-- dump date 20120504_143118 -- class Genbank::misc_feature -- table misc_feature_note -- id note 159087000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 159087000002 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 159087000003 Walker A motif; other site 159087000004 ATP binding site [chemical binding]; other site 159087000005 Walker B motif; other site 159087000006 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000007 arginine finger; other site 159087000008 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 159087000009 DnaA box-binding interface [nucleotide binding]; other site 159087000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 159087000011 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 159087000012 putative DNA binding surface [nucleotide binding]; other site 159087000013 dimer interface [polypeptide binding]; other site 159087000014 beta-clamp/clamp loader binding surface; other site 159087000015 beta-clamp/translesion DNA polymerase binding surface; other site 159087000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 159087000017 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 159087000018 ATP binding site [chemical binding]; other site 159087000019 Mg2+ binding site [ion binding]; other site 159087000020 G-X-G motif; other site 159087000021 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 159087000022 anchoring element; other site 159087000023 dimer interface [polypeptide binding]; other site 159087000024 ATP binding site [chemical binding]; other site 159087000025 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 159087000026 active site 159087000027 putative metal-binding site [ion binding]; other site 159087000028 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 159087000029 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 159087000030 HIT family signature motif; other site 159087000031 catalytic residue [active] 159087000032 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 159087000033 dimerization interface [polypeptide binding]; other site 159087000034 putative tRNAtyr binding site [nucleotide binding]; other site 159087000035 putative active site [active] 159087000036 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 159087000037 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087000038 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000039 active site 159087000040 phosphorylation site [posttranslational modification] 159087000041 intermolecular recognition site; other site 159087000042 dimerization interface [polypeptide binding]; other site 159087000043 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087000044 Zn2+ binding site [ion binding]; other site 159087000045 Mg2+ binding site [ion binding]; other site 159087000046 PAS domain S-box; Region: sensory_box; TIGR00229 159087000047 PAS domain S-box; Region: sensory_box; TIGR00229 159087000048 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 159087000049 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 159087000050 ApbE family; Region: ApbE; cl00643 159087000051 glutathione synthetase; Provisional; Region: PRK05246 159087000052 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 159087000053 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087000054 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 159087000055 Glutamate-cysteine ligase; Region: GshA; pfam08886 159087000056 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000057 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000058 active site 159087000059 phosphorylation site [posttranslational modification] 159087000060 intermolecular recognition site; other site 159087000061 dimerization interface [polypeptide binding]; other site 159087000062 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 159087000063 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000064 Walker A/P-loop; other site 159087000065 ATP binding site [chemical binding]; other site 159087000066 Q-loop/lid; other site 159087000067 ABC transporter signature motif; other site 159087000068 Walker B; other site 159087000069 D-loop; other site 159087000070 H-loop/switch region; other site 159087000071 ABC transporter; Region: ABC_tran_2; pfam12848 159087000072 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087000073 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 159087000074 putative hydrophobic ligand binding site [chemical binding]; other site 159087000075 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 159087000076 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 159087000077 RNA binding surface [nucleotide binding]; other site 159087000078 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 159087000079 active site 159087000080 uracil binding [chemical binding]; other site 159087000081 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087000082 Helix-turn-helix domains; Region: HTH; cl00088 159087000083 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 159087000084 dimerization interface [polypeptide binding]; other site 159087000085 DNA topoisomerase III; Validated; Region: PRK08173 159087000086 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 159087000087 active site 159087000088 putative interdomain interaction site [polypeptide binding]; other site 159087000089 putative metal-binding site [ion binding]; other site 159087000090 putative nucleotide binding site [chemical binding]; other site 159087000091 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 159087000092 domain I; other site 159087000093 DNA binding groove [nucleotide binding] 159087000094 phosphate binding site [ion binding]; other site 159087000095 domain II; other site 159087000096 domain III; other site 159087000097 nucleotide binding site [chemical binding]; other site 159087000098 catalytic site [active] 159087000099 domain IV; other site 159087000100 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 159087000101 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 159087000102 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 159087000103 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; cl00234 159087000104 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 159087000105 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 159087000106 putative active site [active] 159087000107 substrate binding site [chemical binding]; other site 159087000108 putative cosubstrate binding site; other site 159087000109 catalytic site [active] 159087000110 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 159087000111 substrate binding site [chemical binding]; other site 159087000112 Peptidase family M48; Region: Peptidase_M48; cl12018 159087000113 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 159087000114 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 159087000115 conserved cys residue [active] 159087000116 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 159087000117 S1/P1 Nuclease; Region: S1-P1_nuclease; pfam02265 159087000118 16S rRNA methyltransferase B; Provisional; Region: PRK10901 159087000119 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 159087000120 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; cl12011 159087000121 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 159087000122 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 159087000123 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 159087000124 dimerization interface [polypeptide binding]; other site 159087000125 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 159087000126 dimer interface [polypeptide binding]; other site 159087000127 phosphorylation site [posttranslational modification] 159087000128 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 159087000129 ATP binding site [chemical binding]; other site 159087000130 Mg2+ binding site [ion binding]; other site 159087000131 G-X-G motif; other site 159087000132 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087000133 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000134 active site 159087000135 phosphorylation site [posttranslational modification] 159087000136 intermolecular recognition site; other site 159087000137 dimerization interface [polypeptide binding]; other site 159087000138 Helix-turn-helix domains; Region: HTH; cl00088 159087000139 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 159087000140 substrate binding site [chemical binding]; other site 159087000141 active site 159087000142 primosome assembly protein PriA; Validated; Region: PRK05580 159087000143 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 159087000144 ATP binding site [chemical binding]; other site 159087000145 putative Mg++ binding site [ion binding]; other site 159087000146 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000147 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 159087000148 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087000149 putative substrate translocation pore; other site 159087000150 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 159087000151 MOSC domain; Region: MOSC; pfam03473 159087000152 fructokinase; Reviewed; Region: PRK09557 159087000153 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 159087000154 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 159087000155 PAS domain S-box; Region: sensory_box; TIGR00229 159087000156 PAS domain S-box; Region: sensory_box; TIGR00229 159087000157 PAS domain S-box; Region: sensory_box; TIGR00229 159087000158 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 159087000159 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 159087000160 Cupin domain; Region: Cupin_2; cl09118 159087000161 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 159087000162 active site 159087000163 metal binding site [ion binding]; metal-binding site 159087000164 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 159087000165 FAD binding domain; Region: FAD_binding_4; pfam01565 159087000166 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 159087000167 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 159087000168 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 159087000169 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 159087000170 5-methyltetrahydrofolate--homocysteine methyltransferase; Region: metH; TIGR02082 159087000171 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 159087000172 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 159087000173 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 159087000174 active site residue [active] 159087000175 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 159087000176 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 159087000177 putative substrate translocation pore; other site 159087000178 Mg chelatase-related protein; Region: TIGR00368 159087000179 Membrane fusogenic activity; Region: BMFP; cl01115 159087000180 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 159087000181 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087000182 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 159087000183 Isochorismatase family; Region: Isochorismatase; pfam00857 159087000184 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 159087000185 catalytic triad [active] 159087000186 dimer interface [polypeptide binding]; other site 159087000187 conserved cis-peptide bond; other site 159087000188 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 159087000189 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087000190 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 159087000191 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 159087000192 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 159087000193 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087000194 metal binding site [ion binding]; metal-binding site 159087000195 active site 159087000196 I-site; other site 159087000197 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 159087000198 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087000199 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087000200 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 159087000201 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 159087000202 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087000203 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000204 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087000205 ABC transporter; Region: ABC_tran_2; pfam12848 159087000206 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087000207 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 159087000208 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087000209 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087000210 Zn2+ binding site [ion binding]; other site 159087000211 Mg2+ binding site [ion binding]; other site 159087000212 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 159087000213 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 159087000214 minor groove reading motif; other site 159087000215 helix-hairpin-helix signature motif; other site 159087000216 substrate binding pocket [chemical binding]; other site 159087000217 active site 159087000218 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 159087000219 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 159087000220 DNA binding and oxoG recognition site [nucleotide binding] 159087000221 Flavin Reductases; Region: FlaRed; cl00801 159087000222 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 159087000223 aromatic acid decarboxylase; Validated; Region: PRK05920 159087000224 Flavoprotein; Region: Flavoprotein; cl08021 159087000225 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; cl01973 159087000226 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 159087000227 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 159087000228 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000229 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 159087000230 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 159087000231 metal binding site [ion binding]; metal-binding site 159087000232 putative dimer interface [polypeptide binding]; other site 159087000233 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 159087000234 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 159087000235 urea carboxylase; Region: urea_carbox; TIGR02712 159087000236 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087000237 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087000238 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 159087000239 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 159087000240 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 159087000241 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 159087000242 carboxyltransferase (CT) interaction site; other site 159087000243 biotinylation site [posttranslational modification]; other site 159087000244 allophanate hydrolase; Provisional; Region: PRK08186 159087000245 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 159087000246 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 159087000247 Uncharacterised protein family (UPF0156); Region: RHH_2; cl01448 159087000248 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 159087000249 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 159087000250 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 159087000251 Creatinine amidohydrolase; Region: Creatininase; cl00618 159087000252 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 159087000253 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 159087000254 dimer interface [polypeptide binding]; other site 159087000255 conserved gate region; other site 159087000256 putative PBP binding loops; other site 159087000257 ABC-ATPase subunit interface; other site 159087000258 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087000259 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087000260 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 159087000261 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 159087000262 active site 159087000263 catalytic residues [active] 159087000264 metal binding site [ion binding]; metal-binding site 159087000265 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 159087000266 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087000267 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 159087000268 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087000269 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087000270 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 159087000271 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 159087000272 carboxyltransferase (CT) interaction site; other site 159087000273 biotinylation site [posttranslational modification]; other site 159087000274 enoyl-CoA hydratase; Provisional; Region: PRK05995 159087000275 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 159087000276 substrate binding site [chemical binding]; other site 159087000277 oxyanion hole (OAH) forming residues; other site 159087000278 trimer interface [polypeptide binding]; other site 159087000279 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 159087000280 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 159087000281 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 159087000282 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 159087000283 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 159087000284 putative catalytic residue [active] 159087000285 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 159087000286 putative metal binding site [ion binding]; other site 159087000287 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 159087000288 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087000289 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087000290 active site 159087000291 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 159087000292 EamA-like transporter family; Region: EamA; cl01037 159087000293 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 159087000294 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 159087000295 dimer interface [polypeptide binding]; other site 159087000296 active site 159087000297 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 159087000298 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 159087000299 isovaleryl-CoA dehydrogenase; Region: PLN02519 159087000300 substrate binding site [chemical binding]; other site 159087000301 FAD binding site [chemical binding]; other site 159087000302 catalytic base [active] 159087000303 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 159087000304 CoenzymeA binding site [chemical binding]; other site 159087000305 subunit interaction site [polypeptide binding]; other site 159087000306 PHB binding site; other site 159087000307 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 159087000308 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 159087000309 DNA binding residues [nucleotide binding] 159087000310 putative dimer interface [polypeptide binding]; other site 159087000311 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 159087000312 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087000313 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 159087000314 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 159087000315 Ubiquitin-like proteins; Region: UBQ; cl00155 159087000316 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087000317 PAS fold; Region: PAS_4; pfam08448 159087000318 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 159087000319 SCP-2 sterol transfer family; Region: SCP2; cl01225 159087000320 Peptidase family U32; Region: Peptidase_U32; cl03113 159087000321 Peptidase family U32; Region: Peptidase_U32; cl03113 159087000322 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087000323 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000324 active site 159087000325 phosphorylation site [posttranslational modification] 159087000326 intermolecular recognition site; other site 159087000327 dimerization interface [polypeptide binding]; other site 159087000328 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 159087000329 Sporulation related domain; Region: SPOR; cl10051 159087000330 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 159087000331 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 159087000332 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 159087000333 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087000334 rod shape-determining protein MreD; Region: MreD; cl01087 159087000335 rod shape-determining protein MreC; Provisional; Region: PRK13922 159087000336 Protein of unknown function (DUF837); Region: DUF837; pfam05769 159087000337 rod shape-determining protein MreC; Region: MreC; pfam04085 159087000338 rod shape-determining protein MreB; Provisional; Region: PRK13927 159087000339 hypothetical protein; Provisional; Region: PRK10039 159087000340 Cell division protein FtsA; Region: FtsA; cl11496 159087000341 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 159087000342 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 159087000343 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 159087000344 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit; Region: gatB; TIGR00133 159087000345 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087000346 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 159087000347 putative active site [active] 159087000348 putative DNA binding site [nucleotide binding]; other site 159087000349 putative phosphate binding site [ion binding]; other site 159087000350 putative catalytic site [active] 159087000351 metal binding site A [ion binding]; metal-binding site 159087000352 putative AP binding site [nucleotide binding]; other site 159087000353 putative metal binding site B [ion binding]; other site 159087000354 CsbD-like; Region: CsbD; cl01888 159087000355 Protein of unknown function (DUF1469); Region: DUF1469; cl12095 159087000356 YqjK-like protein; Region: YqjK; pfam13997 159087000357 AmpG-related permease; Region: 2A0125; TIGR00901 159087000358 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 159087000359 S-adenosylmethionine binding site [chemical binding]; other site 159087000360 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087000361 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 159087000362 PilZ domain; Region: PilZ; cl01260 159087000363 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 159087000364 N-terminal plug; other site 159087000365 ligand-binding site [chemical binding]; other site 159087000366 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 159087000367 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 159087000368 dimerization interface [polypeptide binding]; other site 159087000369 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087000370 metal binding site [ion binding]; metal-binding site 159087000371 active site 159087000372 I-site; other site 159087000373 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 159087000374 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 159087000375 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087000376 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 159087000377 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 159087000378 cobalamin binding residues [chemical binding]; other site 159087000379 putative BtuC binding residues; other site 159087000380 dimer interface [polypeptide binding]; other site 159087000381 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 159087000382 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 159087000383 cobalamin binding residues [chemical binding]; other site 159087000384 putative BtuC binding residues; other site 159087000385 dimer interface [polypeptide binding]; other site 159087000386 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 159087000387 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 159087000388 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087000389 homodimer interface [polypeptide binding]; other site 159087000390 catalytic residue [active] 159087000391 CobD/Cbib protein; Region: CobD_Cbib; cl00561 159087000392 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 159087000393 putative FMN binding site [chemical binding]; other site 159087000394 cobyric acid synthase; Provisional; Region: PRK00784 159087000395 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000396 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000397 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 159087000398 catalytic triad [active] 159087000399 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000400 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000401 active site 159087000402 phosphorylation site [posttranslational modification] 159087000403 intermolecular recognition site; other site 159087000404 dimerization interface [polypeptide binding]; other site 159087000405 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087000406 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000407 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 159087000408 ATP binding site [chemical binding]; other site 159087000409 Mg2+ binding site [ion binding]; other site 159087000410 G-X-G motif; other site 159087000411 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 159087000412 homotrimer interface [polypeptide binding]; other site 159087000413 Walker A motif; other site 159087000414 GTP binding site [chemical binding]; other site 159087000415 Walker B motif; other site 159087000416 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 159087000417 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 159087000418 putative dimer interface [polypeptide