293 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 60480010294 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 60480010295 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 60480010296 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 60480010297 primosomal replication protein N; Provisional; Region: PRK02801 60480010298 generic binding surface II; other site 60480010299 generic binding surface I; other site 60480010300 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 60480010301 Protein of unknown function, DUF481; Region: DUF481; pfam04338 60480010302 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 60480010303 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480010304 putative substrate translocation pore; other site 60480010305 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 60480010306 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 60480010307 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 60480010308 exoribonuclease R; Provisional; Region: PRK11642 60480010309 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 60480010310 RNB domain; Region: RNB; pfam00773 60480010311 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 60480010312 RNA binding site [nucleotide binding]; other site 60480010313 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 60480010314 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 60480010315 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 60480010316 GDP-binding site [chemical binding]; other site 60480010317 ACT binding site; other site 60480010318 IMP binding site; other site 60480010319 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 60480010320 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 60480010321 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 60480010322 23S rRNA interface [nucleotide binding]; other site 60480010323 L3 interface [polypeptide binding]; other site 60480010324 Predicted ATPase [General function prediction only]; Region: COG1485 60480010325 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 60480010326 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 60480010327 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 60480010328 protein binding site [polypeptide binding]; other site 60480010329 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 60480010330 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 60480010331 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 60480010332 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 60480010333 protein binding site [polypeptide binding]; other site 60480010334 Protein of unknown function (DUF342); Region: DUF342; pfam03961 60480010335 protein structure with unknown function; Region: DUF4144; pfam13642 60480010336 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 60480010337 Peptidase family M50; Region: Peptidase_M50; pfam02163 60480010338 active site 60480010339 putative substrate binding region [chemical binding]; other site 60480010340 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480010341 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 60480010342 dimer interface [polypeptide binding]; other site 60480010343 phosphorylation site [posttranslational modification] 60480010344 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 60480010345 ATP binding site [chemical binding]; other site 60480010346 Mg2+ binding site [ion binding]; other site 60480010347 G-X-G motif; other site 60480010348 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480010349 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480010350 active site 60480010351 phosphorylation site [posttranslational modification] 60480010352 intermolecular recognition site; other site 60480010353 dimerization interface [polypeptide binding]; other site 60480010354 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 60480010355 DNA binding site [nucleotide binding] 60480010356 Spondin_N; Region: Spond_N; pfam06468 60480010357 Spondin_N; Region: Spond_N; pfam06468 60480010358 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 60480010359 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480010360 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 60480010361 N-terminal plug; other site 60480010362 ligand-binding site [chemical binding]; other site 60480010363 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480010364 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480010365 active site 60480010366 phosphorylation site [posttranslational modification] 60480010367 intermolecular recognition site; other site 60480010368 dimerization interface [polypeptide binding]; other site 60480010369 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 60480010370 DNA binding residues [nucleotide binding] 60480010371 dimerization interface [polypeptide binding]; other site 60480010372 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 60480010373 Na binding site [ion binding]; other site 60480010374 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 60480010375 PAS fold; Region: PAS_7; pfam12860 60480010376 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480010377 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 60480010378 dimer interface [polypeptide binding]; other site 60480010379 phosphorylation site [posttranslational modification] 60480010380 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 60480010381 ATP binding site [chemical binding]; other site 60480010382 Mg2+ binding site [ion binding]; other site 60480010383 G-X-G motif; other site 60480010384 Response regulator receiver domain; Region: Response_reg; pfam00072 60480010385 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480010386 active site 60480010387 phosphorylation site [posttranslational modification] 60480010388 intermolecular recognition site; other site 60480010389 dimerization interface [polypeptide binding]; other site 60480010390 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 60480010391 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480010392 putative substrate translocation pore; other site 60480010393 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 60480010394 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 60480010395 substrate binding pocket [chemical binding]; other site 60480010396 amidase; Validated; Region: PRK06565 60480010397 Amidase; Region: Amidase; cl11426 60480010398 Amidase; Region: Amidase; cl11426 60480010399 agmatine deiminase; Provisional; Region: PRK13551 60480010400 agmatine deiminase; Region: agmatine_aguA; TIGR03380 60480010401 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 60480010402 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 60480010403 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480010404 NAD(P) binding site [chemical binding]; other site 60480010405 active site 60480010406 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 60480010407 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 60480010408 CAAX protease self-immunity; Region: Abi; pfam02517 60480010409 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 60480010410 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 60480010411 THF binding site; other site 60480010412 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 60480010413 substrate binding site [chemical binding]; other site 60480010414 THF binding site; other site 60480010415 zinc-binding site [ion binding]; other site 60480010416 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480010417 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480010418 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 60480010419 putative dimerization interface [polypeptide binding]; other site 60480010420 HDOD domain; Region: HDOD; pfam08668 60480010421 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480010422 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 60480010423 N-terminal plug; other site 60480010424 ligand-binding site [chemical binding]; other site 60480010425 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 60480010426 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 60480010427 active site 60480010428 tetramer interface [polypeptide binding]; other site 60480010429 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 60480010430 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 60480010431 substrate binding site [chemical binding]; other site 60480010432 dimer interface [polypeptide binding]; other site 60480010433 ATP binding site [chemical binding]; other site 60480010434 azurin; Region: azurin; TIGR02695 60480010435 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 60480010436 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins; Region: GDPD_EcGlpQ_like_1; cd08560 60480010437 putative active site [active] 60480010438 catalytic site [active] 60480010439 putative metal binding site [ion binding]; other site 60480010440 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480010441 active site 60480010442 PhoD-like phosphatase; Region: PhoD; pfam09423 60480010443 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 60480010444 putative active site [active] 60480010445 putative metal binding site [ion binding]; other site 60480010446 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 60480010447 FOG: CBS domain [General function prediction only]; Region: COG0517 60480010448 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_15; cd04803 60480010449 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 60480010450 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 60480010451 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 60480010452 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 60480010453 substrate binding pocket [chemical binding]; other site 60480010454 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 60480010455 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 60480010456 N-terminal plug; other site 60480010457 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480010458 ligand-binding site [chemical binding]; other site 60480010459 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 60480010460 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 60480010461 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480010462 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480010463 metal binding site [ion binding]; metal-binding site 60480010464 active site 60480010465 I-site; other site 60480010466 YcaO domain protein; Region: TIGR03549 60480010467 OsmC-like protein; Region: OsmC; pfam02566 60480010468 YcaO-like family; Region: YcaO; pfam02624 60480010469 Cache domain; Region: Cache_2; pfam08269 60480010470 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 60480010471 dimerization interface [polypeptide binding]; other site 60480010472 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 60480010473 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480010474 dimer interface [polypeptide binding]; other site 60480010475 putative CheW interface [polypeptide binding]; other site 60480010476 Ribosome recycling factor; Region: RRF_GI; pfam12614 60480010477 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 60480010478 Nuclease-related domain; Region: NERD; pfam08378 60480010479 Domain of unknown function (DUF4297); Region: DUF4297; pfam14130 60480010480 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 60480010481 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 60480010482 ATP binding site [chemical binding]; other site 60480010483 putative Mg++ binding site [ion binding]; other site 60480010484 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 60480010485 nucleotide binding region [chemical binding]; other site 60480010486 ATP-binding site [chemical binding]; other site 60480010487 glycine dehydrogenase; Provisional; Region: PRK05367 60480010488 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 60480010489 tetramer interface [polypeptide binding]; other site 60480010490 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480010491 catalytic residue [active] 60480010492 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 60480010493 tetramer interface [polypeptide binding]; other site 60480010494 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480010495 catalytic residue [active] 60480010496 glycine cleavage system protein H; Provisional; Region: PRK13380 60480010497 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 60480010498 lipoyl attachment site [posttranslational modification]; other site 60480010499 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 60480010500 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 60480010501 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 60480010502 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 60480010503 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 60480010504 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 60480010505 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 60480010506 Cell division protein ZapA; Region: ZapA; pfam05164 60480010507 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 60480010508 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 60480010509 dihydromonapterin reductase; Provisional; Region: PRK06483 60480010510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480010511 NAD(P) binding site [chemical binding]; other site 60480010512 active site 60480010513 Protein of unknown function, DUF393; Region: DUF393; pfam04134 60480010514 malate dehydrogenase; Provisional; Region: PRK05086 60480010515 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 60480010516 NAD binding site [chemical binding]; other site 60480010517 dimerization interface [polypeptide binding]; other site 60480010518 Substrate binding site [chemical binding]; other site 60480010519 arginine repressor; Provisional; Region: PRK05066 60480010520 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 60480010521 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 60480010522 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 60480010523 NADH(P)-binding; Region: NAD_binding_10; pfam13460 60480010524 NAD binding site [chemical binding]; other site 60480010525 substrate binding site [chemical binding]; other site 60480010526 putative active site [active] 60480010527 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480010528 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480010529 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 60480010530 putative effector binding pocket; other site 60480010531 dimerization interface [polypeptide binding]; other site 60480010532 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 60480010533 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 60480010534 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 60480010535 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 60480010536 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 60480010537 Walker A/P-loop; other site 60480010538 ATP binding site [chemical binding]; other site 60480010539 Q-loop/lid; other site 60480010540 ABC transporter signature motif; other site 60480010541 Walker B; other site 60480010542 D-loop; other site 60480010543 H-loop/switch region; other site 60480010544 TOBE domain; Region: TOBE_2; pfam08402 60480010545 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 60480010546 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 60480010547 dimer interface [polypeptide binding]; other site 60480010548 conserved gate region; other site 60480010549 putative PBP binding loops; other site 60480010550 ABC-ATPase subunit interface; other site 60480010551 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 60480010552 dimer interface [polypeptide binding]; other site 60480010553 conserved gate region; other site 60480010554 putative PBP binding loops; other site 60480010555 ABC-ATPase subunit interface; other site 60480010556 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 60480010557 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 60480010558 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 60480010559 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 60480010560 putative C-terminal domain interface [polypeptide binding]; other site 60480010561 putative GSH binding site (G-site) [chemical binding]; other site 60480010562 putative dimer interface [polypeptide binding]; other site 60480010563 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 60480010564 substrate binding pocket (H-site) [chemical binding]; other site 60480010565 N-terminal domain interface [polypeptide binding]; other site 60480010566 ferredoxin-NADP reductase; Provisional; Region: PRK10926 60480010567 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 60480010568 FAD binding pocket [chemical binding]; other site 60480010569 FAD binding motif [chemical binding]; other site 60480010570 phosphate binding motif [ion binding]; other site 60480010571 beta-alpha-beta structure motif; other site 60480010572 NAD binding pocket [chemical binding]; other site 60480010573 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 60480010574 catalytic core [active] 60480010575 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 60480010576 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 60480010577 active site 60480010578 FMN binding site [chemical binding]; other site 60480010579 substrate binding site [chemical binding]; other site 60480010580 3Fe-4S cluster binding site [ion binding]; other site 60480010581 Src Homology 3 domain superfamily; Region: SH3; cl17036 60480010582 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 60480010583 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 60480010584 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480010585 Walker A/P-loop; other site 60480010586 ATP binding site [chemical binding]; other site 60480010587 Q-loop/lid; other site 60480010588 ABC transporter signature motif; other site 60480010589 Walker B; other site 60480010590 D-loop; other site 60480010591 H-loop/switch region; other site 60480010592 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 60480010593 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 60480010594 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 60480010595 binding surface 60480010596 TPR repeat; Region: TPR_11; pfam13414 60480010597 TPR motif; other site 60480010598 TPR repeat; Region: TPR_11; pfam13414 60480010599 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 60480010600 binding surface 60480010601 TPR motif; other site 60480010602 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 60480010603 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 60480010604 Nitrogen regulatory protein P-II; Region: P-II; smart00938 60480010605 Isochorismatase family; Region: Isochorismatase; pfam00857 60480010606 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 60480010607 catalytic triad [active] 60480010608 dimer interface [polypeptide binding]; other site 60480010609 conserved cis-peptide bond; other site 60480010610 LysE type translocator; Region: LysE; cl00565 60480010611 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 60480010612 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 60480010613 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480010614 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480010615 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 60480010616 dimer interface [polypeptide binding]; other site 60480010617 Alkaline phosphatase homologues; Region: alkPPc; smart00098 60480010618 active site 60480010619 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 60480010620 dimer interface [polypeptide binding]; other site 60480010621 Alkaline phosphatase homologues; Region: alkPPc; smart00098 60480010622 active site 60480010623 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 60480010624 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 60480010625 putative active site [active] 60480010626 heme pocket [chemical binding]; other site 60480010627 PAS domain; Region: PAS; smart00091 60480010628 putative active site [active] 60480010629 heme pocket [chemical binding]; other site 60480010630 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480010631 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480010632 metal binding site [ion binding]; metal-binding site 60480010633 active site 60480010634 I-site; other site 60480010635 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 60480010636 DNA-binding site [nucleotide binding]; DNA binding site 60480010637 RNA-binding motif; other site 60480010638 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 60480010639 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 60480010640 Peptidase S8 family domain, uncharacterized subfamily 3; Region: Peptidases_S8_3; cd04852 60480010641 active site 60480010642 catalytic triad [active] 60480010643 PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from...; Region: PA_subtilisin_like; cd02120 60480010644 PA/protease or protease-like domain interface [polypeptide binding]; other site 60480010645 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 60480010646 catalytic residues [active] 60480010647 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 60480010648 catalytic residues [active] 60480010649 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 60480010650 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480010651 Q-loop/lid; other site 60480010652 ABC transporter signature motif; other site 60480010653 Walker B; other site 60480010654 D-loop; other site 60480010655 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480010656 Walker A/P-loop; other site 60480010657 ATP binding site [chemical binding]; other site 60480010658 Q-loop/lid; other site 60480010659 ABC transporter signature motif; other site 60480010660 Walker B; other site 60480010661 D-loop; other site 60480010662 H-loop/switch region; other site 60480010663 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 60480010664 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 60480010665 dimer interface [polypeptide binding]; other site 60480010666 active site 60480010667 heme binding site [chemical binding]; other site 60480010668 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 60480010669 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 60480010670 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 60480010671 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 60480010672 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 60480010673 motif II; other site 60480010674 Oxygen tolerance; Region: BatD; pfam13584 60480010675 von Willebrand factor type A domain; Region: VWA_2; pfam13519 60480010676 metal ion-dependent adhesion site (MIDAS); other site 60480010677 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 60480010678 metal ion-dependent adhesion site (MIDAS); other site 60480010679 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 60480010680 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 60480010681 Protein of unknown function DUF58; Region: DUF58; pfam01882 60480010682 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 60480010683 metal ion-dependent adhesion site (MIDAS); other site 60480010684 MoxR-like ATPases [General function prediction only]; Region: COG0714 60480010685 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 60480010686 Walker A motif; other site 60480010687 ATP binding site [chemical binding]; other site 60480010688 Walker B motif; other site 60480010689 arginine finger; other site 60480010690 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 60480010691 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 60480010692 FeS/SAM binding site; other site 60480010693 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 60480010694 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 60480010695 Sulfatase; Region: Sulfatase; pfam00884 60480010696 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480010697 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480010698 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 60480010699 putative substrate binding pocket [chemical binding]; other site 60480010700 putative dimerization interface [polypeptide binding]; other site 60480010701 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 60480010702 metal ion-dependent adhesion site (MIDAS); other site 60480010703 Domain of unknown function (DUF1973); Region: DUF1973; pfam09315 60480010704 VCBS repeat; Region: VCBS_repeat; TIGR01965 60480010705 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 60480010706 HipA N-terminal domain; Region: Couple_hipA; pfam13657 60480010707 HipA-like N-terminal domain; Region: HipA_N; pfam07805 60480010708 HipA-like C-terminal domain; Region: HipA_C; pfam07804 60480010709 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 60480010710 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 60480010711 non-specific DNA binding site [nucleotide binding]; other site 60480010712 salt bridge; other site 60480010713 sequence-specific DNA binding site [nucleotide binding]; other site 60480010714 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 60480010715 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 60480010716 ring oligomerisation interface [polypeptide binding]; other site 60480010717 ATP/Mg binding site [chemical binding]; other site 60480010718 stacking interactions; other site 60480010719 hinge regions; other site 60480010720 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 60480010721 oligomerisation interface [polypeptide binding]; other site 60480010722 mobile loop; other site 60480010723 roof hairpin; other site 60480010724 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 60480010725 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 60480010726 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480010727 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480010728 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 60480010729 putative effector binding pocket; other site 60480010730 dimerization interface [polypeptide binding]; other site 60480010731 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480010732 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480010733 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 60480010734 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 60480010735 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 60480010736 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 60480010737 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 60480010738 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 60480010739 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 60480010740 DsbD alpha interface [polypeptide binding]; other site 60480010741 catalytic residues [active] 60480010742 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 60480010743 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 60480010744 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 60480010745 TrkA-N domain; Region: TrkA_N; pfam02254 60480010746 galactokinase; Provisional; Region: PRK05101 60480010747 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 60480010748 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 60480010749 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 60480010750 active site 60480010751 catalytic residues [active] 60480010752 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 60480010753 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 60480010754 NAD(P) binding site [chemical binding]; other site 60480010755 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 60480010756 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 60480010757 Leucine rich repeat; Region: LRR_8; pfam13855 60480010758 Substrate binding site [chemical binding]; other site 60480010759 Leucine rich repeat; Region: LRR_8; pfam13855 60480010760 Catalytic domain of Protein Kinases; Region: PKc; cd00180 60480010761 active site 60480010762 ATP binding site [chemical binding]; other site 60480010763 substrate binding site [chemical binding]; other site 60480010764 activation loop (A-loop); other site 60480010765 MltD lipid attachment motif; Region: MLTD_N; pfam06474 60480010766 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 60480010767 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 60480010768 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480010769 catalytic residue [active] 60480010770 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480010771 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 60480010772 Part of AAA domain; Region: AAA_19; pfam13245 60480010773 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 60480010774 AAA domain; Region: AAA_12; pfam13087 60480010775 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 60480010776 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480010777 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480010778 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480010779 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 60480010780 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 60480010781 dimer interface [polypeptide binding]; other site 60480010782 ssDNA binding site [nucleotide binding]; other site 60480010783 tetramer (dimer of dimers) interface [polypeptide binding]; other site 60480010784 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 60480010785 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480010786 putative substrate translocation pore; other site 60480010787 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 60480010788 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 60480010789 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 60480010790 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 60480010791 M28 Zn-Peptidases; Region: M28_like_2; cd05662 60480010792 Peptidase family M28; Region: Peptidase_M28; pfam04389 60480010793 metal binding site [ion binding]; metal-binding site 60480010794 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 60480010795 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 60480010796 ATP binding site [chemical binding]; other site 60480010797 Mg++ binding site [ion binding]; other site 60480010798 motif III; other site 60480010799 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 60480010800 nucleotide binding region [chemical binding]; other site 60480010801 ATP-binding site [chemical binding]; other site 60480010802 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 60480010803 putative RNA binding site [nucleotide binding]; other site 60480010804 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 60480010805 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 60480010806 active site 60480010807 motif I; other site 60480010808 motif II; other site 60480010809 rarD protein; Region: rarD; TIGR00688 60480010810 EamA-like transporter family; Region: EamA; pfam00892 60480010811 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 60480010812 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 60480010813 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 60480010814 Cytochrome c [Energy production and conversion]; Region: COG3258 60480010815 Cytochrome c; Region: Cytochrom_C; pfam00034 60480010816 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 60480010817 Cytochrome c; Region: Cytochrom_C; cl11414 60480010818 Cytochrome c; Region: Cytochrom_C; pfam00034 60480010819 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 60480010820 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 60480010821 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480010822 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480010823 transcriptional regulator SlyA; Provisional; Region: PRK03573 60480010824 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 60480010825 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 60480010826 FAD binding site [chemical binding]; other site 60480010827 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 60480010828 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 60480010829 putative catalytic residues [active] 60480010830 putative nucleotide binding site [chemical binding]; other site 60480010831 putative aspartate binding site [chemical binding]; other site 60480010832 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 60480010833 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 60480010834 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 60480010835 homodimer interface [polypeptide binding]; other site 60480010836 substrate-cofactor binding pocket; other site 60480010837 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480010838 catalytic residue [active] 60480010839 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 60480010840 dimerization interface [polypeptide binding]; other site 60480010841 DNA binding site [nucleotide binding] 60480010842 corepressor binding sites; other site 60480010843 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 60480010844 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 60480010845 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 60480010846 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 60480010847 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 60480010848 thiosulfate reductase PhsA; Provisional; Region: PRK15488 60480010849 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 60480010850 putative [Fe4-S4] binding site [ion binding]; other site 60480010851 putative molybdopterin cofactor binding site [chemical binding]; other site 60480010852 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 60480010853 putative molybdopterin cofactor binding site; other site 60480010854 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 60480010855 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 60480010856 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 60480010857 ATP binding site [chemical binding]; other site 60480010858 active site 60480010859 substrate binding site [chemical binding]; other site 60480010860 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 60480010861 putative catalytic site [active] 60480010862 putative phosphate binding site [ion binding]; other site 60480010863 putative metal binding site [ion binding]; other site 60480010864 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 60480010865 S-adenosylmethionine binding site [chemical binding]; other site 60480010866 Uncharacterized conserved protein [Function unknown]; Region: COG2968 60480010867 oxidative stress defense protein; Provisional; Region: PRK11087 60480010868 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 60480010869 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 60480010870 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 60480010871 FeS/SAM binding site; other site 60480010872 Domain of unknown function; Region: DUF331; pfam03889 60480010873 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 60480010874 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 60480010875 substrate binding pocket [chemical binding]; other site 60480010876 membrane-bound complex binding site; other site 60480010877 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 60480010878 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 60480010879 peptidase PmbA; Provisional; Region: PRK11040 60480010880 hypothetical protein; Provisional; Region: PRK05255 60480010881 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 60480010882 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 60480010883 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 60480010884 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 60480010885 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 60480010886 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 60480010887 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 60480010888 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 60480010889 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 60480010890 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480010891 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480010892 Outer membrane efflux protein; Region: OEP; pfam02321 60480010893 Outer membrane efflux protein; Region: OEP; pfam02321 60480010894 protease TldD; Provisional; Region: tldD; PRK10735 60480010895 nitrilase; Region: PLN02798 60480010896 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 60480010897 putative active site [active] 60480010898 catalytic triad [active] 60480010899 dimer interface [polypeptide binding]; other site 60480010900 TIGR02099 family protein; Region: TIGR02099 60480010901 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 60480010902 ribonuclease G; Provisional; Region: PRK11712 60480010903 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 60480010904 homodimer interface [polypeptide binding]; other site 60480010905 oligonucleotide binding site [chemical binding]; other site 60480010906 Maf-like protein; Region: Maf; pfam02545 60480010907 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 60480010908 active site 60480010909 dimer interface [polypeptide binding]; other site 60480010910 rod shape-determining protein MreD; Region: MreD; cl01087 60480010911 rod shape-determining protein MreC; Region: mreC; TIGR00219 60480010912 rod shape-determining protein MreC; Region: MreC; pfam04085 60480010913 rod shape-determining protein MreB; Provisional; Region: PRK13927 60480010914 MreB and similar proteins; Region: MreB_like; cd10225 60480010915 nucleotide binding site [chemical binding]; other site 60480010916 Mg binding site [ion binding]; other site 60480010917 putative protofilament interaction site [polypeptide binding]; other site 60480010918 RodZ interaction site [polypeptide binding]; other site 60480010919 legume lectins; Region: lectin_L-type; cl14058 60480010920 homotetramer interaction site [polypeptide binding]; other site 60480010921 homodimer interaction site [polypeptide binding]; other site 60480010922 carbohydrate binding site [chemical binding]; other site 60480010923 metal binding site [ion binding]; metal-binding site 60480010924 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 60480010925 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 60480010926 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 60480010927 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 60480010928 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 60480010929 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 60480010930 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 60480010931 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 60480010932 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 60480010933 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 60480010934 Walker A motif; other site 60480010935 ATP binding site [chemical binding]; other site 60480010936 Walker B motif; other site 60480010937 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 60480010938 TPR motif; other site 60480010939 binding surface 60480010940 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 60480010941 binding surface 60480010942 TPR motif; other site 60480010943 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 60480010944 AAA ATPase domain; Region: AAA_16; pfam13191 60480010945 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 60480010946 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 60480010947 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 60480010948 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 60480010949 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 60480010950 regulatory protein CsrD; Provisional; Region: PRK11059 60480010951 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480010952 metal binding site [ion binding]; metal-binding site 60480010953 active site 60480010954 I-site; other site 60480010955 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 60480010956 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 60480010957 Malic enzyme, N-terminal domain; Region: malic; pfam00390 60480010958 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 60480010959 putative NAD(P) binding site [chemical binding]; other site 60480010960 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 60480010961 FimV N-terminal domain; Region: FimV_core; TIGR03505 60480010962 primosome assembly protein PriA; Validated; Region: PRK05580 60480010963 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 60480010964 ATP binding site [chemical binding]; other site 60480010965 putative Mg++ binding site [ion binding]; other site 60480010966 helicase superfamily c-terminal domain; Region: HELICc; smart00490 60480010967 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 60480010968 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 60480010969 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 60480010970 active site 60480010971 HIGH motif; other site 60480010972 KMSK motif region; other site 60480010973 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 60480010974 tRNA binding surface [nucleotide binding]; other site 60480010975 anticodon binding site; other site 60480010976 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 60480010977 Sporulation related domain; Region: SPOR; pfam05036 60480010978 Cupin; Region: Cupin_6; pfam12852 60480010979 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480010980 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 60480010981 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 60480010982 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 60480010983 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 60480010984 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 60480010985 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 60480010986 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 60480010987 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 60480010988 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 60480010989 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 60480010990 uridine phosphorylase; Provisional; Region: PRK11178 60480010991 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 60480010992 Protein of unknown function (DUF465); Region: DUF465; cl01070 60480010993 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 60480010994 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 60480010995 dimer interface [polypeptide binding]; other site 60480010996 active site 60480010997 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 60480010998 catalytic residues [active] 60480010999 substrate binding site [chemical binding]; other site 60480011000 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 60480011001 Conserved TM helix; Region: TM_helix; pfam05552 60480011002 Mechanosensitive ion channel; Region: MS_channel; pfam00924 60480011003 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 60480011004 Sel1-like repeats; Region: SEL1; smart00671 60480011005 Sel1-like repeats; Region: SEL1; smart00671 60480011006 Sel1-like repeats; Region: SEL1; smart00671 60480011007 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 60480011008 Protein of unknown function (DUF3373); Region: DUF3373; pfam11853 60480011009 Mite allergen Blo t 5; Region: Blo-t-5; pfam11642 60480011010 octaheme c-type cytochrome, tetrathionate reductase family; Region: octaheme_Shew; TIGR04315 60480011011 Cytochrome c bacterial; Region: Cytochrome_cB; pfam11783 60480011012 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 60480011013 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 60480011014 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 60480011015 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 60480011016 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 60480011017 ATP binding site [chemical binding]; other site 60480011018 Mg2+ binding site [ion binding]; other site 60480011019 G-X-G motif; other site 60480011020 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 60480011021 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480011022 active site 60480011023 phosphorylation site [posttranslational modification] 60480011024 intermolecular recognition site; other site 60480011025 dimerization interface [polypeptide binding]; other site 60480011026 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 60480011027 DNA binding residues [nucleotide binding] 60480011028 dimerization interface [polypeptide binding]; other site 60480011029 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 60480011030 active site 60480011031 HslU subunit interaction site [polypeptide binding]; other site 60480011032 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 60480011033 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 60480011034 Walker A motif; other site 60480011035 ATP binding site [chemical binding]; other site 60480011036 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 60480011037 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 60480011038 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 60480011039 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 60480011040 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 60480011041 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 60480011042 