binding]; other site 159087000419 active site pocket [active] 159087000420 putative cataytic base [active] 159087000421 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 159087000422 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 159087000423 catalytic core [active] 159087000424 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000425 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 159087000426 putative active site [active] 159087000427 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087000428 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 159087000429 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 159087000430 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 159087000431 Walker A/P-loop; other site 159087000432 ATP binding site [chemical binding]; other site 159087000433 Q-loop/lid; other site 159087000434 ABC transporter signature motif; other site 159087000435 Walker B; other site 159087000436 D-loop; other site 159087000437 H-loop/switch region; other site 159087000438 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087000439 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087000440 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 159087000441 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 159087000442 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000443 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 159087000444 putative active site [active] 159087000445 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087000446 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000447 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 159087000448 putative active site [active] 159087000449 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087000450 O-Antigen ligase; Region: Wzy_C; cl04850 159087000451 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000452 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 159087000453 putative active site [active] 159087000454 DNA polymerase I; Provisional; Region: PRK05755 159087000455 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 159087000456 active site 159087000457 metal binding site 1 [ion binding]; metal-binding site 159087000458 putative 5' ssDNA interaction site; other site 159087000459 metal binding site 3; metal-binding site 159087000460 metal binding site 2 [ion binding]; metal-binding site 159087000461 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 159087000462 putative DNA binding site [nucleotide binding]; other site 159087000463 putative metal binding site [ion binding]; other site 159087000464 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 159087000465 active site 159087000466 substrate binding site [chemical binding]; other site 159087000467 catalytic site [active] 159087000468 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 159087000469 active site 159087000470 DNA binding site [nucleotide binding] 159087000471 catalytic site [active] 159087000472 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 159087000473 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 159087000474 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; cl15691 159087000475 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 159087000476 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 159087000477 active site 159087000478 (T/H)XGH motif; other site 159087000479 Domain of unknown function DUF143; Region: DUF143; cl00519 159087000480 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 159087000481 Maf-like protein; Region: Maf; pfam02545 159087000482 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 159087000483 active site 159087000484 dimer interface [polypeptide binding]; other site 159087000485 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 159087000486 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000487 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 159087000488 non-ribosomal peptide synthetase terminal domain of unknown function; Region: NRPS_term_dom; TIGR02353 159087000489 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 159087000490 putative trimer interface [polypeptide binding]; other site 159087000491 putative CoA binding site [chemical binding]; other site 159087000492 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 159087000493 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 159087000494 putative trimer interface [polypeptide binding]; other site 159087000495 putative CoA binding site [chemical binding]; other site 159087000496 enoyl-CoA hydratase; Provisional; Region: PRK05862 159087000497 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 159087000498 substrate binding site [chemical binding]; other site 159087000499 oxyanion hole (OAH) forming residues; other site 159087000500 trimer interface [polypeptide binding]; other site 159087000501 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 159087000502 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 159087000503 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000504 OpgC protein; Region: OpgC_C; cl00792 159087000505 Peptidase family U32; Region: Peptidase_U32; cl03113 159087000506 ribonuclease G; Provisional; Region: PRK11712 159087000507 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 159087000508 homodimer interface [polypeptide binding]; other site 159087000509 oligonucleotide binding site [chemical binding]; other site 159087000510 Dienelactone hydrolase family; Region: DLH; pfam01738 159087000511 Thiamine pyrophosphokinase; Region: TPK; cl08415 159087000512 dimerization interface [polypeptide binding]; other site 159087000513 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 159087000514 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 159087000515 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 159087000516 FAD binding site [chemical binding]; other site 159087000517 hemolysin TlyA family protein; Region: tly; TIGR00478 159087000518 Membrane protein of unknown function; Region: DUF360; cl00850 159087000519 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 159087000520 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and...; Region: AdoHcyase; cd00401 159087000521 oligomerization interface [polypeptide binding]; other site 159087000522 active site 159087000523 NAD+ binding site [chemical binding]; other site 159087000524 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087000525 S-adenosylmethionine synthetase; Validated; Region: PRK05250 159087000526 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 159087000527 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 159087000528 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 159087000529 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 159087000530 putative acyl-acceptor binding pocket; other site 159087000531 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 159087000532 putative acyl-acceptor binding pocket; other site 159087000533 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 159087000534 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087000535 Coenzyme A binding pocket [chemical binding]; other site 159087000536 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 159087000537 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 159087000538 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 159087000539 Protein of unknown function, DUF484; Region: DUF484; cl01228 159087000540 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 159087000541 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 159087000542 DNA binding site [nucleotide binding] 159087000543 Int/Topo IB signature motif; other site 159087000544 active site 159087000545 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 159087000546 PUA domain; Region: PUA; cl00607 159087000547 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; cl12011 159087000548 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 159087000549 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 159087000550 putative ligand binding site [chemical binding]; other site 159087000551 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087000552 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000553 Walker A/P-loop; other site 159087000554 ATP binding site [chemical binding]; other site 159087000555 Q-loop/lid; other site 159087000556 ABC transporter signature motif; other site 159087000557 Walker B; other site 159087000558 D-loop; other site 159087000559 H-loop/switch region; other site 159087000560 Translocation protein Sec62; Region: Sec62; cl02170 159087000561 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 159087000562 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 159087000563 active site 159087000564 HslU subunit interaction site [polypeptide binding]; other site 159087000565 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 159087000566 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 159087000567 Walker A motif; other site 159087000568 ATP binding site [chemical binding]; other site 159087000569 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000570 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 159087000571 Membrane transport protein; Region: Mem_trans; cl09117 159087000572 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 159087000573 RNA binding surface [nucleotide binding]; other site 159087000574 diaminopimelate decarboxylase; Region: lysA; TIGR01048 159087000575 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 159087000576 active site 159087000577 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087000578 substrate binding site [chemical binding]; other site 159087000579 catalytic residues [active] 159087000580 dimer interface [polypeptide binding]; other site 159087000581 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 in...; Region: Frataxin; cl00238 159087000582 putative iron binding site [ion binding]; other site 159087000583 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 159087000584 Transglycosylase; Region: Transgly; cl07896 159087000585 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087000586 Cell division protein FtsA; Region: FtsA; cl11496 159087000587 Competence protein A; Region: Competence_A; pfam11104 159087000588 Cell division protein FtsA; Region: FtsA; cl11496 159087000589 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 159087000590 Pilus assembly protein, PilO; Region: PilO; cl01234 159087000591 Pilus assembly protein, PilP; Region: PilP; cl01235 159087000592 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 159087000593 Secretin and TonB N terminus short domain; Region: STN; cl06624 159087000594 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 159087000595 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087000596 shikimate kinase; Reviewed; Region: aroK; PRK00131 159087000597 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 159087000598 ADP binding site [chemical binding]; other site 159087000599 magnesium binding site [ion binding]; other site 159087000600 putative shikimate binding site; other site 159087000601 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 159087000602 active site 159087000603 dimer interface [polypeptide binding]; other site 159087000604 metal binding site [ion binding]; metal-binding site 159087000605 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 159087000606 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 159087000607 active site 159087000608 dimer interface [polypeptide binding]; other site 159087000609 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 159087000610 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 159087000611 active site 159087000612 FMN binding site [chemical binding]; other site 159087000613 substrate binding site [chemical binding]; other site 159087000614 3Fe-4S cluster binding site [ion binding]; other site 159087000615 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 159087000616 domain interface; other site 159087000617 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 159087000618 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 159087000619 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 159087000620 Substrate binding site; other site 159087000621 Mg++ binding site; other site 159087000622 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 159087000623 active site 159087000624 substrate binding site [chemical binding]; other site 159087000625 CoA binding site [chemical binding]; other site 159087000626 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so...; Region: EF-G_bact; cd04170 159087000627 elongation factor G; Reviewed; Region: PRK12740 159087000628 G1 box; other site 159087000629 putative GEF interaction site [polypeptide binding]; other site 159087000630 GTP/Mg2+ binding site [chemical binding]; other site 159087000631 Switch I region; other site 159087000632 G2 box; other site 159087000633 G3 box; other site 159087000634 Switch II region; other site 159087000635 G4 box; other site 159087000636 G5 box; other site 159087000637 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 159087000638 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 159087000639 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 159087000640 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 159087000641 putative active site [active] 159087000642 heme pocket [chemical binding]; other site 159087000643 Cache domain; Region: Cache_1; pfam02743 159087000644 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 159087000645 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 159087000646 dimer interface [polypeptide binding]; other site 159087000647 phosphorylation site [posttranslational modification] 159087000648 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 159087000649 ATP binding site [chemical binding]; other site 159087000650 Mg2+ binding site [ion binding]; other site 159087000651 G-X-G motif; other site 159087000652 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000653 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000654 active site 159087000655 phosphorylation site [posttranslational modification] 159087000656 intermolecular recognition site; other site 159087000657 dimerization interface [polypeptide binding]; other site 159087000658 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000659 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000660 active site 159087000661 phosphorylation site [posttranslational modification] 159087000662 intermolecular recognition site; other site 159087000663 dimerization interface [polypeptide binding]; other site 159087000664 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087000665 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000666 active site 159087000667 phosphorylation site [posttranslational modification] 159087000668 intermolecular recognition site; other site 159087000669 dimerization interface [polypeptide binding]; other site 159087000670 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 159087000671 DNA binding site [nucleotide binding] 159087000672 PAS domain S-box; Region: sensory_box; TIGR00229 159087000673 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 159087000674 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; cl00075 159087000675 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 159087000676 acyl-CoA synthetase; Validated; Region: PRK08162 159087000677 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000678 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000679 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 159087000680 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 159087000681 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087000682 active site 159087000683 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 159087000684 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 159087000685 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087000686 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 159087000687 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 159087000688 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 159087000689 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087000690 metal binding site [ion binding]; metal-binding site 159087000691 active site 159087000692 I-site; other site 159087000693 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 159087000694 Walker A motif; other site 159087000695 ATP binding site [chemical binding]; other site 159087000696 Walker B motif; other site 159087000697 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 159087000698 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 159087000699 dimer interface [polypeptide binding]; other site 159087000700 phosphorylation site [posttranslational modification] 159087000701 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 159087000702 ATP binding site [chemical binding]; other site 159087000703 Mg2+ binding site [ion binding]; other site 159087000704 G-X-G motif; other site 159087000705 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000706 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000707 active site 159087000708 phosphorylation site [posttranslational modification] 159087000709 intermolecular recognition site; other site 159087000710 dimerization interface [polypeptide binding]; other site 159087000711 Sulfatase; Region: Sulfatase; cl10460 159087000712 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 159087000713 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 159087000714 phosphatidylinositol kinase; Provisional; Region: PTZ00303 159087000715 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 159087000716 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 159087000717 putative active site [active] 159087000718 catalytic site [active] 159087000719 putative metal binding site [ion binding]; other site 159087000720 Integral membrane protein TerC family; Region: TerC; cl10468 159087000721 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 159087000722 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000723 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 159087000724 dimerization interface [polypeptide binding]; other site 159087000725 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 159087000726 dimer interface [polypeptide binding]; other site 159087000727 phosphorylation site [posttranslational modification] 159087000728 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 159087000729 ATP binding site [chemical binding]; other site 159087000730 Mg2+ binding site [ion binding]; other site 159087000731 G-X-G motif; other site 159087000732 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000733 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000734 active site 159087000735 phosphorylation site [posttranslational modification] 159087000736 intermolecular recognition site; other site 159087000737 dimerization interface [polypeptide binding]; other site 159087000738 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000739 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000740 active site 159087000741 phosphorylation site [posttranslational modification] 159087000742 intermolecular recognition site; other site 159087000743 dimerization interface [polypeptide binding]; other site 159087000744 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 159087000745 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087000746 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087000747 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 159087000748 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087000749 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087000750 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 159087000751 B12 binding site [chemical binding]; other site 159087000752 cobalt ligand [ion binding]; other site 159087000753 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 159087000754 Walker A; other site 159087000755 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, unknown subfamily 1; composed of uncharacterized bacterial proteins containing a C-terminal MCM domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The...; Region: MM_CoA_mutase_1; cd03678 159087000756 Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid metabolism]; Region: Sbm; COG1884 159087000757 putative active site [active] 159087000758 putative substrate binding site [chemical binding]; other site 159087000759 putative coenzyme B12 binding site [chemical binding]; other site 159087000760 Cache domain; Region: Cache_2; cl07034 159087000761 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 159087000762 Cache domain; Region: Cache_2; cl07034 159087000763 PAS domain S-box; Region: sensory_box; TIGR00229 159087000764 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 159087000765 putative active site [active] 159087000766 heme pocket [chemical binding]; other site 159087000767 PAS fold; Region: PAS_4; pfam08448 159087000768 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 159087000769 dimer interface [polypeptide binding]; other site 159087000770 phosphorylation site [posttranslational modification] 159087000771 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 159087000772 ATP binding site [chemical binding]; other site 159087000773 Mg2+ binding site [ion binding]; other site 159087000774 G-X-G motif; other site 159087000775 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000776 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000777 active site 159087000778 phosphorylation site [posttranslational modification] 159087000779 intermolecular recognition site; other site 159087000780 dimerization interface [polypeptide binding]; other site 159087000781 Autotransporter beta-domain; Region: Autotransporter; cl02365 159087000782 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087000783 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087000784 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 159087000785 ligand binding site [chemical binding]; other site 159087000786 flexible hinge region; other site 159087000787 Helix-turn-helix domains; Region: HTH; cl00088 159087000788 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 159087000789 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000790 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000791 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087000792 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087000793 Walker A/P-loop; other site 159087000794 ATP binding site [chemical binding]; other site 159087000795 Q-loop/lid; other site 159087000796 ABC transporter signature motif; other site 159087000797 Walker B; other site 159087000798 D-loop; other site 159087000799 H-loop/switch region; other site 159087000800 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087000801 TM-ABC transporter signature motif; other site 159087000802 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087000803 TM-ABC transporter signature motif; other site 159087000804 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 159087000805 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087000806 putative ligand binding site [chemical binding]; other site 159087000807 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087000808 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087000809 Walker A/P-loop; other site 159087000810 ATP binding site [chemical binding]; other site 159087000811 Q-loop/lid; other site 159087000812 ABC transporter signature motif; other site 159087000813 Walker B; other site 159087000814 D-loop; other site 159087000815 H-loop/switch region; other site 159087000816 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087000817 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 159087000818 CoA-transferase family III; Region: CoA_transf_3; pfam02515 159087000819 cyclase homology domain; Region: CHD; cd07302 159087000820 metal binding site [ion binding]; metal-binding site 159087000821 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087000822 phosphopeptide binding site; other site 159087000823 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 159087000824 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 159087000825 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 159087000826 Membrane transport protein; Region: Mem_trans; cl09117 159087000827 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087000828 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087000829 active site 159087000830 phosphorylation site [posttranslational modification] 159087000831 intermolecular recognition site; other site 159087000832 dimerization interface [polypeptide binding]; other site 159087000833 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 159087000834 DNA binding residues [nucleotide binding] 159087000835 dimerization interface [polypeptide binding]; other site 159087000836 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000837 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 159087000838 dimer interface [polypeptide binding]; other site 159087000839 phosphorylation site [posttranslational modification] 159087000840 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 159087000841 ATP binding site [chemical binding]; other site 159087000842 Mg2+ binding site [ion binding]; other site 159087000843 G-X-G motif; other site 159087000844 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; cl12011 159087000845 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 159087000846 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087000847 dimer interface [polypeptide binding]; other site 159087000848 PYR/PP interface [polypeptide binding]; other site 159087000849 TPP binding site [chemical binding]; other site 159087000850 substrate binding site [chemical binding]; other site 159087000851 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 159087000852 TPP-binding site; other site 159087000853 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 159087000854 D-lactate dehydrogenase [cytochrome]; Region: PLN02805 159087000855 FAD binding domain; Region: FAD_binding_4; pfam01565 159087000856 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087000857 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087000858 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 159087000859 dimerization interface [polypeptide binding]; other site 159087000860 ligand binding site [chemical binding]; other site 159087000861 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087000862 TM-ABC transporter signature motif; other site 159087000863 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087000864 TM-ABC transporter signature motif; other site 159087000865 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087000866 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087000867 Walker A/P-loop; other site 159087000868 ATP binding site [chemical binding]; other site 159087000869 Q-loop/lid; other site 159087000870 ABC transporter signature motif; other site 159087000871 Walker B; other site 159087000872 D-loop; other site 159087000873 H-loop/switch region; other site 159087000874 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087000875 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087000876 Walker A/P-loop; other site 159087000877 ATP binding site [chemical binding]; other site 159087000878 Q-loop/lid; other site 159087000879 ABC transporter signature motif; other site 159087000880 Walker B; other site 159087000881 D-loop; other site 159087000882 H-loop/switch region; other site 159087000883 septum formation inhibitor; Reviewed; Region: minC; PRK03511 159087000884 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 159087000885 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 159087000886 cell division inhibitor MinD; Provisional; Region: PRK10818 159087000887 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 159087000888 Switch I; other site 159087000889 Switch II; other site 159087000890 Septum formation topological specificity factor MinE; Region: MinE; cl00538 159087000891 Predicted membrane protein [Function unknown]; Region: COG3650 159087000892 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087000893 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 159087000894 catalytic loop [active] 159087000895 iron binding site [ion binding]; other site 159087000896 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 159087000897 FAD binding pocket [chemical binding]; other site 159087000898 FAD binding motif [chemical binding]; other site 159087000899 phosphate binding motif [ion binding]; other site 159087000900 beta-alpha-beta structure motif; other site 159087000901 NAD binding pocket [chemical binding]; other site 159087000902 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 159087000903 putative NAD(P) binding site [chemical binding]; other site 159087000904 Uncharacterised protein family (UPF0093); Region: UPF0093; cl00863 159087000905 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 159087000906 THUMP domain; Region: THUMP; cl12076 159087000907 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; cl12011 159087000908 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 159087000909 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 159087000910 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 159087000911 lipoyl synthase; Provisional; Region: PRK05481 159087000912 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 159087000913 FeS/SAM binding site; other site 159087000914 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 159087000915 Protein of unknown function (DUF493); Region: DUF493; cl01102 159087000916 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 159087000917 homodimer interface [polypeptide binding]; other site 159087000918 substrate-cofactor binding pocket; other site 159087000919 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087000920 Aminotransferase class IV; Region: Aminotran_4; pfam01063 159087000921 catalytic residue [active] 159087000922 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 159087000923 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 159087000924 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 159087000925 Helix-turn-helix domains; Region: HTH; cl00088 159087000926 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 159087000927 dimerization interface [polypeptide binding]; other site 159087000928 Peptidase family M48; Region: Peptidase_M48; cl12018 159087000929 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087000930 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087000931 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087000932 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087000933 GAF domain; Region: GAF; cl00853 159087000934 PAS fold; Region: PAS; pfam00989 159087000935 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 159087000936 putative active site [active] 159087000937 heme pocket [chemical binding]; other site 159087000938 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087000939 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 159087000940 dimer interface [polypeptide binding]; other site 159087000941 substrate binding site [chemical binding]; other site 159087000942 metal binding site [ion binding]; metal-binding site 159087000943 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 159087000944 Dehydratase family; Region: ILVD_EDD; cl00340 159087000945 LysE type translocator; Region: LysE; cl00565 159087000946 Cytochrome c; Region: Cytochrom_C; cl11414 159087000947 translation elongation factor TU; Region: EF-Tu; TIGR00485 159087000948 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087000949 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 159087000950 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 159087000951 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 159087000952 putative homodimer interface [polypeptide binding]; other site 159087000953 KOW motif; Region: KOW; cl00354 159087000954 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 159087000955 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 159087000956 23S rRNA interface [nucleotide binding]; other site 159087000957 L7/L12 interface [polypeptide binding]; other site 159087000958 putative thiostrepton binding site; other site 159087000959 L25 interface [polypeptide binding]; other site 159087000960 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 159087000961 mRNA/rRNA interface [nucleotide binding]; other site 159087000962 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 159087000963 23S rRNA interface [nucleotide binding]; other site 159087000964 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 159087000965 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 159087000966 core dimer interface [polypeptide binding]; other site 159087000967 peripheral dimer interface [polypeptide binding]; other site 159087000968 L10 interface [polypeptide binding]; other site 159087000969 L11 interface [polypeptide binding]; other site 159087000970 putative EF-Tu interaction site [polypeptide binding]; other site 159087000971 putative EF-G interaction site [polypeptide binding]; other site 159087000972 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 159087000973 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; cl04593 159087000974 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 159087000975 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; cl04593 159087000976 RPB11 interaction site [polypeptide binding]; other site 159087000977 RPB12 interaction site [polypeptide binding]; other site 159087000978 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 159087000979 RPB3 interaction site [polypeptide binding]; other site 159087000980 RPB1 interaction site [polypeptide binding]; other site 159087000981 RPB11 interaction site [polypeptide binding]; other site 159087000982 RPB10 interaction site [polypeptide binding]; other site 159087000983 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 159087000984 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 159087000985 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 159087000986 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 159087000987 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 159087000988 DNA-directed RNA polymerase subunit A''; Provisional; Region: PRK14898 159087000989 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 159087000990 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 159087000991 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 159087000992 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 159087000993 DNA binding site [nucleotide binding] 159087000994 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 159087000995 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 159087000996 S17 interaction site [polypeptide binding]; other site 159087000997 S8 interaction site; other site 159087000998 16S rRNA interaction site [nucleotide binding]; other site 159087000999 streptomycin interaction site [chemical binding]; other site 159087001000 23S rRNA interaction site [nucleotide binding]; other site 159087001001 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 159087001002 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 159087001003 elongation factor G; Reviewed; Region: PRK00007 159087001004 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so...; Region: EF-G; cd01886 159087001005 G1 box; other site 159087001006 putative GEF interaction site [polypeptide binding]; other site 159087001007 GTP/Mg2+ binding site [chemical binding]; other site 159087001008 Switch I region; other site 159087001009 G2 box; other site 159087001010 G3 box; other site 159087001011 Switch II region; other site 159087001012 G4 box; other site 159087001013 G5 box; other site 159087001014 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 159087001015 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 159087001016 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 159087001017 translation elongation factor TU; Region: EF-Tu; TIGR00485 159087001018 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087001019 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 159087001020 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 159087001021 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 159087001022 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 159087001023 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 159087001024 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 159087001025 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 159087001026 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 159087001027 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 159087001028 putative translocon binding site; other site 159087001029 protein-rRNA interface [nucleotide binding]; other site 159087001030 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 159087001031 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 159087001032 G-X-X-G motif; other site 159087001033 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 159087001034 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 159087001035 23S rRNA interface [nucleotide binding]; other site 159087001036 5S rRNA interface [nucleotide binding]; other site 159087001037 putative antibiotic binding site [chemical binding]; other site 159087001038 L25 interface [polypeptide binding]; other site 159087001039 L27 interface [polypeptide binding]; other site 159087001040 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 159087001041 23S rRNA interface [nucleotide binding]; other site 159087001042 putative translocon interaction site; other site 159087001043 signal recognition particle (SRP54) interaction site; other site 159087001044 L23 interface [polypeptide binding]; other site 159087001045 trigger factor interaction site; other site 159087001046 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 159087001047 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 159087001048 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 159087001049 KOW motif; Region: KOW; cl00354 159087001050 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 159087001051 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 159087001052 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 159087001053 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 159087001054 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 159087001055 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 159087001056 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 159087001057 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 159087001058 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 159087001059 5S rRNA interface [nucleotide binding]; other site 159087001060 23S rRNA interface [nucleotide binding]; other site 159087001061 L5 interface [polypeptide binding]; other site 159087001062 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 159087001063 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 159087001064 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 159087001065 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 159087001066 23S rRNA binding site [nucleotide binding]; other site 159087001067 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 159087001068 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 159087001069 SecY translocase; Region: SecY; pfam00344 159087001070 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 159087001071 rRNA binding site [nucleotide binding]; other site 159087001072 predicted 30S ribosome binding site; other site 159087001073 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 159087001074 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 159087001075 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 159087001076 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 159087001077 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 159087001078 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 159087001079 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 159087001080 RNA binding surface [nucleotide binding]; other site 159087001081 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 159087001082 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 159087001083 alphaNTD homodimer interface [polypeptide binding]; other site 159087001084 alphaNTD - beta interaction site [polypeptide binding]; other site 159087001085 alphaNTD - beta' interaction site [polypeptide binding]; other site 159087001086 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 159087001087 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 159087001088 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001089 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001090 active site 159087001091 phosphorylation site [posttranslational modification] 159087001092 intermolecular recognition site; other site 159087001093 dimerization interface [polypeptide binding]; other site 159087001094 PAS domain S-box; Region: sensory_box; TIGR00229 159087001095 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 159087001096 putative active site [active] 159087001097 heme pocket [chemical binding]; other site 159087001098 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 159087001099 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 159087001100 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 159087001101 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087001102 Walker A/P-loop; other site 159087001103 ATP binding site [chemical binding]; other site 159087001104 Q-loop/lid; other site 159087001105 ABC transporter signature motif; other site 159087001106 Walker B; other site 159087001107 D-loop; other site 159087001108 H-loop/switch region; other site 159087001109 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 159087001110 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 159087001111 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 159087001112 Sporulation related domain; Region: SPOR; cl10051 159087001113 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 159087001114 binding surface 159087001115 TPR motif; other site 159087001116 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 159087001117 homotrimer interaction site [polypeptide binding]; other site 159087001118 putative active site [active] 159087001119 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 159087001120 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 159087001121 generic binding surface II; other site 159087001122 ssDNA binding site; other site 159087001123 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 159087001124 ATP binding site [chemical binding]; other site 159087001125 putative Mg++ binding site [ion binding]; other site 159087001126 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 159087001127 nucleotide binding region [chemical binding]; other site 159087001128 ATP-binding site [chemical binding]; other site 159087001129 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087001130 Helix-turn-helix domains; Region: HTH; cl00088 159087001131 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 159087001132 dimerization interface [polypeptide binding]; other site 159087001133 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 159087001134 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 159087001135 putative substrate translocation pore; other site 159087001136 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 159087001137 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 159087001138 NADP binding site [chemical binding]; other site 159087001139 dimer interface [polypeptide binding]; other site 159087001140 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 159087001141 active site 1 [active] 159087001142 dimer interface [polypeptide binding]; other site 159087001143 hexamer interface [polypeptide binding]; other site 159087001144 active site 2 [active] 159087001145 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 159087001146 active site 159087001147 FMN binding site [chemical binding]; other site 159087001148 substrate binding site [chemical binding]; other site 159087001149 homotetramer interface [polypeptide binding]; other site 159087001150 catalytic residue [active] 159087001151 Flagellin N-methylase; Region: FliB; cl00497 159087001152 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 159087001153 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087001154 nucleophilic elbow; other site 159087001155 catalytic triad; other site 159087001156 Uncharacterized conserved protein [Function unknown]; Region: COG3945 159087001157 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087001158 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087001159 Walker A/P-loop; other site 159087001160 ATP binding site [chemical binding]; other site 159087001161 Q-loop/lid; other site 159087001162 ABC transporter signature motif; other site 159087001163 Walker B; other site 159087001164 D-loop; other site 159087001165 H-loop/switch region; other site 159087001166 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 159087001167 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087001168 Walker A/P-loop; other site 159087001169 ATP binding site [chemical binding]; other site 159087001170 Q-loop/lid; other site 159087001171 ABC transporter signature motif; other site 159087001172 Walker B; other site 159087001173 D-loop; other site 159087001174 H-loop/switch region; other site 159087001175 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087001176 TM-ABC transporter signature motif; other site 159087001177 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087001178 TM-ABC transporter signature motif; other site 159087001179 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087001180 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 159087001181 catalytic loop [active] 159087001182 iron binding site [ion binding]; other site 159087001183 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 159087001184 FAD binding pocket [chemical binding]; other site 159087001185 FAD binding motif [chemical binding]; other site 159087001186 phosphate binding motif [ion binding]; other site 159087001187 beta-alpha-beta structure motif; other site 159087001188 NAD binding pocket [chemical binding]; other site 159087001189 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 159087001190 NAD(P) binding site [chemical binding]; other site 159087001191 catalytic residues [active] 159087001192 enoyl-CoA hydratase; Provisional; Region: PRK08140 159087001193 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 159087001194 substrate binding site [chemical binding]; other site 159087001195 oxyanion hole (OAH) forming residues; other site 159087001196 trimer interface [polypeptide binding]; other site 159087001197 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 159087001198 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; cl12011 159087001199 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087001200 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087001201 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 159087001202 CoenzymeA binding site [chemical binding]; other site 159087001203 subunit interaction site [polypeptide binding]; other site 159087001204 PHB binding site; other site 159087001205 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087001206 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 159087001207 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 159087001208 dimer interface [polypeptide binding]; other site 159087001209 active site 159087001210 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087001211 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087001212 putative ligand binding site [chemical binding]; other site 159087001213 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 159087001214 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 159087001215 Phenylacetic acid degradation B; Region: PaaB; cl01371 159087001216 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 159087001217 Domain of unknown function DUF59; Region: DUF59; cl00941 159087001218 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 159087001219 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 159087001220 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 159087001221 FAD binding pocket [chemical binding]; other site 159087001222 FAD binding motif [chemical binding]; other site 159087001223 phosphate binding motif [ion binding]; other site 159087001224 beta-alpha-beta structure motif; other site 159087001225 NAD(p) ribose binding residues [chemical binding]; other site 159087001226 NAD binding pocket [chemical binding]; other site 159087001227 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 159087001228 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 159087001229 catalytic loop [active] 159087001230 iron binding site [ion binding]; other site 159087001231 enoyl-CoA hydratase; Provisional; Region: PRK05862 159087001232 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 159087001233 substrate binding site [chemical binding]; other site 159087001234 oxyanion hole (OAH) forming residues; other site 159087001235 trimer interface [polypeptide binding]; other site 159087001236 enoyl-CoA hydratase; Provisional; Region: PRK05995 159087001237 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 159087001238 substrate binding site [chemical binding]; other site 159087001239 oxyanion hole (OAH) forming residues; other site 159087001240 trimer interface [polypeptide binding]; other site 159087001241 Transcriptional regulator [Transcription]; Region: IclR; COG1414 159087001242 Helix-turn-helix domains; Region: HTH; cl00088 159087001243 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087001244 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 159087001245 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 159087001246 putative trimer interface [polypeptide binding]; other site 159087001247 putative metal binding site [ion binding]; other site 159087001248 PaaX-like protein; Region: PaaX; pfam07848 159087001249 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 159087001250 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 159087001251 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 159087001252 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 159087001253 MG2 domain; Region: A2M_N; pfam01835 159087001254 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 159087001255 Alpha-2-macroglobulin family; Region: A2M; pfam00207 159087001256 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 159087001257 surface patch; other site 159087001258 thioester region; other site 159087001259 specificity defining residues; other site 159087001260 penicillin-binding protein 1C; Provisional; Region: PRK11240 159087001261 Transglycosylase; Region: Transgly; cl07896 159087001262 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087001263 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 159087001264 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 159087001265 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087001266 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 159087001267 Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Region: PLDc_vPLD1_2_like_1; cd09104 159087001268 putative active site [active] 159087001269 catalytic site [active] 159087001270 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 159087001271 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Region: PLDc_vPLD1_2_yPLD_like_2; cd09141 159087001272 putative active site [active] 159087001273 catalytic site [active] 159087001274 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 159087001275 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087001276 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 159087001277 Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Region: PLDc_vPLD1_2_like_1; cd09104 159087001278 putative active site [active] 159087001279 catalytic site [active] 159087001280 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 159087001281 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 159087001282 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Region: PLDc_vPLD1_2_yPLD_like_2; cd09141 159087001283 putative active site [active] 159087001284 catalytic site [active] 159087001285 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 159087001286 putative active site [active] 159087001287 catalytic site [active] 159087001288 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 159087001289 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 159087001290 dimerization interface [polypeptide binding]; other site 159087001291 putative DNA binding site [nucleotide binding]; other site 159087001292 putative Zn2+ binding site [ion binding]; other site 159087001293 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 159087001294 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087001295 putative acyl-acceptor binding pocket; other site 159087001296 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087001297 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 159087001298 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 159087001299 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087001300 putative acyl-acceptor binding pocket; other site 159087001301 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 159087001302 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG1964 159087001303 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 159087001304 FeS/SAM binding site; other site 159087001305 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 159087001306 PAS fold; Region: PAS_3; pfam08447 159087001307 putative active site [active] 159087001308 heme pocket [chemical binding]; other site 159087001309 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001310 metal binding site [ion binding]; metal-binding site 159087001311 active site 159087001312 I-site; other site 159087001313 UbiA prenyltransferase family; Region: UbiA; cl00337 159087001314 Cytochrome C'; Region: Cytochrom_C_2; cl01610 159087001315 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 159087001316 modified peptide precursor CbpA; Region: cobo_pep; TIGR04164 159087001317 peptide-modifying radical SAM enzyme CbpB; Region: rSAM_cobopep; TIGR04163 159087001318 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 159087001319 FeS/SAM binding site; other site 159087001320 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; cl14869 159087001321 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 159087001322 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087001323 Coenzyme A binding pocket [chemical binding]; other site 159087001324 Predicted membrane protein [Function unknown]; Region: COG3671 159087001325 sensory histidine kinase AtoS; Provisional; Region: PRK11360 159087001326 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 159087001327 dimer interface [polypeptide binding]; other site 159087001328 phosphorylation site [posttranslational modification] 159087001329 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 159087001330 ATP binding site [chemical binding]; other site 159087001331 Mg2+ binding site [ion binding]; other site 159087001332 G-X-G motif; other site 159087001333 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001334 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001335 active site 159087001336 phosphorylation site [posttranslational modification] 159087001337 intermolecular recognition site; other site 159087001338 dimerization interface [polypeptide binding]; other site 159087001339 Uncharacterized conserved protein [Function unknown]; Region: COG1284 159087001340 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 159087001341 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 159087001342 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 159087001343 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl15297 159087001344 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087001345 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087001346 PAS domain S-box; Region: sensory_box; TIGR00229 159087001347 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087001348 PAS domain S-box; Region: sensory_box; TIGR00229 159087001349 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 159087001350 putative active site [active] 159087001351 heme pocket [chemical binding]; other site 159087001352 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001353 metal binding site [ion binding]; metal-binding site 159087001354 active site 159087001355 I-site; other site 159087001356 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 159087001357 oligomerisation interface [polypeptide binding]; other site 159087001358 mobile loop; other site 159087001359 roof hairpin; other site 159087001360 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 159087001361 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 159087001362 ring oligomerisation interface [polypeptide binding]; other site 159087001363 ATP/Mg binding site [chemical binding]; other site 159087001364 stacking interactions; other site 159087001365 hinge regions; other site 159087001366 Protein of unknown function, DUF485; Region: DUF485; cl01231 159087001367 Sodium:solute symporter family; Region: SSF; cl00456 159087001368 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 159087001369 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 159087001370 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001371 active site 159087001372 phosphorylation site [posttranslational modification] 159087001373 intermolecular recognition site; other site 159087001374 dimerization interface [polypeptide binding]; other site 159087001375 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 159087001376 DNA binding site [nucleotide binding] 159087001377 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087001378 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087001379 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 159087001380 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 159087001381 dimer interface [polypeptide binding]; other site 159087001382 phosphorylation site [posttranslational modification] 159087001383 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 159087001384 ATP binding site [chemical binding]; other site 159087001385 Mg2+ binding site [ion binding]; other site 159087001386 G-X-G motif; other site 159087001387 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; cl12011 159087001388 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 159087001389 catalytic core [active] 159087001390 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 159087001391 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 159087001392 CoenzymeA binding site [chemical binding]; other site 159087001393 subunit interaction site [polypeptide binding]; other site 159087001394 PHB binding site; other site 159087001395 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 159087001396 Protein phosphatase 2C; Region: PP2C; pfam00481 159087001397 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087001398 active site 159087001399 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087001400 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087001401 active site 159087001402 ATP binding site [chemical binding]; other site 159087001403 substrate binding site [chemical binding]; other site 159087001404 activation loop (A-loop); other site 159087001405 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087001406 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 159087001407 E3 interaction surface; other site 159087001408 lipoyl attachment site [posttranslational modification]; other site 159087001409 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001410 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 159087001411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001412 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 159087001413 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 159087001414 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 159087001415 E3 interaction surface; other site 159087001416 lipoyl attachment site [posttranslational modification]; other site 159087001417 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 159087001418 E3 interaction surface; other site 159087001419 lipoyl attachment site [posttranslational modification]; other site 159087001420 e3 binding domain; Region: E3_binding; pfam02817 159087001421 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 159087001422 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 159087001423 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 159087001424 dimer interface [polypeptide binding]; other site 159087001425 TPP-binding site [chemical binding]; other site 159087001426 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 159087001427 Subunit I/III interface [polypeptide binding]; other site 159087001428 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 159087001429 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087001430 dimer interface [polypeptide binding]; other site 159087001431 PYR/PP interface [polypeptide binding]; other site 159087001432 TPP binding site [chemical binding]; other site 159087001433 substrate binding site [chemical binding]; other site 159087001434 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 159087001435 TPP-binding site; other site 159087001436 4Fe-4S binding domain; Region: Fer4; cl02805 159087001437 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 159087001438 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 159087001439 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 159087001440 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 159087001441 homodimer interface [polypeptide binding]; other site 159087001442 NADP binding site [chemical binding]; other site 159087001443 substrate binding site [chemical binding]; other site 159087001444 AIR carboxylase; Region: AIRC; cl00310 159087001445 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 159087001446 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 159087001447 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087001448 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 159087001449 SUA5 domain; Region: SUA5; pfam03481 159087001450 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 159087001451 aromatic arch; other site 159087001452 DCoH dimer interaction site [polypeptide binding]; other site 159087001453 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 159087001454 DCoH tetramer interaction site [polypeptide binding]; other site 159087001455 substrate binding site [chemical binding]; other site 159087001456 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 159087001457 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 159087001458 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 159087001459 Walker A motif; other site 159087001460 ATP binding site [chemical binding]; other site 159087001461 Walker B motif; other site 159087001462 arginine finger; other site 159087001463 Helix-turn-helix domains; Region: HTH; cl00088 159087001464 Citrate transporter; Region: CitMHS; pfam03600 159087001465 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 159087001466 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 159087001467 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 159087001468 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087001469 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087001470 Protein export membrane protein; Region: SecD_SecF; cl14618 159087001471 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087001472 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 159087001473 dimer interface [polypeptide binding]; other site 159087001474 phosphorylation site [posttranslational modification] 159087001475 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 159087001476 ATP binding site [chemical binding]; other site 159087001477 Mg2+ binding site [ion binding]; other site 159087001478 G-X-G motif; other site 159087001479 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001480 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001481 active site 159087001482 phosphorylation site [posttranslational modification] 159087001483 intermolecular recognition site; other site 159087001484 dimerization interface [polypeptide binding]; other site 159087001485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 159087001486 Family of unknown function (DUF490); Region: DUF490; pfam04357 159087001487 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 159087001488 Surface antigen; Region: Bac_surface_Ag; cl03097 159087001489 Site-specific recombinase; Region: SpecificRecomb; cl15411 159087001490 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087001491 ligand binding site [chemical binding]; other site 159087001492 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 159087001493 nucleophile elbow; other site 159087001494 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 159087001495 Surface antigen; Region: Bac_surface_Ag; cl03097 159087001496 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 159087001497 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 159087001498 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 159087001499 probable DNA repair protein; Region: TIGR03623 159087001500 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 159087001501 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 159087001502 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 159087001503 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087001504 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087001505 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 159087001506 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 159087001507 substrate binding pocket [chemical binding]; other site 159087001508 membrane-bound complex binding site; other site 159087001509 hinge residues; other site 159087001510 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001511 metal binding site [ion binding]; metal-binding site 159087001512 active site 159087001513 I-site; other site 159087001514 putative metal dependent hydrolase; Provisional; Region: PRK11598 159087001515 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 159087001516 Sulfatase; Region: Sulfatase; cl10460 159087001517 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 159087001518 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 159087001519 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 159087001520 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 159087001521 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 159087001522 Peptidase family M48; Region: Peptidase_M48; cl12018 159087001523 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087001524 Helix-turn-helix domains; Region: HTH; cl00088 159087001525 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 159087001526 dimerization interface [polypeptide binding]; other site 159087001527 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087001528 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001529 active site 159087001530 phosphorylation site [posttranslational modification] 159087001531 intermolecular recognition site; other site 159087001532 dimerization interface [polypeptide binding]; other site 159087001533 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 159087001534 Walker A motif; other site 159087001535 ATP binding site [chemical binding]; other site 159087001536 Walker B motif; other site 159087001537 arginine finger; other site 159087001538 Helix-turn-helix domains; Region: HTH; cl00088 159087001539 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087001540 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 159087001541 dimer interface [polypeptide binding]; other site 159087001542 phosphorylation site [posttranslational modification] 159087001543 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 159087001544 ATP binding site [chemical binding]; other site 159087001545 Mg2+ binding site [ion binding]; other site 159087001546 G-X-G motif; other site 159087001547 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087001548 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087001549 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 159087001550 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 159087001551 Aspartase; Region: Aspartase; cd01357 159087001552 active sites [active] 159087001553 tetramer interface [polypeptide binding]; other site 159087001554 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 159087001555 putative substrate translocation pore; other site 159087001556 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 159087001557 dimer interface [polypeptide binding]; other site 159087001558 ssDNA binding site [nucleotide binding]; other site 159087001559 tetramer (dimer of dimers) interface [polypeptide binding]; other site 159087001560 HDOD domain; Region: HDOD; pfam08668 159087001561 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087001562 Amino acid permease; Region: AA_permease; cl00524 159087001563 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087001564 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 159087001565 active site 159087001566 HIGH motif; other site 159087001567 nucleotide binding site [chemical binding]; other site 159087001568 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 159087001569 DNA binding residues [nucleotide binding] 159087001570 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 159087001571 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 159087001572 catalytic residues [active] 159087001573 dimer interface [polypeptide binding]; other site 159087001574 Uncharacterized ACR, COG1469; Region: DUF198; cl00642 159087001575 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 159087001576 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001577 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001578 Uncharacterized conserved protein [Function unknown]; Region: COG3496 159087001579 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 159087001580 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 159087001581 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; cl12011 159087001582 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 159087001583 S-adenosylmethionine binding site [chemical binding]; other site 159087001584 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 159087001585 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 159087001586 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001587 NAD(P) binding site [chemical binding]; other site 159087001588 active site 159087001589 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 159087001590 Ion channel; Region: Ion_trans_2; cl11596 159087001591 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001592 acetolactate synthase catalytic subunit; Reviewed; Region: PRK07282 159087001593 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 159087001594 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001595 outer membrane lipoprotein; Provisional; Region: PRK11023 159087001596 BON domain; Region: BON; cl02771 159087001597 BON domain; Region: BON; cl02771 159087001598 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 159087001599 dimer interface [polypeptide binding]; other site 159087001600 active site 159087001601 HIRAN domain; Region: HIRAN; cl07418 159087001602 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 159087001603 Predicted methyltransferases [General function prediction only]; Region: COG0313 159087001604 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087001605 PAS fold; Region: PAS_4; pfam08448 159087001606 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 159087001607 putative active site [active] 159087001608 heme pocket [chemical binding]; other site 159087001609 PAS domain S-box; Region: sensory_box; TIGR00229 159087001610 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 159087001611 putative active site [active] 159087001612 heme pocket [chemical binding]; other site 159087001613 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001614 metal binding site [ion binding]; metal-binding site 159087001615 active site 159087001616 I-site; other site 159087001617 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 159087001618 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 159087001619 active site 159087001620 substrate binding pocket [chemical binding]; other site 159087001621 dimer interface [polypeptide binding]; other site 159087001622 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 159087001623 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 159087001624 rRNA binding site [nucleotide binding]; other site 159087001625 predicted 30S ribosome binding site; other site 159087001626 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087001627 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087001628 2-isopropylmalate synthase; Validated; Region: PRK03739 159087001629 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 159087001630 active site 159087001631 catalytic residues [active] 159087001632 metal binding site [ion binding]; metal-binding site 159087001633 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 159087001634 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087001635 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 159087001636 putative DNA binding site [nucleotide binding]; other site 159087001637 putative Zn2+ binding site [ion binding]; other site 159087001638 Helix-turn-helix domains; Region: HTH; cl00088 159087001639 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; cl12011 159087001640 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; cl12011 159087001641 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 159087001642 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 159087001643 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 159087001644 Walker A motif; other site 159087001645 ATP binding site [chemical binding]; other site 159087001646 Walker B motif; other site 159087001647 arginine finger; other site 159087001648 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 159087001649 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 159087001650 S-adenosylmethionine binding site [chemical binding]; other site 159087001651 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 159087001652 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 159087001653 RNA polymerase sigma factor; Provisional; Region: PRK12511 159087001654 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087001655 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 159087001656 DNA binding residues [nucleotide binding] 159087001657 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 159087001658 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 159087001659 putative heme binding pocket [chemical binding]; other site 159087001660 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087001661 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087001662 putative ligand binding site [chemical binding]; other site 159087001663 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 159087001664 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 159087001665 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 159087001666 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 159087001667 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087001668 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 159087001669 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 159087001670 DNA binding residues [nucleotide binding] 159087001671 DNA primase; Validated; Region: dnaG; PRK05667 159087001672 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087001673 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 159087001674 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 159087001675 active site 159087001676 metal binding site [ion binding]; metal-binding site 159087001677 interdomain interaction site; other site 159087001678 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 159087001679 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 159087001680 GatB domain; Region: GatB_Yqey; cl11497 159087001681 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 159087001682 UGMP family protein; Validated; Region: PRK09604 159087001683 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 159087001684 Cupin domain; Region: Cupin_2; cl09118 159087001685 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 159087001686 dimer interface [polypeptide binding]; other site 159087001687 catalytic triad [active] 159087001688 peroxidatic and resolving cysteines [active] 159087001689 Domain