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 60480011043 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 60480011044 C factor cell-cell signaling protein; Provisional; Region: PRK09009 60480011045 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 60480011046 NAD(P) binding site [chemical binding]; other site 60480011047 active site 60480011048 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 60480011049 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480011050 active site 60480011051 phosphorylation site [posttranslational modification] 60480011052 intermolecular recognition site; other site 60480011053 dimerization interface [polypeptide binding]; other site 60480011054 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480011055 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 60480011056 ATP binding site [chemical binding]; other site 60480011057 Mg2+ binding site [ion binding]; other site 60480011058 G-X-G motif; other site 60480011059 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 60480011060 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 60480011061 NADP binding site [chemical binding]; other site 60480011062 active site 60480011063 putative substrate binding site [chemical binding]; other site 60480011064 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 60480011065 metal binding site [ion binding]; metal-binding site 60480011066 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 60480011067 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 60480011068 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 60480011069 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480011070 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 60480011071 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 60480011072 DXD motif; other site 60480011073 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 60480011074 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 60480011075 active site 60480011076 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 60480011077 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 60480011078 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 60480011079 N-terminal plug; other site 60480011080 ligand-binding site [chemical binding]; other site 60480011081 Domain of unknown function (DUF386); Region: DUF386; cl01047 60480011082 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 60480011083 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 60480011084 DHHA2 domain; Region: DHHA2; pfam02833 60480011085 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 60480011086 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 60480011087 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 60480011088 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 60480011089 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 60480011090 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 60480011091 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 60480011092 active site 60480011093 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 60480011094 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 60480011095 putative active site [active] 60480011096 putative metal binding site [ion binding]; other site 60480011097 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 60480011098 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 60480011099 S-adenosylmethionine binding site [chemical binding]; other site 60480011100 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 60480011101 SCP-2 sterol transfer family; Region: SCP2; pfam02036 60480011102 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 60480011103 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 60480011104 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 60480011105 sec-independent translocase; Provisional; Region: PRK01770 60480011106 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 60480011107 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 60480011108 active site 60480011109 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 60480011110 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 60480011111 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480011112 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480011113 metal binding site [ion binding]; metal-binding site 60480011114 active site 60480011115 I-site; other site 60480011116 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 60480011117 dimer interface [polypeptide binding]; other site 60480011118 allosteric magnesium binding site [ion binding]; other site 60480011119 active site 60480011120 aspartate-rich active site metal binding site; other site 60480011121 Schiff base residues; other site 60480011122 preprotein translocase subunit SecA; Reviewed; Region: PRK13107 60480011123 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 60480011124 SEC-C motif; Region: SEC-C; pfam02810 60480011125 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 60480011126 Peptidase family M23; Region: Peptidase_M23; pfam01551 60480011127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 60480011128 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 60480011129 cell division protein FtsZ; Validated; Region: PRK09330 60480011130 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 60480011131 nucleotide binding site [chemical binding]; other site 60480011132 SulA interaction site; other site 60480011133 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 60480011134 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 60480011135 nucleotide binding site [chemical binding]; other site 60480011136 Cell division protein FtsA; Region: FtsA; pfam14450 60480011137 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 60480011138 Cell division protein FtsQ; Region: FtsQ; pfam03799 60480011139 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 60480011140 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 60480011141 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 60480011142 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 60480011143 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 60480011144 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 60480011145 active site 60480011146 homodimer interface [polypeptide binding]; other site 60480011147 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 60480011148 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 60480011149 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 60480011150 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 60480011151 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 60480011152 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 60480011153 Mg++ binding site [ion binding]; other site 60480011154 putative catalytic motif [active] 60480011155 putative substrate binding site [chemical binding]; other site 60480011156 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 60480011157 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 60480011158 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 60480011159 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 60480011160 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 60480011161 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 60480011162 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 60480011163 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 60480011164 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 60480011165 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 60480011166 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 60480011167 Cell division protein FtsL; Region: FtsL; pfam04999 60480011168 MraW methylase family; Region: Methyltransf_5; pfam01795 60480011169 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 60480011170 cell division protein MraZ; Reviewed; Region: PRK00326 60480011171 MraZ protein; Region: MraZ; pfam02381 60480011172 MraZ protein; Region: MraZ; pfam02381 60480011173 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 60480011174 glycerol kinase; Provisional; Region: glpK; PRK00047 60480011175 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 60480011176 N- and C-terminal domain interface [polypeptide binding]; other site 60480011177 active site 60480011178 MgATP binding site [chemical binding]; other site 60480011179 catalytic site [active] 60480011180 metal binding site [ion binding]; metal-binding site 60480011181 glycerol binding site [chemical binding]; other site 60480011182 homotetramer interface [polypeptide binding]; other site 60480011183 homodimer interface [polypeptide binding]; other site 60480011184 FBP binding site [chemical binding]; other site 60480011185 protein IIAGlc interface [polypeptide binding]; other site 60480011186 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 60480011187 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 60480011188 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 60480011189 substrate binding site [chemical binding]; other site 60480011190 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 60480011191 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 60480011192 substrate binding site [chemical binding]; other site 60480011193 ligand binding site [chemical binding]; other site 60480011194 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 60480011195 tartrate dehydrogenase; Region: TTC; TIGR02089 60480011196 2-isopropylmalate synthase; Validated; Region: PRK00915 60480011197 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 60480011198 active site 60480011199 catalytic residues [active] 60480011200 metal binding site [ion binding]; metal-binding site 60480011201 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 60480011202 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480011203 metal binding site [ion binding]; metal-binding site 60480011204 active site 60480011205 I-site; other site 60480011206 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 60480011207 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 60480011208 ATP binding site [chemical binding]; other site 60480011209 putative Mg++ binding site [ion binding]; other site 60480011210 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 60480011211 nucleotide binding region [chemical binding]; other site 60480011212 ATP-binding site [chemical binding]; other site 60480011213 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 60480011214 HRDC domain; Region: HRDC; pfam00570 60480011215 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 60480011216 CoenzymeA binding site [chemical binding]; other site 60480011217 subunit interaction site [polypeptide binding]; other site 60480011218 PHB binding site; other site 60480011219 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 60480011220 N-acetylglutamate synthase; Validated; Region: PRK05279 60480011221 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 60480011222 putative feedback inhibition sensing region; other site 60480011223 putative nucleotide binding site [chemical binding]; other site 60480011224 putative substrate binding site [chemical binding]; other site 60480011225 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480011226 Coenzyme A binding pocket [chemical binding]; other site 60480011227 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 60480011228 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 60480011229 hypothetical protein; Reviewed; Region: PRK00024 60480011230 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 60480011231 MPN+ (JAMM) motif; other site 60480011232 Zinc-binding site [ion binding]; other site 60480011233 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 60480011234 Flavoprotein; Region: Flavoprotein; pfam02441 60480011235 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 60480011236 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 60480011237 trimer interface [polypeptide binding]; other site 60480011238 active site 60480011239 division inhibitor protein; Provisional; Region: slmA; PRK09480 60480011240 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480011241 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480011242 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480011243 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 60480011244 GTP cyclohydrolase I; Provisional; Region: PLN03044 60480011245 active site 60480011246 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 60480011247 active site 60480011248 ribonuclease PH; Reviewed; Region: rph; PRK00173 60480011249 Ribonuclease PH; Region: RNase_PH_bact; cd11362 60480011250 hexamer interface [polypeptide binding]; other site 60480011251 active site 60480011252 hypothetical protein; Provisional; Region: PRK11820 60480011253 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 60480011254 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 60480011255 dUMP phosphatase; Provisional; Region: PRK09449 60480011256 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 60480011257 motif II; other site 60480011258 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480011259 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480011260 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 60480011261 putative effector binding pocket; other site 60480011262 dimerization interface [polypeptide binding]; other site 60480011263 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 60480011264 Major Facilitator Superfamily; Region: MFS_1; pfam07690 60480011265 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 60480011266 putative substrate translocation pore; other site 60480011267 Phosphotransferase enzyme family; Region: APH; pfam01636 60480011268 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 60480011269 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 60480011270 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 60480011271 active site 60480011272 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 60480011273 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 60480011274 catalytic site [active] 60480011275 G-X2-G-X-G-K; other site 60480011276 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 60480011277 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 60480011278 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480011279 Zn2+ binding site [ion binding]; other site 60480011280 Mg2+ binding site [ion binding]; other site 60480011281 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 60480011282 synthetase active site [active] 60480011283 NTP binding site [chemical binding]; other site 60480011284 metal binding site [ion binding]; metal-binding site 60480011285 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 60480011286 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 60480011287 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 60480011288 homotrimer interaction site [polypeptide binding]; other site 60480011289 putative active site [active] 60480011290 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 60480011291 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 60480011292 acyl-activating