of unknown function (DUF205); Region: DUF205; cl00410 159087001690 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 159087001691 active site 159087001692 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 159087001693 putative deacylase active site [active] 159087001694 RF-1 domain; Region: RF-1; cl02875 159087001695 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 159087001696 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 159087001697 Int/Topo IB signature motif; other site 159087001698 active site 159087001699 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 159087001700 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 159087001701 DNA binding site [nucleotide binding] 159087001702 active site 159087001703 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 159087001704 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087001705 FAD binding site [chemical binding]; other site 159087001706 substrate binding pocket [chemical binding]; other site 159087001707 catalytic base [active] 159087001708 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 159087001709 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 159087001710 putative catalytic cysteine [active] 159087001711 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 159087001712 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 159087001713 Lipopolysaccharide-assembly; Region: LptE; cl01125 159087001714 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 159087001715 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 159087001716 HIGH motif; other site 159087001717 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087001718 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087001719 active site 159087001720 KMSKS motif; other site 159087001721 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 159087001722 tRNA binding surface [nucleotide binding]; other site 159087001723 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 159087001724 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087001725 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 159087001726 putative active site [active] 159087001727 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 159087001728 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 159087001729 NADP binding site [chemical binding]; other site 159087001730 dimer interface [polypeptide binding]; other site 159087001731 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 159087001732 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087001733 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 159087001734 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 159087001735 P-loop; other site 159087001736 Magnesium ion binding site [ion binding]; other site 159087001737 CHASE domain; Region: CHASE; cl01369 159087001738 PAS fold; Region: PAS_4; pfam08448 159087001739 PAS domain S-box; Region: sensory_box; TIGR00229 159087001740 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 159087001741 putative active site [active] 159087001742 heme pocket [chemical binding]; other site 159087001743 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087001744 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 159087001745 dimer interface [polypeptide binding]; other site 159087001746 phosphorylation site [posttranslational modification] 159087001747 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 159087001748 ATP binding site [chemical binding]; other site 159087001749 G-X-G motif; other site 159087001750 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001751 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001752 active site 159087001753 phosphorylation site [posttranslational modification] 159087001754 intermolecular recognition site; other site 159087001755 dimerization interface [polypeptide binding]; other site 159087001756 Helix-turn-helix domains; Region: HTH; cl00088 159087001757 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 159087001758 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 159087001759 putative dimerization interface [polypeptide binding]; other site 159087001760 Pirin-related protein [General function prediction only]; Region: COG1741 159087001761 Cupin domain; Region: Cupin_2; cl09118 159087001762 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087001763 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087001764 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087001765 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001766 active site 159087001767 phosphorylation site [posttranslational modification] 159087001768 intermolecular recognition site; other site 159087001769 dimerization interface [polypeptide binding]; other site 159087001770 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 159087001771 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001772 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001773 active site 159087001774 phosphorylation site [posttranslational modification] 159087001775 intermolecular recognition site; other site 159087001776 dimerization interface [polypeptide binding]; other site 159087001777 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cl01922 159087001778 enoyl-CoA hydratase; Validated; Region: PRK08139 159087001779 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 159087001780 substrate binding site [chemical binding]; other site 159087001781 oxyanion hole (OAH) forming residues; other site 159087001782 trimer interface [polypeptide binding]; other site 159087001783 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 159087001784 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 159087001785 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 159087001786 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 159087001787 generic binding surface II; other site 159087001788 generic binding surface I; other site 159087001789 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087001790 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087001791 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 159087001792 DNA binding residues [nucleotide binding] 159087001793 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001794 active site 159087001795 phosphorylation site [posttranslational modification] 159087001796 intermolecular recognition site; other site 159087001797 peroxidase; Provisional; Region: PRK15000 159087001798 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 159087001799 dimer interface [polypeptide binding]; other site 159087001800 decamer (pentamer of dimers) interface [polypeptide binding]; other site 159087001801 catalytic triad [active] 159087001802 peroxidatic and resolving cysteines [active] 159087001803 proton-translocating NADH-quinone oxidoreductase, chain M; Region: NDH_I_M; TIGR01972 159087001804 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087001805 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 159087001806 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 159087001807 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 159087001808 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087001809 proton-translocating NADH-quinone oxidoreductase, chain M; Region: NDH_I_M; TIGR01972 159087001810 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087001811 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 159087001812 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087001813 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 159087001814 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 159087001815 PhnA protein; Region: PhnA; pfam03831 159087001816 putative transporter; Provisional; Region: PRK11660 159087001817 Permease family; Region: Xan_ur_permease; cl00967 159087001818 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 159087001819 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15375 159087001820 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 159087001821 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 159087001822 active site 159087001823 HIGH motif; other site 159087001824 KMSKS motif; other site 159087001825 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 159087001826 tRNA binding surface [nucleotide binding]; other site 159087001827 anticodon binding site; other site 159087001828 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 159087001829 dimer interface [polypeptide binding]; other site 159087001830 putative tRNA-binding site [nucleotide binding]; other site 159087001831 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087001832 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087001833 active site 159087001834 phosphorylation site [posttranslational modification] 159087001835 intermolecular recognition site; other site 159087001836 dimerization interface [polypeptide binding]; other site 159087001837 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 159087001838 DNA binding site [nucleotide binding] 159087001839 Domain of unknown function DUF59; Region: DUF59; cl00941 159087001840 antiporter inner membrane protein; Provisional; Region: PRK11670 159087001841 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 159087001842 Walker A motif; other site 159087001843 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 159087001844 trimer interface [polypeptide binding]; other site 159087001845 active site 159087001846 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 159087001847 lysine decarboxylase LdcC; Provisional; Region: PRK15399 159087001848 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 159087001849 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087001850 catalytic residue [active] 159087001851 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 159087001852 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 159087001853 folate binding site [chemical binding]; other site 159087001854 NADP+ binding site [chemical binding]; other site 159087001855 glycogen synthase; Provisional; Region: glgA; PRK00654 159087001856 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 159087001857 ADP-binding pocket [chemical binding]; other site 159087001858 homodimer interface [polypeptide binding]; other site 159087001859 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 159087001860 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 159087001861 active site 159087001862 dimer interface [polypeptide binding]; other site 159087001863 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 159087001864 dimer interface [polypeptide binding]; other site 159087001865 active site 159087001866 This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important...; Region: GT1_Glycogen_Phosphorylase_like; cd04299 159087001867 putative homodimer interface [polypeptide binding]; other site 159087001868 putative active site pocket [active] 159087001869 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 159087001870 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 159087001871 Glycosyl hydrolases family 38 N-terminal domain; Region: Glyco_hydro_38; pfam01074 159087001872 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 159087001873 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 159087001874 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]; Region: COG1449 159087001875 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 159087001876 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 159087001877 ligand binding site; other site 159087001878 oligomer interface; other site 159087001879 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 159087001880 dimer interface [polypeptide binding]; other site 159087001881 N-terminal domain interface [polypeptide binding]; other site 159087001882 sulfate 1 binding site; other site 159087001883 glycogen branching enzyme; Provisional; Region: PRK12313 159087001884 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 159087001885 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 159087001886 active site 159087001887 catalytic site [active] 159087001888 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 159087001889 Protein of unknown function (DUF1345); Region: DUF1345; cl01753 159087001890 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 159087001891 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 159087001892 dimerization interface [polypeptide binding]; other site 159087001893 active site 159087001894 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 159087001895 MPT binding site; other site 159087001896 trimer interface [polypeptide binding]; other site 159087001897 Protein of unknown function (DUF615); Region: DUF615; cl01147 159087001898 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 159087001899 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 159087001900 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087001901 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087001902 Ferritin-like domain; Region: Ferritin; pfam00210 159087001903 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 159087001904 dimerization interface [polypeptide binding]; other site 159087001905 DPS ferroxidase diiron center [ion binding]; other site 159087001906 ion pore; other site 159087001907 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 159087001908 DctM-like transporters; Region: DctM; pfam06808 159087001909 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 159087001910 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 159087001911 catalytic core [active] 159087001912 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 159087001913 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 159087001914 dimer interface [polypeptide binding]; other site 159087001915 glycine-pyridoxal phosphate binding site [chemical binding]; other site 159087001916 active site 159087001917 folate binding site [chemical binding]; other site 159087001918 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 159087001919 ATP cone domain; Region: ATP-cone; pfam03477 159087001920 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 159087001921 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 159087001922 catalytic motif [active] 159087001923 Zn binding site [ion binding]; other site 159087001924 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; cl00161 159087001925 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 159087001926 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 159087001927 ATP binding site [chemical binding]; other site 159087001928 substrate interface [chemical binding]; other site 159087001929 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 159087001930 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 159087001931 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 159087001932 protein binding site [polypeptide binding]; other site 159087001933 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 159087001934 Catalytic dyad [active] 159087001935 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 159087001936 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 159087001937 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 159087001938 dimerization interface [polypeptide binding]; other site 159087001939 putative DNA binding site [nucleotide binding]; other site 159087001940 putative Zn2+ binding site [ion binding]; other site 159087001941 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 159087001942 active site residue [active] 159087001943 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 159087001944 GSH binding site [chemical binding]; other site 159087001945 catalytic residues [active] 159087001946 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; cl00251 159087001947 SecA binding site; other site 159087001948 Preprotein binding site; other site 159087001949 Bacterial SH3 domain; Region: SH3_3; cl02551 159087001950 Bacterial SH3 domain; Region: SH3_3; cl02551 159087001951 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 159087001952 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001953 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 159087001954 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 159087001955 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 159087001956 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087001957 biotin synthase; Region: bioB; TIGR00433 159087001958 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 159087001959 FeS/SAM binding site; other site 159087001960 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 159087001961 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 159087001962 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 159087001963 S-adenosylmethionine binding site [chemical binding]; other site 159087001964 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 159087001965 TMAO/DMSO reductase; Reviewed; Region: PRK05363 159087001966 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 159087001967 Moco binding site; other site 159087001968 metal coordination site [ion binding]; other site 159087001969 HDOD domain; Region: HDOD; pfam08668 159087001970 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087001971 FOG: CBS domain [General function prediction only]; Region: COG0517 159087001972 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 159087001973 Cytochrome c; Region: Cytochrom_C; cl11414 159087001974 Cytochrome c; Region: Cytochrom_C; cl11414 159087001975 Predicted GTPase [General function prediction only]; Region: COG0218 159087001976 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 159087001977 G1 box; other site 159087001978 GTP/Mg2+ binding site [chemical binding]; other site 159087001979 Switch I region; other site 159087001980 G2 box; other site 159087001981 G3 box; other site 159087001982 Switch II region; other site 159087001983 G4 box; other site 159087001984 G5 box; other site 159087001985 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 159087001986 dimer interface [polypeptide binding]; other site 159087001987 active site 159087001988 aspartate-rich active site metal binding site; other site 159087001989 allosteric magnesium binding site [ion binding]; other site 159087001990 Schiff base residues; other site 159087001991 division inhibitor protein; Provisional; Region: slmA; PRK09480 159087001992 Helix-turn-helix domains; Region: HTH; cl00088 159087001993 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 159087001994 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 159087001995 motif II; other site 159087001996 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 159087001997 feedback inhibition sensing region; other site 159087001998 homohexameric interface [polypeptide binding]; other site 159087001999 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 159087002000 nucleotide binding site [chemical binding]; other site 159087002001 N-acetyl-L-glutamate binding site [chemical binding]; other site 159087002002 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 159087002003 putative dimer interface [polypeptide binding]; other site 159087002004 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_7; cd04664 159087002005 nudix motif; other site 159087002006 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 159087002007 putative RNAase interaction site [polypeptide binding]; other site 159087002008 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 159087002009 active site 159087002010 barstar interaction site; other site 159087002011 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 159087002012 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 159087002013 dimer interface [polypeptide binding]; other site 159087002014 anticodon binding site; other site 159087002015 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 the...; Region: AspRS_core; cd00777 159087002016 homodimer interface [polypeptide binding]; other site 159087002017 motif 1; other site 159087002018 active site 159087002019 motif 2; other site 159087002020 GAD domain; Region: GAD; pfam02938 159087002021 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 the...; Region: AspRS_core; cd00777 159087002022 motif 3; other site 159087002023 Protein of unknown function (DUF502); Region: DUF502; cl01107 159087002024 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 159087002025 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 159087002026 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 159087002027 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 159087002028 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 159087002029 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087002030 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087002031 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087002032 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 159087002033 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 159087002034 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 159087002035 Walker A motif; other site 159087002036 ATP binding site [chemical binding]; other site 159087002037 Walker B motif; other site 159087002038 Domain of unknown function DUF21; Region: DUF21; pfam01595 159087002039 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 159087002040 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 159087002041 Transporter associated domain; Region: CorC_HlyC; cl08393 159087002042 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 159087002043 signal recognition particle protein; Provisional; Region: PRK10867 159087002044 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 159087002045 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 159087002046 P loop; other site 159087002047 GTP binding site [chemical binding]; other site 159087002048 Signal peptide binding domain; Region: SRP_SPB; pfam02978 159087002049 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087002050 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 catalyze...; Region: LT_GEWL; cd00254 159087002051 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087002052 catalytic residue [active] 159087002053 prolyl-tRNA synthetase; Provisional; Region: PRK09194 159087002054 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 formation of...; Region: ProRS_core_prok; cd00779 159087002055 dimer interface [polypeptide binding]; other site 159087002056 motif 1; other site 159087002057 active site 159087002058 motif 2; other site 159087002059 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 159087002060 putative deacylase active site [active] 159087002061 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 attaches...; Region: class_II_aaRS-like_core; cl00268 159087002062 active site 159087002063 motif 3; other site 159087002064 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 159087002065 anticodon binding site; other site 159087002066 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 159087002067 putative active site [active] 159087002068 Ap4A binding site [chemical binding]; other site 159087002069 nudix motif; other site 159087002070 putative metal binding site [ion binding]; other site 159087002071 CNP1-like family; Region: CNP1; pfam08750 159087002072 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 159087002073 diiron binding motif [ion binding]; other site 159087002074 OsmC-like protein; Region: OsmC; cl00767 159087002075 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 159087002076 23S rRNA interface [nucleotide binding]; other site 159087002077 L3 interface [polypeptide binding]; other site 159087002078 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 159087002079 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 159087002080 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 159087002081 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087002082 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 159087002083 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 159087002084 putative ATP binding site [chemical binding]; other site 159087002085 putative substrate interface [chemical binding]; other site 159087002086 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 159087002087 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087002088 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 159087002089 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 159087002090 substrate binding pocket [chemical binding]; other site 159087002091 chain length determination region; other site 159087002092 substrate-Mg2+ binding site; other site 159087002093 catalytic residues [active] 159087002094 aspartate-rich region 1; other site 159087002095 active site lid residues [active] 159087002096 aspartate-rich region 2; other site 159087002097 Protein of unknown function (DUF3553); Region: DUF3553; pfam12073 159087002098 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 159087002099 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 159087002100 dimer interface [polypeptide binding]; other site 159087002101 phosphorylation site [posttranslational modification] 159087002102 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 159087002103 ATP binding site [chemical binding]; other site 159087002104 Mg2+ binding site [ion binding]; other site 159087002105 G-X-G motif; other site 159087002106 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087002107 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002108 active site 159087002109 phosphorylation site [posttranslational modification] 159087002110 intermolecular recognition site; other site 159087002111 dimerization interface [polypeptide binding]; other site 159087002112 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 159087002113 Walker A motif; other site 159087002114 ATP binding site [chemical binding]; other site 159087002115 Walker B motif; other site 159087002116 arginine finger; other site 159087002117 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087002118 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; cl02712 159087002119 aminotransferase; Validated; Region: PRK07337 159087002120 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 159087002121 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087002122 homodimer interface [polypeptide binding]; other site 159087002123 catalytic residue [active] 159087002124 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 159087002125 Phosphoenolpyruvate carboxykinase; Region: PEPCK; pfam00821 159087002126 active site 159087002127 substrate-binding site [chemical binding]; other site 159087002128 metal-binding site [ion binding] 159087002129 GTP binding site [chemical binding]; other site 159087002130 malic enzyme; Reviewed; Region: PRK12862 159087002131 Malic enzyme, N-terminal domain; Region: malic; pfam00390 159087002132 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 159087002133 putative NAD(P) binding site [chemical binding]; other site 159087002134 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 159087002135 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 159087002136 Transcriptional regulator [Transcription]; Region: IclR; COG1414 159087002137 Helix-turn-helix domains; Region: HTH; cl00088 159087002138 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087002139 glycerol-3-phosphate dehydrogenase, anaerobic, C subunit; Region: glycerol3P_GlpC; TIGR03379 159087002140 Cysteine-rich domain; Region: CCG; pfam02754 159087002141 Cysteine-rich domain; Region: CCG; pfam02754 159087002142 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 159087002143 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 159087002144 4Fe-4S binding domain; Region: Fer4; cl02805 159087002145 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 159087002146 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 159087002147 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 159087002148 NAD(P) binding site [chemical binding]; other site 159087002149 glycerate dehydrogenase; Provisional; Region: PRK06487 159087002150 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087002151 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 159087002152 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 159087002153 PAS fold; Region: PAS_3; pfam08447 159087002154 putative active site [active] 159087002155 heme pocket [chemical binding]; other site 159087002156 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002157 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087002158 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087002159 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 159087002160 putative active site [active] 159087002161 heme pocket [chemical binding]; other site 159087002162 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 159087002163 putative active site [active] 159087002164 heme pocket [chemical binding]; other site 159087002165 PAS domain S-box; Region: sensory_box; TIGR00229 159087002166 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 159087002167 putative active site [active] 159087002168 heme pocket [chemical binding]; other site 159087002169 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087002170 metal binding site [ion binding]; metal-binding site 159087002171 active site 159087002172 I-site; other site 159087002173 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 159087002174 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 159087002175 RNA binding surface [nucleotide binding]; other site 159087002176 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 159087002177 putative acyl-acceptor binding pocket; other site 159087002178 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 159087002179 Phosphate transporter family; Region: PHO4; cl00396 159087002180 Phosphate transporter family; Region: PHO4; cl00396 159087002181 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_3; cd09321 159087002182 gating phenylalanine in ion channel; other site 159087002183 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087002184 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087002185 4Fe-4S binding domain; Region: Fer4; cl02805 159087002186 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087002187 PAS fold; Region: PAS_4; pfam08448 159087002188 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087002189 putative active site [active] 159087002190 heme pocket [chemical binding]; other site 159087002191 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 159087002192 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 159087002193 Walker A motif; other site 159087002194 ATP binding site [chemical binding]; other site 159087002195 Walker B motif; other site 159087002196 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 159087002197 arginine finger; other site 159087002198 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087002199 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; cl15357 159087002200 transmembrane helices; other site 159087002201 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002202 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002203 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002204 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002205 secreted effector protein PipB2; Provisional; Region: PRK15196 159087002206 MASE1; Region: MASE1; pfam05231 159087002207 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 159087002208 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; cl00075 159087002209 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087002210 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002211 active site 159087002212 phosphorylation site [posttranslational modification] 159087002213 intermolecular recognition site; other site 159087002214 dimerization interface [polypeptide binding]; other site 159087002215 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 159087002216 DNA binding residues [nucleotide binding] 159087002217 dimerization interface [polypeptide binding]; other site 159087002218 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 159087002219 dimerization interface [polypeptide binding]; other site 159087002220 putative DNA binding site [nucleotide binding]; other site 159087002221 putative Zn2+ binding site [ion binding]; other site 159087002222 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 159087002223 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 159087002224 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 159087002225 putative active site [active] 159087002226 putative NTP binding site [chemical binding]; other site 159087002227 putative nucleic acid binding site [nucleotide binding]; other site 159087002228 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 159087002229 Cytochrome c; Region: Cytochrom_C; cl11414 159087002230 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087002231 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002232 ligand binding site [chemical binding]; other site 159087002233 Transcriptional regulators [Transcription]; Region: MarR; COG1846 159087002234 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087002235 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002236 ligand binding site [chemical binding]; other site 159087002237 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 159087002238 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 159087002239 putative ion selectivity filter; other site 159087002240 putative pore gating glutamate residue; other site 159087002241 putative H+/Cl- coupling transport residue; other site 159087002242 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 159087002243 putative DNA binding site [nucleotide binding]; other site 159087002244 putative Zn2+ binding site [ion binding]; other site 159087002245 Low molecular weight phosphatase family; Region: LMWPc; cd00115 159087002246 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 159087002247 active site 159087002248 Membrane transport protein; Region: Mem_trans; cl09117 159087002249 Predicted permease; Region: DUF318; cl00487 159087002250 Predicted permease; Region: DUF318; cl00487 159087002251 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087002252 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl08302 159087002253 Ca2+ binding site [ion binding]; other site 159087002254 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087002255 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002256 active site 159087002257 phosphorylation site [posttranslational modification] 159087002258 intermolecular recognition site; other site 159087002259 dimerization interface [polypeptide binding]; other site 159087002260 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 159087002261 DNA binding site [nucleotide binding] 159087002262 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087002263 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 159087002264 dimerization interface [polypeptide binding]; other site 159087002265 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 159087002266 dimer interface [polypeptide binding]; other site 159087002267 phosphorylation site [posttranslational modification] 159087002268 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 159087002269 ATP binding site [chemical binding]; other site 159087002270 Mg2+ binding site [ion binding]; other site 159087002271 G-X-G motif; other site 159087002272 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 159087002273 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 159087002274 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 159087002275 substrate binding site [chemical binding]; other site 159087002276 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 159087002277 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002278 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002279 active site 159087002280 phosphorylation site [posttranslational modification] 159087002281 intermolecular recognition site; other site 159087002282 dimerization interface [polypeptide binding]; other site 159087002283 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087002284 metal binding site [ion binding]; metal-binding site 159087002285 active site 159087002286 I-site; other site 159087002287 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 159087002288 NAD binding site [chemical binding]; other site 159087002289 homotetramer interface [polypeptide binding]; other site 159087002290 homodimer interface [polypeptide binding]; other site 159087002291 active site 159087002292 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 159087002293 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087002294 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 159087002295 metal-binding site [ion binding] 159087002296 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087002297 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087002298 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 159087002299 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 159087002300 Low-spin heme binding site [chemical binding]; other site 159087002301 Putative water exit pathway; other site 159087002302 Binuclear center (active site) [active] 159087002303 Putative proton exit pathway; other site 159087002304 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 159087002305 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 159087002306 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 159087002307 Cytochrome c; Region: Cytochrom_C; cl11414 159087002308 Cytochrome c; Region: Cytochrom_C; cl11414 159087002309 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087002310 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087002311 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087002312 FixH; Region: FixH; cl01254 159087002313 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087002314 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 159087002315 nudix motif; other site 159087002316 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 159087002317 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 159087002318 flagellar motor protein MotB; Validated; Region: motB; PRK09041 159087002319 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002320 ligand binding site [chemical binding]; other site 159087002321 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002322 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002323 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002324 active site 159087002325 phosphorylation site [posttranslational modification] 159087002326 intermolecular recognition site; other site 159087002327 dimerization interface [polypeptide binding]; other site 159087002328 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087002329 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 159087002330 putative binding surface; other site 159087002331 active site 159087002332 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087002333 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 159087002334 ATP binding site [chemical binding]; other site 159087002335 Mg2+ binding site [ion binding]; other site 159087002336 G-X-G motif; other site 159087002337 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 159087002338 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 159087002339 putative CheA interaction surface; other site 159087002340 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 159087002341 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 159087002342 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002343 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087002344 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 159087002345 PAS fold; Region: PAS_3; pfam08447 159087002346 putative active site [active] 159087002347 heme pocket [chemical binding]; other site 159087002348 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087002349 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002350 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 159087002351 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002352 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087002353 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 159087002354 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 159087002355 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; cl12011 159087002356 CheD chemotactic sensory transduction; Region: CheD; cl00810 159087002357 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 159087002358 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002359 active site 159087002360 phosphorylation site [posttranslational modification] 159087002361 intermolecular recognition site; other site 159087002362 dimerization interface [polypeptide binding]; other site 159087002363 CheB methylesterase; Region: CheB_methylest; pfam01339 159087002364 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 159087002365 anti sigma factor interaction site; other site 159087002366 regulatory phosphorylation site [posttranslational modification]; other site 159087002367 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087002368 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087002369 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002370 active site 159087002371 phosphorylation site [posttranslational modification] 159087002372 intermolecular recognition site; other site 159087002373 dimerization interface [polypeptide binding]; other site 159087002374 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087002375 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087002376 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002377 active site 159087002378 phosphorylation site [posttranslational modification] 159087002379 intermolecular recognition site; other site 159087002380 dimerization interface [polypeptide binding]; other site 159087002381 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002382 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002383 active site 159087002384 phosphorylation site [posttranslational modification] 159087002385 intermolecular recognition site; other site 159087002386 dimerization interface [polypeptide binding]; other site 159087002387 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 159087002388 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 159087002389 putative binding surface; other site 159087002390 active site 159087002391 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087002392 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 159087002393 ATP binding site [chemical binding]; other site 159087002394 Mg2+ binding site [ion binding]; other site 159087002395 G-X-G motif; other site 159087002396 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087002397 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 159087002398 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 159087002399 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 159087002400 FHIPEP family; Region: FHIPEP; pfam00771 159087002401 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 159087002402 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087002403 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 159087002404 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087002405 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 159087002406 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087002407 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 159087002408 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 159087002409 DNA binding residues [nucleotide binding] 159087002410 flagellar motor protein MotA; Validated; Region: PRK08124 159087002411 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 159087002412 flagellar motor protein MotD; Reviewed; Region: PRK09038 159087002413 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002414 ligand binding site [chemical binding]; other site 159087002415 FlgN protein; Region: FlgN; cl09176 159087002416 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 159087002417 SAF domain; Region: SAF; cl00555 159087002418 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 159087002419 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 159087002420 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 159087002421 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 159087002422 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 159087002423 Flagellar hook capping protein; Region: FlgD; cl04347 159087002424 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 159087002425 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 159087002426 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 159087002427 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 159087002428 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 159087002429 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 159087002430 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 159087002431 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 159087002432 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 159087002433 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 159087002434 Flagellar L-ring protein; Region: FlgH; cl00905 159087002435 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 159087002436 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 159087002437 Rod binding protein; Region: Rod-binding; cl01626 159087002438 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 159087002439 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 159087002440 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 159087002441 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 159087002442 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 159087002443 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 159087002444 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 159087002445 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 159087002446 FliP family; Region: FliP; cl00593 159087002447 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 159087002448 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 159087002449 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 159087002450 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 159087002451 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 159087002452 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 159087002453 Flagellar FliJ protein; Region: FliJ; cl09161 159087002454 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 159087002455 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 159087002456 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 159087002457 Walker A motif/ATP binding site; other site 159087002458 Walker B motif; other site 159087002459 flagellar assembly protein H; Validated; Region: fliH; PRK05687 159087002460 Flagellar assembly protein FliH; Region: FliH; pfam02108 159087002461 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 159087002462 FliG C-terminal domain; Region: FliG_C; pfam01706 159087002463 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 159087002464 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 159087002465 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 159087002466 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 159087002467 dimer interface [polypeptide binding]; other site 159087002468 phosphorylation site [posttranslational modification] 159087002469 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 159087002470 ATP binding site [chemical binding]; other site 159087002471 Mg2+ binding site [ion binding]; other site 159087002472 G-X-G motif; other site 159087002473 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087002474 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002475 active site 159087002476 phosphorylation site [posttranslational modification] 159087002477 intermolecular recognition site; other site 159087002478 dimerization interface [polypeptide binding]; other site 159087002479 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 159087002480 Walker A motif; other site 159087002481 ATP binding site [chemical binding]; other site 159087002482 Walker B motif; other site 159087002483 arginine finger; other site 159087002484 Helix-turn-helix domains; Region: HTH; cl00088 159087002485 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 159087002486 Flagellar regulator YcgR; Region: YcgR; pfam07317 159087002487 PilZ domain; Region: PilZ; cl01260 159087002488 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 159087002489 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 159087002490 Flagellar protein FliT; Region: FliT; cl05125 159087002491 Flagellar protein FliS; Region: FliS; cl00654 159087002492 flagellar capping protein; Reviewed; Region: fliD; PRK08032 159087002493 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 159087002494 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 159087002495 FlaG protein; Region: FlaG; cl00591 159087002496 flagellin; Provisional; Region: PRK12802 159087002497 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 159087002498 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 159087002499 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 159087002500 binding surface 159087002501 TPR motif; other site 159087002502 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 159087002503 TPR motif; other site 159087002504 binding surface 159087002505 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 159087002506 TPR motif; other site 159087002507 binding surface 159087002508 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 159087002509 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 159087002510 binding surface 159087002511 TPR motif; other site 159087002512 cellulose synthase subunit BcsC; Provisional; Region: PRK11447 159087002513 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; cl12011 159087002514 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 159087002515 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087002516 metal binding site [ion binding]; metal-binding site 159087002517 active site 159087002518 I-site; other site 159087002519 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 159087002520 DNA binding site [nucleotide binding] 159087002521 Int/Topo IB signature motif; other site 159087002522 active site 159087002523 BRO family, N-terminal domain; Region: Bro-N; cl10591 159087002524 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 159087002525 KilA-N domain; Region: KilA-N; pfam04383 159087002526 BRO family, N-terminal domain; Region: Bro-N; cl10591 159087002527 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 159087002528 K-box region; Region: K-box; pfam01486 159087002529 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 159087002530 catalytic residues [active] 159087002531 catalytic nucleophile [active] 159087002532 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087002533 Transcriptional regulator [Transcription]; Region: IclR; COG1414 159087002534 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087002535 ParA-like protein; Provisional; Region: PHA02518 159087002536 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 159087002537 P-loop; other site 159087002538 Magnesium ion binding site [ion binding]; other site 159087002539 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 159087002540 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 159087002541 Walker