enzyme (AAE) consensus motif; other site 60480011293 putative AMP binding site [chemical binding]; other site 60480011294 putative active site [active] 60480011295 putative CoA binding site [chemical binding]; other site 60480011296 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 60480011297 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 60480011298 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 60480011299 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 60480011300 Histidine kinase; Region: HisKA_3; pfam07730 60480011301 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 60480011302 ATP binding site [chemical binding]; other site 60480011303 Mg2+ binding site [ion binding]; other site 60480011304 G-X-G motif; other site 60480011305 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480011306 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480011307 active site 60480011308 phosphorylation site [posttranslational modification] 60480011309 intermolecular recognition site; other site 60480011310 dimerization interface [polypeptide binding]; other site 60480011311 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 60480011312 DNA binding residues [nucleotide binding] 60480011313 dimerization interface [polypeptide binding]; other site 60480011314 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 60480011315 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 60480011316 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 60480011317 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 60480011318 Walker A motif; other site 60480011319 ATP binding site [chemical binding]; other site 60480011320 Walker B motif; other site 60480011321 arginine finger; other site 60480011322 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 60480011323 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 60480011324 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 60480011325 putative acyl-acceptor binding pocket; other site 60480011326 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 60480011327 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 60480011328 putative acyl-acceptor binding pocket; other site 60480011329 Uncharacterized conserved protein [Function unknown]; Region: COG1683 60480011330 Transcriptional regulators [Transcription]; Region: GntR; COG1802 60480011331 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 60480011332 DNA-binding site [nucleotide binding]; DNA binding site 60480011333 FCD domain; Region: FCD; pfam07729 60480011334 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 60480011335 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 60480011336 tetramer interface [polypeptide binding]; other site 60480011337 active site 60480011338 Mg2+/Mn2+ binding site [ion binding]; other site 60480011339 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 60480011340 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 60480011341 dimer interface [polypeptide binding]; other site 60480011342 active site 60480011343 citrylCoA binding site [chemical binding]; other site 60480011344 oxalacetate/citrate binding site [chemical binding]; other site 60480011345 coenzyme A binding site [chemical binding]; other site 60480011346 catalytic triad [active] 60480011347 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 60480011348 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 60480011349 substrate binding site [chemical binding]; other site 60480011350 ligand binding site [chemical binding]; other site 60480011351 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 60480011352 substrate binding site [chemical binding]; other site 60480011353 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 60480011354 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 60480011355 starch binding site [chemical binding]; other site 60480011356 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 60480011357 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 60480011358 PAS domain S-box; Region: sensory_box; TIGR00229 60480011359 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 60480011360 putative active site [active] 60480011361 heme pocket [chemical binding]; other site 60480011362 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 60480011363 PAS domain; Region: PAS_9; pfam13426 60480011364 putative active site [active] 60480011365 heme pocket [chemical binding]; other site 60480011366 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480011367 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480011368 metal binding site [ion binding]; metal-binding site 60480011369 active site 60480011370 I-site; other site 60480011371 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 60480011372 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 60480011373 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 60480011374 homodimer interface [polypeptide binding]; other site 60480011375 substrate-cofactor binding pocket; other site 60480011376 catalytic residue [active] 60480011377 Protein of unknown function (DUF1223); Region: DUF1223; pfam06764 60480011378 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; pfam07073 60480011379 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 60480011380 homotrimer interaction site [polypeptide binding]; other site 60480011381 putative active site [active] 60480011382 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 60480011383 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 60480011384 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 60480011385 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 60480011386 catalytic residues [active] 60480011387 hinge region; other site 60480011388 alpha helical domain; other site 60480011389 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 60480011390 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 60480011391 active site 60480011392 substrate binding site [chemical binding]; other site 60480011393 ATP binding site [chemical binding]; other site 60480011394 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 60480011395 Uncharacterized conserved protein [Function unknown]; Region: COG0397 60480011396 hypothetical protein; Validated; Region: PRK00029 60480011397 DsrE/DsrF-like family; Region: DrsE; cl00672 60480011398 Nitrous oxide-stimulated promoter; Region: YgbA_NO; pfam11756 60480011399 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 60480011400 putative amphipathic alpha helix; other site 60480011401 Acyltransferase family; Region: Acyl_transf_3; pfam01757 60480011402 Uncharacterized conserved protein [Function unknown]; Region: COG3339 60480011403 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 60480011404 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 60480011405 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480011406 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480011407 dimerization interface [polypeptide binding]; other site 60480011408 LysR substrate binding domain; Region: LysR_substrate; pfam03466 60480011409 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 60480011410 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 60480011411 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 60480011412 putative [4Fe-4S] binding site [ion binding]; other site 60480011413 putative molybdopterin cofactor binding site [chemical binding]; other site 60480011414 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 60480011415 molybdopterin cofactor binding site; other site 60480011416 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 60480011417 4Fe-4S binding domain; Region: Fer4; pfam00037 60480011418 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 60480011419 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 60480011420 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 60480011421 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480011422 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 60480011423 eyelet of channel; other site 60480011424 trimer interface [polypeptide binding]; other site 60480011425 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 60480011426 substrate binding site [chemical binding]; other site 60480011427 Protein of unknown function (DUF2618); Region: DUF2618; pfam10940 60480011428 ornithine decarboxylase; Provisional; Region: PRK13578 60480011429 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 60480011430 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 60480011431 homodimer interface [polypeptide binding]; other site 60480011432 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480011433 catalytic residue [active] 60480011434 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 60480011435 putrescine transporter; Provisional; Region: potE; PRK10655 60480011436 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 60480011437 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 60480011438 trimer interface [polypeptide binding]; other site 60480011439 eyelet of channel; other site 60480011440 hypothetical protein; Provisional; Region: PRK01254 60480011441 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 60480011442 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 60480011443 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 60480011444 MAPEG family; Region: MAPEG; cl09190 60480011445 Uncharacterized conserved protein [Function unknown]; Region: COG2966 60480011446 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 60480011447 Uncharacterized conserved protein [Function unknown]; Region: COG3610 60480011448 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 60480011449 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 60480011450 Conjugative relaxosome accessory transposon protein; Region: TraH; cl05580 60480011451 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 60480011452 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 60480011453 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 60480011454 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 60480011455 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 60480011456 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 60480011457 molybdopterin cofactor binding site; other site 60480011458 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_CT_DmsA-EC; cd02794 60480011459 putative molybdopterin cofactor binding site; other site 60480011460 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 60480011461 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 60480011462 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 60480011463 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 60480011464 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 60480011465 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 60480011466 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 60480011467 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 60480011468 putative SAM binding site [chemical binding]; other site 60480011469 putative homodimer interface [polypeptide binding]; other site 60480011470 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 60480011471 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 60480011472 putative ligand binding site [chemical binding]; other site 60480011473 hypothetical protein; Reviewed; Region: PRK12497 60480011474 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 60480011475 dimer interface [polypeptide binding]; other site 60480011476 active site 60480011477 outer membrane lipoprotein; Provisional; Region: PRK11023 60480011478 BON domain; Region: BON; pfam04972 60480011479 BON domain; Region: BON; pfam04972 60480011480 EamA-like transporter family; Region: EamA; pfam00892 60480011481 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 60480011482 EamA-like transporter family; Region: EamA; cl17759 60480011483 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 60480011484 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480011485 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 60480011486 dimerization interface [polypeptide binding]; other site 60480011487 substrate binding pocket [chemical binding]; other site 60480011488 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 60480011489 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 60480011490 active site 60480011491 HIGH motif; other site 60480011492 dimer interface [polypeptide binding]; other site 60480011493 KMSKS motif; other site 60480011494 phosphoglycolate phosphatase; Provisional; Region: PRK13222 60480011495 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 60480011496 motif II; other site 60480011497 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 60480011498 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 60480011499 substrate binding site [chemical binding]; other site 60480011500 hexamer interface [polypeptide binding]; other site 60480011501 metal binding site [ion binding]; metal-binding site 60480011502 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 60480011503 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 60480011504 AAA domain; Region: AAA_22; pfam13401 60480011505 Sporulation related domain; Region: SPOR; pfam05036 60480011506 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 60480011507 active site 60480011508 dimer interface [polypeptide binding]; other site 60480011509 metal binding site [ion binding]; metal-binding site 60480011510 shikimate kinase; Reviewed; Region: aroK; PRK00131 60480011511 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 60480011512 ADP binding site [chemical binding]; other site 60480011513 magnesium binding site [ion binding]; other site 60480011514 putative shikimate binding site; other site 60480011515 AMIN domain; Region: AMIN; pfam11741 60480011516 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 60480011517 Secretin and TonB N terminus short domain; Region: STN; smart00965 60480011518 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 60480011519 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 60480011520 Pilus assembly protein, PilP; Region: PilP; pfam04351 60480011521 Pilus assembly protein, PilO; Region: PilO; pfam04350 60480011522 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 60480011523 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 60480011524 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 60480011525 Competence protein A; Region: Competence_A; pfam11104 60480011526 nucleotide binding site [chemical binding]; other site 60480011527 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 60480011528 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 60480011529 Transglycosylase; Region: Transgly; pfam00912 60480011530 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 60480011531 argininosuccinate lyase; Provisional; Region: PRK04833 60480011532 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 60480011533 active sites [active] 60480011534 tetramer interface [polypeptide binding]; other site 60480011535 argininosuccinate synthase; Provisional; Region: PRK13820 60480011536 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 