A motif; other site 159087002542 ATP binding site [chemical binding]; other site 159087002543 Walker B motif; other site 159087002544 arginine finger; other site 159087002545 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 159087002546 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 159087002547 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 159087002548 recombination protein RecR; Reviewed; Region: recR; PRK00076 159087002549 RecR protein; Region: RecR; pfam02132 159087002550 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 159087002551 putative active site [active] 159087002552 putative metal-binding site [ion binding]; other site 159087002553 tetramer interface [polypeptide binding]; other site 159087002554 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 159087002555 [2Fe-2S] cluster binding site [ion binding]; other site 159087002556 cytochrome b; Provisional; Region: CYTB; MTH00145 159087002557 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 159087002558 Qi binding site; other site 159087002559 intrachain domain interface; other site 159087002560 interchain domain interface [polypeptide binding]; other site 159087002561 heme bH binding site [chemical binding]; other site 159087002562 heme bL binding site [chemical binding]; other site 159087002563 Qo binding site; other site 159087002564 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; cl00193 159087002565 interchain domain interface [polypeptide binding]; other site 159087002566 intrachain domain interface; other site 159087002567 Qi binding site; other site 159087002568 Qo binding site; other site 159087002569 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 159087002570 stringent starvation protein A; Provisional; Region: sspA; PRK09481 159087002571 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 159087002572 C-terminal domain interface [polypeptide binding]; other site 159087002573 putative GSH binding site (G-site) [chemical binding]; other site 159087002574 dimer interface [polypeptide binding]; other site 159087002575 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 159087002576 dimer interface [polypeptide binding]; other site 159087002577 N-terminal domain interface [polypeptide binding]; other site 159087002578 Stringent starvation protein B; Region: SspB; cl01120 159087002579 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 159087002580 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 159087002581 [4Fe-4S] binding site [ion binding]; other site 159087002582 molybdopterin cofactor binding site; other site 159087002583 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 159087002584 molybdopterin cofactor binding site; other site 159087002585 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 159087002586 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 159087002587 glycosyl transferase family protein; Provisional; Region: PRK08136 159087002588 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 159087002589 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 159087002590 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087002591 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 159087002592 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 159087002593 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 159087002594 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 159087002595 [2Fe-2S] cluster binding site [ion binding]; other site 159087002596 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 159087002597 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 159087002598 active site 159087002599 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087002600 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087002601 active site 159087002602 ATP binding site [chemical binding]; other site 159087002603 substrate binding site [chemical binding]; other site 159087002604 activation loop (A-loop); other site 159087002605 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_3; cd04327 159087002606 Astacin (Peptidase family M12A); Region: Astacin; pfam01400 159087002607 active site 159087002608 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 159087002609 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 159087002610 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 159087002611 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087002612 active site 159087002613 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087002614 active site 159087002615 ATP binding site [chemical binding]; other site 159087002616 substrate binding site [chemical binding]; other site 159087002617 activation loop (A-loop); other site 159087002618 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 159087002619 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087002620 putative substrate translocation pore; other site 159087002621 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 159087002622 putative active site [active] 159087002623 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 159087002624 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002625 active site 159087002626 phosphorylation site [posttranslational modification] 159087002627 intermolecular recognition site; other site 159087002628 dimerization interface [polypeptide binding]; other site 159087002629 ANTAR domain; Region: ANTAR; cl04297 159087002630 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 159087002631 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 159087002632 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 159087002633 dimer interface [polypeptide binding]; other site 159087002634 conserved gate region; other site 159087002635 putative PBP binding loops; other site 159087002636 ABC-ATPase subunit interface; other site 159087002637 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 159087002638 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 159087002639 Walker A/P-loop; other site 159087002640 ATP binding site [chemical binding]; other site 159087002641 Q-loop/lid; other site 159087002642 ABC transporter signature motif; other site 159087002643 Walker B; other site 159087002644 D-loop; other site 159087002645 H-loop/switch region; other site 159087002646 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 159087002647 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 159087002648 dimerization interface [polypeptide binding]; other site 159087002649 GAF domain; Region: GAF; cl00853 159087002650 Histidine kinase; Region: HisKA_3; pfam07730 159087002651 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 159087002652 ATP binding site [chemical binding]; other site 159087002653 Mg2+ binding site [ion binding]; other site 159087002654 G-X-G motif; other site 159087002655 transcriptional regulator NarL; Provisional; Region: PRK10651 159087002656 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002657 active site 159087002658 phosphorylation site [posttranslational modification] 159087002659 intermolecular recognition site; other site 159087002660 dimerization interface [polypeptide binding]; other site 159087002661 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 159087002662 DNA binding residues [nucleotide binding] 159087002663 dimerization interface [polypeptide binding]; other site 159087002664 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; cl12011 159087002665 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 159087002666 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 159087002667 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087002668 ABC transporter ATPase component; Reviewed; Region: PRK11147 159087002669 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087002670 Walker A/P-loop; other site 159087002671 ATP binding site [chemical binding]; other site 159087002672 Q-loop/lid; other site 159087002673 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087002674 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087002675 ABC transporter; Region: ABC_tran_2; pfam12848 159087002676 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087002677 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087002678 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 159087002679 putative substrate translocation pore; other site 159087002680 HDOD domain; Region: HDOD; pfam08668 159087002681 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087002682 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 159087002683 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 159087002684 endonuclease III; Region: ENDO3c; smart00478 159087002685 minor groove reading motif; other site 159087002686 helix-hairpin-helix signature motif; other site 159087002687 substrate binding pocket [chemical binding]; other site 159087002688 active site 159087002689 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 159087002690 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; cl14780 159087002691 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 159087002692 Ligand Binding Site [chemical binding]; other site 159087002693 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 159087002694 dihydrodipicolinate synthase; Region: dapA; TIGR00674 159087002695 dimer interface [polypeptide binding]; other site 159087002696 active site 159087002697 catalytic residue [active] 159087002698 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 159087002699 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087002700 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 159087002701 TRAM domain; Region: TRAM; cl01282 159087002702 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 159087002703 S-adenosylmethionine binding site [chemical binding]; other site 159087002704 YccA-like proteins; Region: YccA_like; cd10433 159087002705 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 159087002706 active site 159087002707 nucleophile elbow; other site 159087002708 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 159087002709 active site 159087002710 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 159087002711 FeS/SAM binding site; other site 159087002712 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 159087002713 non-specific DNA binding site [nucleotide binding]; other site 159087002714 salt bridge; other site 159087002715 sequence-specific DNA binding site [nucleotide binding]; other site 159087002716 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 159087002717 FOG: CBS domain [General function prediction only]; Region: COG0517 159087002718 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 159087002719 Tetramer interface [polypeptide binding]; other site 159087002720 active site 159087002721 FMN-binding site [chemical binding]; other site 159087002722 Protein of unknown function (DUF465); Region: DUF465; cl01070 159087002723 MFS_1 like family; Region: MFS_1_like; pfam12832 159087002724 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 159087002725 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 159087002726 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 159087002727 substrate binding site [chemical binding]; other site 159087002728 ligand binding site [chemical binding]; other site 159087002729 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 159087002730 substrate binding site [chemical binding]; other site 159087002731 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 159087002732 tartrate dehydrogenase; Provisional; Region: PRK08194 159087002733 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 159087002734 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087002735 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 159087002736 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 159087002737 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 159087002738 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 159087002739 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 159087002740 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 159087002741 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 159087002742 dimerization interface 3.5A [polypeptide binding]; other site 159087002743 active site 159087002744 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 monomeric; Region: PRAI; cd00405 159087002745 active site 159087002746 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 159087002747 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 159087002748 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087002749 catalytic residue [active] 159087002750 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 159087002751 substrate binding site [chemical binding]; other site 159087002752 active site 159087002753 catalytic residues [active] 159087002754 heterodimer interface [polypeptide binding]; other site 159087002755 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 159087002756 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; cl14780 159087002757 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 159087002758 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087002759 Sporulation related domain; Region: SPOR; cl10051 159087002760 Colicin V production protein; Region: Colicin_V; cl00567 159087002761 amidophosphoribosyltransferase; Provisional; Region: PRK09246 159087002762 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 159087002763 tetramer interface [polypeptide binding]; other site 159087002764 active site 159087002765 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087002766 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 159087002767 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 159087002768 homodimer interface [polypeptide binding]; other site 159087002769 substrate-cofactor binding pocket; other site 159087002770 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087002771 catalytic residue [active] 159087002772 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 159087002773 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 159087002774 ATP binding site [chemical binding]; other site 159087002775 Mg++ binding site [ion binding]; other site 159087002776 motif III; other site 159087002777 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 159087002778 nucleotide binding region [chemical binding]; other site 159087002779 ATP-binding site [chemical binding]; other site 159087002780 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 159087002781 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 159087002782 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 159087002783 Walker A motif; other site 159087002784 ATP binding site [chemical binding]; other site 159087002785 Walker B motif; other site 159087002786 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087002787 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087002788 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087002789 legume lectins; Region: lectin_L-type; cl14058 159087002790 homotetramer interaction site [polypeptide binding]; other site 159087002791 homodimer interaction site [polypeptide binding]; other site 159087002792 carbohydrate binding site [chemical binding]; other site 159087002793 metal binding site [ion binding]; metal-binding site 159087002794 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 159087002795 Secretin and TonB N terminus short domain; Region: STN; cl06624 159087002796 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 159087002797 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 159087002798 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087002799 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 159087002800 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 159087002801 Walker A motif; other site 159087002802 ATP binding site [chemical binding]; other site 159087002803 Walker B motif; other site 159087002804 arginine finger; other site 159087002805 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 159087002806 binding surface 159087002807 TPR motif; other site 159087002808 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 159087002809 TPR motif; other site 159087002810 binding surface 159087002811 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 159087002812 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087002813 DNA-binding transcriptional activator MhpR; Provisional; Region: PRK09834 159087002814 Helix-turn-helix domains; Region: HTH; cl00088 159087002815 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087002816 Transcriptional regulators [Transcription]; Region: GntR; COG1802 159087002817 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087002818 DNA-binding site [nucleotide binding]; DNA binding site 159087002819 FCD domain; Region: FCD; cl11656 159087002820 FAD binding domain; Region: FAD_binding_3; pfam01494 159087002821 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087002822 3-(3-hydroxyphenyl)propionate hydroxylase; Validated; Region: mhpA; PRK06183 159087002823 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087002824 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087002825 putative ligand binding site [chemical binding]; other site 159087002826 Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate; Region: MhpB_like; cd07365 159087002827 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087002828 putative active site [active] 159087002829 Fe(II) binding site [ion binding]; other site 159087002830 putative dimer interface [polypeptide binding]; other site 159087002831 putative tetramer interface [polypeptide binding]; other site 159087002832 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087002833 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087002834 active site 159087002835 Flavin Reductases; Region: FlaRed; cl00801 159087002836 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087002837 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087002838 putative ligand binding site [chemical binding]; other site 159087002839 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087002840 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087002841 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087002842 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087002843 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087002844 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087002845 active site 159087002846 catalytic residues [active] 159087002847 metal binding site [ion binding]; metal-binding site 159087002848 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087002849 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087002850 TM-ABC transporter signature motif; other site 159087002851 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087002852 TM-ABC transporter signature motif; other site 159087002853 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087002854 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087002855 Walker A/P-loop; other site 159087002856 ATP binding site [chemical binding]; other site 159087002857 Q-loop/lid; other site 159087002858 ABC transporter signature motif; other site 159087002859 Walker B; other site 159087002860 D-loop; other site 159087002861 H-loop/switch region; other site 159087002862 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087002863 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087002864 Walker A/P-loop; other site 159087002865 ATP binding site [chemical binding]; other site 159087002866 Q-loop/lid; other site 159087002867 ABC transporter signature motif; other site 159087002868 Walker B; other site 159087002869 D-loop; other site 159087002870 H-loop/switch region; other site 159087002871 Uncharacterized conserved protein [Function unknown]; Region: COG3945 159087002872 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087002873 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087002874 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 159087002875 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 159087002876 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 159087002877 ATP binding site [chemical binding]; other site 159087002878 putative Mg++ binding site [ion binding]; other site 159087002879 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 159087002880 nucleotide binding region [chemical binding]; other site 159087002881 ATP-binding site [chemical binding]; other site 159087002882 RQC domain; Region: RQC; cl09632 159087002883 HRDC domain; Region: HRDC; cl02578 159087002884 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087002885 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 159087002886 putative active site [active] 159087002887 putative metal binding site [ion binding]; other site 159087002888 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 159087002889 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 159087002890 substrate binding site [chemical binding]; other site 159087002891 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 159087002892 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 159087002893 substrate binding site [chemical binding]; other site 159087002894 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 159087002895 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 159087002896 binding surface 159087002897 TPR motif; other site 159087002898 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 159087002899 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 159087002900 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 159087002901 active site 159087002902 HIGH motif; other site 159087002903 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 159087002904 KMSKS motif; other site 159087002905 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 159087002906 tRNA binding surface [nucleotide binding]; other site 159087002907 anticodon binding site; other site 159087002908 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087002909 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087002910 putative ligand binding site [chemical binding]; other site 159087002911 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087002912 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087002913 putative ligand binding site [chemical binding]; other site 159087002914 chaperone protein DnaJ; Provisional; Region: PRK10767 159087002915 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 159087002916 HSP70 interaction site [polypeptide binding]; other site 159087002917 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 159087002918 substrate binding site [polypeptide binding]; other site 159087002919 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 159087002920 Zn binding sites [ion binding]; other site 159087002921 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 159087002922 dimer interface [polypeptide binding]; other site 159087002923 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 159087002924 heat shock protein GrpE; Provisional; Region: PRK14140 159087002925 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 159087002926 dimer interface [polypeptide binding]; other site 159087002927 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 159087002928 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087002929 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087002930 active site 159087002931 ATP binding site [chemical binding]; other site 159087002932 substrate binding site [chemical binding]; other site 159087002933 activation loop (A-loop); other site 159087002934 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; cl00047 159087002935 ligand binding site [chemical binding]; other site 159087002936 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 159087002937 dimerization interface [polypeptide binding]; other site 159087002938 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002939 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087002940 thioredoxin 2; Provisional; Region: PRK10996 159087002941 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 159087002942 catalytic residues [active] 159087002943 ferrochelatase; Reviewed; Region: hemH; PRK00035 159087002944 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 159087002945 C-terminal domain interface [polypeptide binding]; other site 159087002946 active site 159087002947 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 159087002948 active site 159087002949 N-terminal domain interface [polypeptide binding]; other site 159087002950 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 159087002951 Helix-turn-helix domains; Region: HTH; cl00088 159087002952 HrcA protein C terminal domain; Region: HrcA; pfam01628 159087002953 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 159087002954 recombination and repair protein; Provisional; Region: PRK10869 159087002955 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 159087002956 Walker A/P-loop; other site 159087002957 ATP binding site [chemical binding]; other site 159087002958 Q-loop/lid; other site 159087002959 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 159087002960 ABC transporter signature motif; other site 159087002961 Walker B; other site 159087002962 D-loop; other site 159087002963 H-loop/switch region; other site 159087002964 Predicted membrane protein [Function unknown]; Region: COG2119 159087002965 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087002966 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087002967 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 159087002968 metal binding site 2 [ion binding]; metal-binding site 159087002969 putative DNA binding helix; other site 159087002970 metal binding site 1 [ion binding]; metal-binding site 159087002971 dimer