60480011537 ANP binding site [chemical binding]; other site 60480011538 Substrate Binding Site II [chemical binding]; other site 60480011539 Substrate Binding Site I [chemical binding]; other site 60480011540 ornithine carbamoyltransferase; Provisional; Region: PRK14805 60480011541 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 60480011542 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 60480011543 acetylglutamate kinase; Provisional; Region: PRK00942 60480011544 nucleotide binding site [chemical binding]; other site 60480011545 substrate binding site [chemical binding]; other site 60480011546 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 60480011547 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 60480011548 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 60480011549 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 60480011550 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 60480011551 competence damage-inducible protein A; Provisional; Region: PRK00549 60480011552 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 60480011553 putative MPT binding site; other site 60480011554 Competence-damaged protein; Region: CinA; pfam02464 60480011555 Helix-turn-helix domain; Region: HTH_17; pfam12728 60480011556 PBP superfamily domain; Region: PBP_like; pfam12727 60480011557 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 60480011558 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 60480011559 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 60480011560 Ferredoxin [Energy production and conversion]; Region: COG1146 60480011561 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 60480011562 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 60480011563 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 60480011564 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 60480011565 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 60480011566 [4Fe-4S] binding site [ion binding]; other site 60480011567 molybdopterin cofactor binding site; other site 60480011568 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 60480011569 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 60480011570 molybdopterin cofactor binding site; other site 60480011571 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 60480011572 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 60480011573 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 60480011574 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 60480011575 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 60480011576 [4Fe-4S] binding site [ion binding]; other site 60480011577 molybdopterin cofactor binding site; other site 60480011578 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 60480011579 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 60480011580 molybdopterin cofactor binding site; other site 60480011581 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 60480011582 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 60480011583 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 60480011584 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480011585 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 60480011586 N-terminal plug; other site 60480011587 ligand-binding site [chemical binding]; other site 60480011588 HAMP domain; Region: HAMP; pfam00672 60480011589 dimerization interface [polypeptide binding]; other site 60480011590 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480011591 dimer interface [polypeptide binding]; other site 60480011592 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 60480011593 putative CheW interface [polypeptide binding]; other site 60480011594 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 60480011595 Sodium Bile acid symporter family; Region: SBF; cl17470 60480011596 coproporphyrinogen III oxidase; Provisional; Region: PRK08629 60480011597 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 60480011598 FeS/SAM binding site; other site 60480011599 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 60480011600 Domain of unknown function (DUF4424); Region: DUF4424; pfam14415 60480011601 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 60480011602 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 60480011603 active site 60480011604 nucleophile elbow; other site 60480011605 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 60480011606 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480011607 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 60480011608 substrate binding pocket [chemical binding]; other site 60480011609 dimerization interface [polypeptide binding]; other site 60480011610 EamA-like transporter family; Region: EamA; pfam00892 60480011611 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 60480011612 EamA-like transporter family; Region: EamA; pfam00892 60480011613 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 60480011614 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480011615 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 60480011616 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480011617 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 60480011618 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480011619 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480011620 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 60480011621 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 60480011622 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 60480011623 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 60480011624 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 60480011625 metal binding site [ion binding]; metal-binding site 60480011626 putative dimer interface [polypeptide binding]; other site 60480011627 HTH domain; Region: HTH_11; cl17392 60480011628 WYL domain; Region: WYL; pfam13280 60480011629 cell division protein FtsZ; Validated; Region: PRK09330 60480011630 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 60480011631 nucleotide binding site [chemical binding]; other site 60480011632 SulA interaction site; other site 60480011633 Methyltransferase domain; Region: Methyltransf_23; pfam13489 60480011634 Methyltransferase domain; Region: Methyltransf_11; pfam08241 60480011635 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 60480011636 PAS domain; Region: PAS_9; pfam13426 60480011637 putative active site [active] 60480011638 heme pocket [chemical binding]; other site 60480011639 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480011640 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480011641 metal binding site [ion binding]; metal-binding site 60480011642 active site 60480011643 I-site; other site 60480011644 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 60480011645 DTW domain; Region: DTW; cl01221 60480011646 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 60480011647 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 60480011648 putative substrate translocation pore; other site 60480011649 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 60480011650 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480011651 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 60480011652 substrate binding pocket [chemical binding]; other site 60480011653 dimerization interface [polypeptide binding]; other site 60480011654 Cache domain; Region: Cache_1; pfam02743 60480011655 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 60480011656 dimerization interface [polypeptide binding]; other site 60480011657 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480011658 dimer interface [polypeptide binding]; other site 60480011659 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 60480011660 putative CheW interface [polypeptide binding]; other site 60480011661 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 60480011662 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 60480011663 Sel1-like repeats; Region: SEL1; smart00671 60480011664 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 60480011665 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 60480011666 putative metal binding site [ion binding]; other site 60480011667 HDOD domain; Region: HDOD; pfam08668 60480011668 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 60480011669 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 60480011670 putative transporter; Provisional; Region: PRK11021 60480011671 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 60480011672 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 60480011673 dimerization interface [polypeptide binding]; other site 60480011674 putative Zn2+ binding site [ion binding]; other site 60480011675 putative DNA binding site [nucleotide binding]; other site 60480011676 AsnC family; Region: AsnC_trans_reg; pfam01037 60480011677 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 60480011678 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 60480011679 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 60480011680 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 60480011681 cytochrome c nitrite reductase, pentaheme subunit; Region: cyt_nit_nrfB; TIGR03146 60480011682 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 60480011683 Transcriptional regulator [Transcription]; Region: LysR; COG0583 60480011684 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 60480011685 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 60480011686 dimerization interface [polypeptide binding]; other site 60480011687 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 60480011688 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 60480011689 dimer interface [polypeptide binding]; other site 60480011690 tetramer interface [polypeptide binding]; other site 60480011691 PYR/PP interface [polypeptide binding]; other site 60480011692 TPP binding site [chemical binding]; other site 60480011693 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 60480011694 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 60480011695 TPP-binding site; other site 60480011696 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 60480011697 O-succinylbenzoate synthase; Provisional; Region: PRK05105 60480011698 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 60480011699 active site 60480011700 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 60480011701 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 60480011702 acyl-activating enzyme (AAE) consensus motif; other site 60480011703 putative AMP binding site [chemical binding]; other site 60480011704 putative active site [active] 60480011705 putative CoA binding site [chemical binding]; other site 60480011706 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 60480011707 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 60480011708 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 60480011709 DNA binding residues [nucleotide binding] 60480011710 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 60480011711 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 60480011712 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 60480011713 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480011714 Walker A/P-loop; other site 60480011715 ATP binding site [chemical binding]; other site 60480011716 Q-loop/lid; other site 60480011717 ABC transporter signature motif; other site 60480011718 Walker B; other site 60480011719 D-loop; other site 60480011720 H-loop/switch region; other site 60480011721 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 60480011722 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 60480011723 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 60480011724 P loop; other site 60480011725 GTP binding site [chemical binding]; other site 60480011726 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 60480011727 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 60480011728 S-adenosylmethionine binding site [chemical binding]; other site 60480011729 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 60480011730 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 60480011731 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 60480011732 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 60480011733 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 60480011734 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480011735 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 60480011736 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 60480011737 B1 nucleotide binding pocket [chemical binding]; other site 60480011738 B2 nucleotide binding pocket [chemical binding]; other site 60480011739 CAS motifs; other site 60480011740 active site 60480011741 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 60480011742 dimerization interface [polypeptide binding]; other site 60480011743 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480011744 dimer interface [polypeptide binding]; other site 60480011745 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 60480011746 putative CheW interface [polypeptide binding]; other site 60480011747 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 60480011748 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 60480011749 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 60480011750 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 60480011751 aromatic amino acid transport protein; Region: araaP; TIGR00837 60480011752 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 60480011753 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 60480011754 putative acyl-acceptor binding pocket; other site 60480011755 LexA repressor; Validated; Region: PRK00215 60480011756 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 60480011757 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 60480011758 Catalytic site [active] 60480011759 Cell division inhibitor SulA; Region: SulA; cl01880 60480011760 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 60480011761 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 60480011762 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 60480011763 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 60480011764 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 60480011765 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 60480011766 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 60480011767 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 60480011768 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 60480011769 Subunit I/III interface [polypeptide binding]; other site 60480011770 D-pathway; other site 60480011771 Subunit I/VIIc interface [polypeptide binding]; other site 60480011772 Subunit I/IV interface [polypeptide binding]; other site 60480011773 Subunit I/II interface [polypeptide binding]; other site 60480011774 Low-spin heme (heme a) binding site [chemical binding]; other site 60480011775 Subunit I/VIIa interface [polypeptide binding]; other site 60480011776 Subunit I/VIa interface [polypeptide binding]; other site 60480011777 Dimer interface; other site 60480011778 Putative water exit pathway; other site 60480011779 Binuclear center (heme a3/CuB) [ion binding]; other site 60480011780 K-pathway; other site 60480011781 Subunit I/Vb interface [polypeptide binding]; other site 60480011782 Putative proton exit pathway; other site 60480011783 Subunit I/VIb interface; other site 60480011784 Subunit I/VIc interface [polypeptide binding]; other site 60480011785 Electron transfer pathway; other site 60480011786 Subunit I/VIIIb interface [polypeptide binding]; other site 60480011787 Subunit I/VIIb interface [polypeptide binding]; other site 60480011788 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 60480011789 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 60480011790 Subunit III/VIIa interface [polypeptide binding]; other site 60480011791 Phospholipid binding site [chemical binding]; other site 60480011792 Subunit I/III interface [polypeptide binding]; other site 60480011793 Subunit III/VIb interface [polypeptide binding]; other site 60480011794 Subunit III/VIa interface; other site 60480011795 Subunit III/Vb interface [polypeptide binding]; other site 60480011796 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 60480011797 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 60480011798 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 60480011799 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 60480011800 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 60480011801 UbiA prenyltransferase family; Region: UbiA; pfam01040 60480011802 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 60480011803 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 60480011804 Cu(I) binding site [ion binding]; other site 60480011805 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 60480011806 putative active site [active] 60480011807 putative metal binding site [ion binding]; other site 60480011808 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 60480011809 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 60480011810 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 60480011811 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 60480011812 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 60480011813 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 60480011814 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 60480011815 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 60480011816 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 60480011817 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 60480011818 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 60480011819 Sulfatase; Region: Sulfatase; pfam00884 60480011820 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 60480011821 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 60480011822 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 60480011823 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 60480011824 RNA binding site [nucleotide binding]; other site 60480011825 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 60480011826 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 60480011827 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 60480011828 osmolarity response regulator; Provisional; Region: ompR; PRK09468 60480011829 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480011830 active site 60480011831 phosphorylation site [posttranslational modification] 60480011832 intermolecular recognition site; other site 60480011833 dimerization interface [polypeptide binding]; other site 60480011834 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 60480011835 DNA binding site [nucleotide binding] 60480011836 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 60480011837 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 60480011838 dimerization interface [polypeptide binding]; other site 60480011839 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 60480011840 dimer interface [polypeptide binding]; other site 60480011841 phosphorylation site [posttranslational modification] 60480011842 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 60480011843 ATP binding site [chemical binding]; other site 60480011844 Mg2+ binding site [ion binding]; other site 60480011845 G-X-G motif; other site 60480011846 Negative regulator of septation ring formation [Cell division and chromosome partitioning]; Region: EzrA; COG4477 60480011847 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 60480011848 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 60480011849 dimerization interface [polypeptide binding]; other site 60480011850 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 60480011851 dimer interface [polypeptide binding]; other site 60480011852 putative CheW interface [polypeptide binding]; other site 60480011853 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 60480011854 catalytic triad [active] 60480011855 dimer interface [polypeptide binding]; other site 60480011856 Predicted membrane protein [Function unknown]; Region: COG3212 60480011857 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 60480011858 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 60480011859 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480011860 active site 60480011861 phosphorylation site [posttranslational modification] 60480011862 intermolecular recognition site; other site 60480011863 dimerization interface [polypeptide binding]; other site 60480011864 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 60480011865 DNA binding site [nucleotide binding] 60480011866 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 60480011867 dimer interface [polypeptide binding]; other site 60480011868 phosphorylation site [posttranslational modification] 60480011869 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 60480011870 ATP binding site [chemical binding]; other site 60480011871 Mg2+ binding site [ion binding]; other site 60480011872 G-X-G motif; other site 60480011873 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 60480011874 MASE1; Region: MASE1; cl17823 60480011875 CHASE domain; Region: CHASE; pfam03924 60480011876 PAS domain S-box; Region: sensory_box; TIGR00229 60480011877 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 60480011878 putative active site [active] 60480011879 heme pocket [chemical binding]; other site 60480011880 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 60480011881 PAS domain; Region: PAS_9; pfam13426 60480011882 putative active site [active] 60480011883 heme pocket [chemical binding]; other site 60480011884 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 60480011885 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480011886 metal binding site [ion binding]; metal-binding site 60480011887 active site 60480011888 I-site; other site 60480011889 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 60480011890 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 60480011891 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 60480011892 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 60480011893 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 60480011894 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 60480011895 D-pathway; other site 60480011896 Putative ubiquinol binding site [chemical binding]; other site 60480011897 Low-spin heme (heme b) binding site [chemical binding]; other site 60480011898 Putative water exit pathway; other site 60480011899 Binuclear center (heme o3/CuB) [ion binding]; other site 60480011900 K-pathway; other site 60480011901 Putative proton exit pathway; other site 60480011902 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 60480011903 Subunit I/III interface [polypeptide binding]; other site 60480011904 Subunit III/IV interface [polypeptide binding]; other site 60480011905 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 60480011906 protoheme IX farnesyltransferase; Provisional; Region: PRK13362 60480011907 UbiA prenyltransferase family; Region: UbiA; pfam01040 60480011908 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 60480011909 S-adenosylmethionine binding site [chemical binding]; other site 60480011910 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 60480011911 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 60480011912 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 60480011913 N-acetyl-D-glucosamine binding site [chemical binding]; other site 60480011914 catalytic residue [active] 60480011915 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 60480011916 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 60480011917 AbgT putative transporter family; Region: ABG_transport; pfam03806 60480011918 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 60480011919 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 60480011920 Protein export membrane protein; Region: SecD_SecF; cl14618 60480011921 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 60480011922 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 60480011923 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480011924 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 60480011925 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 60480011926 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 60480011927 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 60480011928 C-terminal domain interface [polypeptide binding]; other site 60480011929 GSH binding site (G-site) [chemical binding]; other site 60480011930 dimer interface [polypeptide binding]; other site 60480011931 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 60480011932 N-terminal domain interface [polypeptide binding]; other site 60480011933 dimer interface [polypeptide binding]; other site 60480011934 substrate binding pocket (H-site) [chemical binding]; other site 60480011935 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 60480011936 active site 60480011937 oligopeptidase A; Provisional; Region: PRK10911 60480011938 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 60480011939 active site 60480011940 Zn binding site [ion binding]; other site 60480011941 glutathione reductase; Validated; Region: PRK06116 60480011942 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 60480011943 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 60480011944 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 60480011945 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 60480011946 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 60480011947 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 60480011948 Na binding site [ion binding]; other site 60480011949 gamma-glutamyl kinase; Provisional; Region: PRK13402 60480011950 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 60480011951 nucleotide binding site [chemical binding]; other site 60480011952 homotetrameric interface [polypeptide binding]; other site 60480011953 putative phosphate binding site [ion binding]; other site 60480011954 putative allosteric binding site; other site 60480011955 PUA domain; Region: PUA; cl00607 60480011956 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 60480011957 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 60480011958 putative catalytic cysteine [active] 60480011959 Hypothetical protein (DUF2513); Region: DUF2513; pfam10711 60480011960 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 60480011961 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 60480011962 non-specific DNA binding site [nucleotide binding]; other site 60480011963 salt bridge; other site 60480011964 sequence-specific DNA binding site [nucleotide binding]; other site 60480011965 Domain of unknown function (DUF955); Region: DUF955; cl01076 60480011966 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 60480011967 malate synthase; Provisional; Region: PRK08951 60480011968 Predicted membrane protein [Function unknown]; Region: COG2855 60480011969 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 60480011970 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 60480011971 DNA binding residues [nucleotide binding] 60480011972 dimerization interface [polypeptide binding]; other site 60480011973 HlyD family secretion protein; Region: HlyD_2; pfam12700 60480011974 HlyD family secretion protein; Region: HlyD_3; pfam13437 60480011975 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 60480011976 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 60480011977 Paraquat-inducible protein A; Region: PqiA; pfam04403 60480011978 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 60480011979 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 60480011980 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 60480011981 Zn2+ binding site [ion binding]; other site 60480011982 Mg2+ binding site [ion binding]; other site 60480011983 Cobalt transport protein; Region: CbiQ; cl00463 60480011984 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 60480011985 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 60480011986 Walker A/P-loop; other site 60480011987 ATP binding site [chemical binding]; other site 60480011988 Q-loop/lid; other site 60480011989 ABC transporter signature motif; other site 60480011990 Walker B; other site 60480011991 D-loop; other site 60480011992 H-loop/switch region; other site 60480011993 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 60480011994 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 60480011995 Walker A/P-loop; other site 60480011996 ATP binding site [chemical binding]; other site 60480011997 Q-loop/lid; other site 60480011998 ABC transporter signature motif; other site 60480011999 Walker B; other site 60480012000 D-loop; other site 60480012001 H-loop/switch region; other site 60480012002 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 60480012003 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 60480012004 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 60480012005 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 60480012006 chorismate binding enzyme; Region: Chorismate_bind; cl10555 60480012007 hypothetical protein; Provisional; Region: PRK11212 60480012008 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 60480012009 Coenzyme A binding pocket [chemical binding]; other site 60480012010 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 60480012011 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 60480012012 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 60480012013 dimer interface [polypeptide binding]; other site 60480012014 phosphorylation site [posttranslational modification] 60480012015 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 60480012016 ATP binding site [chemical binding]; other site 60480012017 G-X-G motif; other site 60480012018 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 60480012019 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 60480012020 active site 60480012021 phosphorylation site [posttranslational modification] 60480012022 intermolecular recognition site; other site 60480012023 dimerization interface [polypeptide binding]; other site 60480012024 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 60480012025 Walker A motif; other site 60480012026 ATP binding site [chemical binding]; other site 60480012027 Walker B motif; other site 60480012028 arginine finger; other site 60480012029 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 60480012030 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 60480012031 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 60480012032 dimerization interface [polypeptide binding]; other site 60480012033 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 60480012034 dimer interface [polypeptide binding]; other site 60480012035 conserved gate region; other site 60480012036 putative PBP binding loops; other site 60480012037 ABC-ATPase subunit interface; other site 60480012038 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 60480012039 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 60480012040 Walker A/P-loop; other site 60480012041 ATP binding site [chemical binding]; other site 60480012042 Q-loop/lid; other site 60480012043 ABC transporter signature motif; other site 60480012044 Walker B; other site 60480012045 D-loop; other site 60480012046 H-loop/switch region; other site 60480012047 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 60480012048 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 60480012049 GTP binding site; other site 60480012050 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 60480012051 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 60480012052 Walker A motif; other site 60480012053 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 60480012054 dimer interface [polypeptide binding]; other site 60480012055 putative functional site; other site 60480012056 putative MPT binding site; other site 60480012057 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 60480012058 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 60480012059 FeS/SAM binding site; other site 60480012060 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 60480012061 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 60480012062 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 60480012063 DNA binding site [nucleotide binding] 60480012064 catalytic residue [active] 60480012065 H2TH interface [polypeptide binding]; other site 60480012066 putative catalytic residues [active] 60480012067 turnover-facilitating residue; other site 60480012068 intercalation triad [nucleotide binding]; other site 60480012069 8OG recognition residue [nucleotide binding]; other site 60480012070 putative reading head residues; other site 60480012071 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 60480012072 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 60480012073 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 60480012074 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 60480012075 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 60480012076 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 60480012077 Ligand binding site; other site 60480012078 Putative Catalytic site; other site 60480012079 DXD motif; other site 60480012080 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 60480012081 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 60480012082 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 60480012083 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 60480012084 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 60480012085 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 60480012086 putative NAD(P) binding site [chemical binding]; other site 60480012087 active site 60480012088 putative substrate binding site [chemical binding]; other site 60480012089 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 60480012090 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 60480012091 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 60480012092 active site 60480012093 (T/H)XGH motif; other site 60480012094 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 60480012095 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 60480012096 putative ADP-binding pocket [chemical binding]; other site 60480012097 capsule biosynthesis phosphatase; Region: EcbF-BcbF; TIGR01689 60480012098 GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule; Region: GT2_BcE_like; cd04183 60480012099 Ligand binding site; other site 60480012100 WavE lipopolysaccharide synthesis; Region: WavE; pfam07507 60480012101 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 60480012102 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 60480012103 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 60480012104 putative ADP-binding pocket [chemical binding]; other site 60480012105 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 60480012106 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 60480012107 putative active site [active] 60480012108 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 60480012109 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 60480012110 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 60480012111 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 60480012112 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 60480012113 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 60480012114 Bacterial transcriptional repressor; Region: TetR; pfam13972 60480012115 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 60480012116 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 60480012117 substrate-cofactor binding pocket; other site 60480012118 pyridoxal 5'-phosphate binding site [chemical binding]; other site 60480012119 catalytic residue [active] 60480012120 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 60480012121 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 60480012122 NAD(P) binding site [chemical binding]; other site 60480012123 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 60480012124 active site residue [active] 60480012125 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 60480012126 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 60480012127 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 60480012128 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 60480012129 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 60480012130 conserved cys residue [active] 60480012131 DNA polymerase I; Provisional; Region: PRK05755 60480012132 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 60480012133 active site 60480012134 metal binding site 1 [ion binding]; metal-binding site 60480012135 putative 5' ssDNA interaction site; other site 60480012136 metal binding site 3; metal-binding site 60480012137 metal binding site 2 [ion binding]; metal-binding site 60480012138 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 60480012139 putative DNA binding site [nucleotide binding]; other site 60480012140 putative metal binding site [ion binding]; other site 60480012141 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 60480012142 active site 60480012143 catalytic site [active] 60480012144 substrate binding site [chemical binding]; other site 60480012145 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 60480012146 active site 60480012147 DNA binding site [nucleotide binding] 60480012148 catalytic site [active] 60480012149 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 60480012150 G1 box; other site 60480012151 GTP/Mg2+ binding site [chemical binding]; other site 60480012152 Switch I region; other site 60480012153 G2 box; other site 60480012154 G3 box; other site 60480012155 Switch II region; other site 60480012156 G4 box; other site 60480012157 G5 box; other site 60480012158 Cytochrome c553 [Energy production and conversion]; Region: COG2863 60480012159 Cytochrome c; Region: Cytochrom_C; cl11414 60480012160 Methyltransferase domain; Region: Methyltransf_12; pfam08242 60480012161 Methyltransferase domain; Region: Methyltransf_23; pfam13489 60480012162 Der GTPase activator (YihI); Region: YihI; pfam04220 60480012163 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 60480012164 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 60480012165 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 60480012166 FeS/SAM binding site; other site 60480012167 HemN C-terminal domain; Region: HemN_C; pfam06969 60480012168 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 60480012169 adenosine deaminase; Provisional; Region: PRK09358 60480012170 active site 60480012171 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 60480012172 lysophospholipase L2; Provisional; Region: PRK10749 60480012173 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 60480012174 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 60480012175 PAS fold; Region: PAS_3; pfam08447 60480012176 putative active site [active] 60480012177 heme pocket [chemical binding]; other site 60480012178 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 60480012179 metal binding site [ion binding]; metal-binding site 60480012180 I-site; other site 60480012181 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 60480012182 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 60480012183 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 60480012184 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 60480012185 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 60480012186 substrate binding site [chemical binding]; other site 60480012187 oxyanion hole (OAH) forming residues; other site 60480012188 trimer interface [polypeptide binding]; other site 60480012189 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 60480012190 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 60480012191 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 60480012192 glutaminase active site [active] 60480012193 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 60480012194 dimer interface [polypeptide binding]; other site 60480012195 active site 60480012196 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 60480012197 dimer interface [polypeptide binding]; other site 60480012198 active site 60480012199 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 60480012200 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 60480012201 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 60480012202 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 60480012203 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 60480012204 N-terminal plug; other site 60480012205 ligand-binding site [chemical binding]; other site 60480012206 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 60480012207 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 60480012208 Substrate binding site; other site 60480012209 Mg++ binding site; other site 60480012210 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 60480012211 active site 60480012212 substrate binding site [chemical binding]; other site 60480012213 CoA binding site [chemical binding]; other site 60480012214 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 60480012215 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 60480012216 gamma subunit interface [polypeptide binding]; other site 60480012217 epsilon subunit interface [polypeptide binding]; other site 60480012218 LBP interface [polypeptide binding]; other site 60480012219 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 60480012220 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 60480012221 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 60480012222 alpha subunit interaction interface [polypeptide binding]; other site 60480012223 Walker A motif; other site 60480012224 ATP binding site [chemical binding]; other site 60480012225 Walker B motif; other site 60480012226 inhibitor binding site; inhibition site 60480012227 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 60480012228 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 60480012229 core domain interface [polypeptide binding]; other site 60480012230 delta subunit interface [polypeptide binding]; other site 60480012231 epsilon subunit interface [polypeptide binding]; other site 60480012232 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 60480012233 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 60480012234 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 60480012235 beta subunit interaction interface [polypeptide binding]; other site 60480012236 Walker A motif; other site 60480012237 ATP binding site [chemical binding]; other site 60480012238 Walker B motif; other site 60480012239 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 60480012240 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 60480012241 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 60480012242 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 60480012243 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 60480012244 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 60480012245 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 60480012246 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 60480012247 F0F1 ATP synthase subunit I; Validated; Region: PRK05760 60480012248 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 60480012249 ParB-like nuclease domain; Region: ParBc; pfam02195 60480012250 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 60480012251 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 60480012252 P-loop; other site 60480012253 Magnesium ion binding site [ion binding]; other site 60480012254 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 60480012255 Magnesium ion binding site [ion binding]; other site 60480012256 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 60480012257 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 60480012258 S-adenosylmethionine binding site [chemical binding]; other site 60480012259 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 60480012260 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 60480012261 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 60480012262 FMN-binding protein MioC; Provisional; Region: PRK09004 60480012263 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 60480012264 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 60480012265 POT family; Region: PTR2; cl17359 60480012266 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 60480012267 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 60480012268 trmE is a tRNA modification GTPase; Region: trmE; cd04164 60480012269 G1 box; other site 60480012270 GTP/Mg2+ binding site [chemical binding]; other site 60480012271 Switch I region; other site 60480012272 G2 box; other site 60480012273 Switch II region; other site 60480012274 G3 box; other site 60480012275 G4 box; other site 60480012276 G5 box; other site 60480012277 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 60480012278 membrane protein insertase; Provisional; Region: PRK01318 60480012279 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 60480012280 Haemolytic domain; Region: Haemolytic; pfam01809 60480012281 ribonuclease P; Reviewed; Region: rnpA; PRK01732 60480012282 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399