interface [polypeptide binding]; other site 159087002972 structural Zn2+ binding site [ion binding]; other site 159087002973 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 159087002974 dihydrodipicolinate reductase; Provisional; Region: PRK00048 159087002975 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087002976 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 159087002977 PAS fold; Region: PAS_3; pfam08447 159087002978 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087002979 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 159087002980 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 159087002981 dimer interface [polypeptide binding]; other site 159087002982 phosphorylation site [posttranslational modification] 159087002983 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 159087002984 ATP binding site [chemical binding]; other site 159087002985 Mg2+ binding site [ion binding]; other site 159087002986 G-X-G motif; other site 159087002987 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087002988 active site 159087002989 phosphorylation site [posttranslational modification] 159087002990 intermolecular recognition site; other site 159087002991 dimerization interface [polypeptide binding]; other site 159087002992 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 159087002993 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 159087002994 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 159087002995 catalytic site [active] 159087002996 subunit interface [polypeptide binding]; other site 159087002997 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 159087002998 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087002999 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087003000 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087003001 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087003002 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 159087003003 IMP binding site; other site 159087003004 dimer interface [polypeptide binding]; other site 159087003005 interdomain contacts; other site 159087003006 partial ornithine binding site; other site 159087003007 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 159087003008 domain; Region: GreA_GreB_N; pfam03449 159087003009 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 159087003010 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 159087003011 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 159087003012 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; cl12011 159087003013 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 159087003014 FtsH Extracellular; Region: FtsH_ext; pfam06480 159087003015 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 159087003016 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 159087003017 Walker A motif; other site 159087003018 ATP binding site [chemical binding]; other site 159087003019 Walker B motif; other site 159087003020 arginine finger; other site 159087003021 Peptidase family M41; Region: Peptidase_M41; pfam01434 159087003022 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 159087003023 dihydropteroate synthase; Region: DHPS; TIGR01496 159087003024 substrate binding pocket [chemical binding]; other site 159087003025 dimer interface [polypeptide binding]; other site 159087003026 inhibitor binding site; inhibition site 159087003027 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 159087003028 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 159087003029 active site 159087003030 substrate binding site [chemical binding]; other site 159087003031 metal binding site [ion binding]; metal-binding site 159087003032 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 159087003033 substrate binding site [chemical binding]; other site 159087003034 dimer interface [polypeptide binding]; other site 159087003035 catalytic triad [active] 159087003036 Preprotein translocase SecG subunit; Region: SecG; cl09123 159087003037 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 159087003038 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 159087003039 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 159087003040 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087003041 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 159087003042 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 159087003043 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 159087003044 putative dimer interface [polypeptide binding]; other site 159087003045 [2Fe-2S] cluster binding site [ion binding]; other site 159087003046 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 159087003047 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 159087003048 SLBB domain; Region: SLBB; pfam10531 159087003049 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 159087003050 NADH dehydrogenase subunit G; Validated; Region: PRK09129 159087003051 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 159087003052 catalytic loop [active] 159087003053 iron binding site [ion binding]; other site 159087003054 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 159087003055 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 159087003056 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 159087003057 NADH dehydrogenase; Region: NADHdh; cl00469 159087003058 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 159087003059 4Fe-4S binding domain; Region: Fer4; cl02805 159087003060 4Fe-4S binding domain; Region: Fer4; cl02805 159087003061 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 159087003062 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 159087003063 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 159087003064 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 159087003065 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 159087003066 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 159087003067 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087003068 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 159087003069 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087003070 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 159087003071 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 159087003072 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 159087003073 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 159087003074 dimer interface [polypeptide binding]; other site 159087003075 ADP-ribose binding site [chemical binding]; other site 159087003076 active site 159087003077 nudix motif; other site 159087003078 metal binding site [ion binding]; metal-binding site 159087003079 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 159087003080 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 159087003081 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 159087003082 active site 159087003083 dimer interface [polypeptide binding]; other site 159087003084 effector binding site; other site 159087003085 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087003086 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087003087 octamerization interface [polypeptide binding]; other site 159087003088 diferric-oxygen binding site [ion binding]; other site 159087003089 PAS domain S-box; Region: sensory_box; TIGR00229 159087003090 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087003091 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 159087003092 dimer interface [polypeptide binding]; other site 159087003093 phosphorylation site [posttranslational modification] 159087003094 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 159087003095 ATP binding site [chemical binding]; other site 159087003096 Mg2+ binding site [ion binding]; other site 159087003097 G-X-G motif; other site 159087003098 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003099 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003100 active site 159087003101 phosphorylation site [posttranslational modification] 159087003102 intermolecular recognition site; other site 159087003103 dimerization interface [polypeptide binding]; other site 159087003104 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 159087003105 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 159087003106 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 159087003107 Walker A motif; other site 159087003108 ATP binding site [chemical binding]; other site 159087003109 Walker B motif; other site 159087003110 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 159087003111 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 159087003112 dimer interface [polypeptide binding]; other site 159087003113 phosphorylation site [posttranslational modification] 159087003114 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 159087003115 ATP binding site [chemical binding]; other site 159087003116 Mg2+ binding site [ion binding]; other site 159087003117 G-X-G motif; other site 159087003118 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras; Region: Ras_like_GTPase; cd00882 159087003119 G1 box; other site 159087003120 GTP/Mg2+ binding site [chemical binding]; other site 159087003121 G2 box; other site 159087003122 Switch I region; other site 159087003123 G3 box; other site 159087003124 Switch II region; other site 159087003125 G4 box; other site 159087003126 G5 box; other site 159087003127 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003128 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003129 active site 159087003130 phosphorylation site [posttranslational modification] 159087003131 intermolecular recognition site; other site 159087003132 dimerization interface [polypeptide binding]; other site 159087003133 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087003134 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003135 active site 159087003136 phosphorylation site [posttranslational modification] 159087003137 intermolecular recognition site; other site 159087003138 dimerization interface [polypeptide binding]; other site 159087003139 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087003140 Zn2+ binding site [ion binding]; other site 159087003141 Mg2+ binding site [ion binding]; other site 159087003142 PAS domain S-box; Region: sensory_box; TIGR00229 159087003143 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 159087003144 putative active site [active] 159087003145 heme pocket [chemical binding]; other site 159087003146 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 159087003147 PAS fold; Region: PAS_3; pfam08447 159087003148 putative active site [active] 159087003149 heme pocket [chemical binding]; other site 159087003150 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087003151 GAF domain; Region: GAF; cl00853 159087003152 sensory histidine kinase AtoS; Provisional; Region: PRK11360 159087003153 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087003154 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 159087003155 dimer interface [polypeptide binding]; other site 159087003156 phosphorylation site [posttranslational modification] 159087003157 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 159087003158 ATP binding site [chemical binding]; other site 159087003159 Mg2+ binding site [ion binding]; other site 159087003160 G-X-G motif; other site 159087003161 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003162 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003163 active site 159087003164 phosphorylation site [posttranslational modification] 159087003165 intermolecular recognition site; other site 159087003166 dimerization interface [polypeptide binding]; other site 159087003167 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 159087003168 PAS fold; Region: PAS_3; pfam08447 159087003169 putative active site [active] 159087003170 heme pocket [chemical binding]; other site 159087003171 PAS fold; Region: PAS; pfam00989 159087003172 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 159087003173 putative active site [active] 159087003174 heme pocket [chemical binding]; other site 159087003175 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087003176 metal binding site [ion binding]; metal-binding site 159087003177 active site 159087003178 I-site; other site 159087003179 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 159087003180 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003181 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003182 active site 159087003183 phosphorylation site [posttranslational modification] 159087003184 intermolecular recognition site; other site 159087003185 dimerization interface [polypeptide binding]; other site 159087003186 PAS fold; Region: PAS_4; pfam08448 159087003187 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087003188 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 159087003189 putative active site [active] 159087003190 heme pocket [chemical binding]; other site 159087003191 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 159087003192 dimer interface [polypeptide binding]; other site 159087003193 phosphorylation site [posttranslational modification] 159087003194 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 159087003195 ATP binding site [chemical binding]; other site 159087003196 Mg2+ binding site [ion binding]; other site 159087003197 G-X-G motif; other site 159087003198 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003199 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003200 active site 159087003201 phosphorylation site [posttranslational modification] 159087003202 intermolecular recognition site; other site 159087003203 dimerization interface [polypeptide binding]; other site 159087003204 Acetokinase family; Region: Acetate_kinase; cl01029 159087003205 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 159087003206 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 159087003207 dimer interaction site [polypeptide binding]; other site 159087003208 substrate-binding tunnel; other site 159087003209 active site 159087003210 catalytic site [active] 159087003211 substrate binding site [chemical binding]; other site 159087003212 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 159087003213 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 159087003214 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 159087003215 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 159087003216 NAD binding site [chemical binding]; other site 159087003217 homotetramer interface [polypeptide binding]; other site 159087003218 homodimer interface [polypeptide binding]; other site 159087003219 substrate binding site [chemical binding]; other site 159087003220 active site 159087003221 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase...; Region: TRX_Fd_NuoE_hoxF; cd03083 159087003222 putative dimer interface [polypeptide binding]; other site 159087003223 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 159087003224 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 159087003225 SLBB domain; Region: SLBB; pfam10531 159087003226 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 159087003227 NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]; Region: NuoG; COG1034 159087003228 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 159087003229 catalytic loop [active] 159087003230 iron binding site [ion binding]; other site 159087003231 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 159087003232 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 159087003233 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087003234 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 159087003235 nickel binding site [ion binding]; other site 159087003236 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 159087003237 Aminotransferase class-V; Region: Aminotran_5; pfam00266 159087003238 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087003239 catalytic residue [active] 159087003240 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 159087003241 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087003242 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 159087003243 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 159087003244 Walker A/P-loop; other site 159087003245 ATP binding site [chemical binding]; other site 159087003246 Q-loop/lid; other site 159087003247 ABC transporter signature motif; other site 159087003248 Walker B; other site 159087003249 D-loop; other site 159087003250 H-loop/switch region; other site 159087003251 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 159087003252 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003253 Walker A/P-loop; other site 159087003254 ATP binding site [chemical binding]; other site 159087003255 Q-loop/lid; other site 159087003256 ABC transporter signature motif; other site 159087003257 Walker B; other site 159087003258 D-loop; other site 159087003259 H-loop/switch region; other site 159087003260 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 159087003261 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087003262 ABC-2 type transporter; Region: ABC2_membrane; cl11417 159087003263 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 159087003264 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087003265 ABC-2 type transporter; Region: ABC2_membrane; cl11417 159087003266 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 159087003267 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 159087003268 Ligand Binding Site [chemical binding]; other site 159087003269 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 159087003270 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087003271 Beta-Casp domain; Region: Beta-Casp; cl12567 159087003272 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 159087003273 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 159087003274 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 159087003275 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087003276 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087003277 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 159087003278 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087003279 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 159087003280 CPxP motif; other site 159087003281 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 159087003282 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 159087003283 GAF domain; Region: GAF; cl00853 159087003284 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 159087003285 Walker A motif; other site 159087003286 ATP binding site [chemical binding]; other site 159087003287 Walker B motif; other site 159087003288 arginine finger; other site 159087003289 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087003290 Cytochrome c; Region: Cytochrom_C; cl11414 159087003291 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 159087003292 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; cl15306 159087003293 membrane-bound complex binding site; other site 159087003294 hinge residues; other site 159087003295 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 159087003296 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 159087003297 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 159087003298 structural tetrad; other site 159087003299 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 159087003300 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 159087003301 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 159087003302 dimer interface [polypeptide binding]; other site 159087003303 phosphorylation site [posttranslational modification] 159087003304 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 159087003305 ATP binding site [chemical binding]; other site 159087003306 Mg2+ binding site [ion binding]; other site 159087003307 G-X-G motif; other site 159087003308 Cytochrome c; Region: Cytochrom_C; cl11414 159087003309 Protein of unknown function (DUF779); Region: DUF779; cl01432 159087003310 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 159087003311 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 159087003312 NAD(P) binding site [chemical binding]; other site 159087003313 catalytic residues [active] 159087003314 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087003315 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 159087003316 dimer interface [polypeptide binding]; other site 159087003317 phosphorylation site [posttranslational modification] 159087003318 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 159087003319 ATP binding site [chemical binding]; other site 159087003320 Mg2+ binding site [ion binding]; other site 159087003321 G-X-G motif; other site 159087003322 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003323 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003324 active site 159087003325 phosphorylation site [posttranslational modification] 159087003326 intermolecular recognition site; other site 159087003327 dimerization interface [polypeptide binding]; other site 159087003328 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 159087003329 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 159087003330 Immunoglobulin I-set domain; Region: I-set; pfam07679 159087003331 Immunoglobulin domain; Region: Ig; cl11960 159087003332 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 159087003333 active site 159087003334 catalytic site [active] 159087003335 substrate binding site [chemical binding]; other site 159087003336 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 159087003337 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087003338 putative substrate translocation pore; other site 159087003339 Transglycosylase; Region: Transgly; cl07896 159087003340 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087003341 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 159087003342 GAF domain; Region: GAF; cl00853 159087003343 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 159087003344 Walker A motif; other site 159087003345 ATP binding site [chemical binding]; other site 159087003346 Walker B motif; other site 159087003347 arginine finger; other site 159087003348 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087003349 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 159087003350 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 159087003351 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 159087003352 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 159087003353 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 159087003354 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 159087003355 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 159087003356 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 159087003357 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 159087003358 Cytochrome c; Region: Cytochrom_C; cl11414 159087003359 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 159087003360 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 159087003361 dimer interface [polypeptide binding]; other site 159087003362 Trp docking motif [polypeptide binding]; other site 159087003363 active site 159087003364 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 159087003365 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 159087003366 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087003367 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087003368 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 159087003369 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 159087003370 N-terminal plug; other site 159087003371 ligand-binding site [chemical binding]; other site 159087003372 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 159087003373 dimerization interface [polypeptide binding]; other site 159087003374 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 159087003375 Histidine kinase; Region: HisKA_3; pfam07730 159087003376 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 159087003377 ATP binding site [chemical binding]; other site 159087003378 Mg2+ binding site [ion binding]; other site 159087003379 G-X-G motif; other site 159087003380 response regulator; Provisional; Region: PRK09483 159087003381 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003382 active site 159087003383 phosphorylation site [posttranslational modification] 159087003384 intermolecular recognition site; other site 159087003385 dimerization interface [polypeptide binding]; other site 159087003386 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 159087003387 DNA binding residues [nucleotide binding] 159087003388 dimerization interface [polypeptide binding]; other site 159087003389 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 159087003390 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 159087003391 homodimer interface [polypeptide binding]; other site 159087003392 putative active site [active] 159087003393 catalytic site [active] 159087003394 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 159087003395 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 159087003396 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 159087003397 catalytic residues [active] 159087003398 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087003399 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 159087003400 ligand binding site [chemical binding]; other site 159087003401 flexible hinge region; other site 159087003402 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087003403 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 159087003404 Phage integrase family; Region: Phage_integrase; pfam00589 159087003405 DNA binding site [nucleotide binding] 159087003406 Int/Topo IB signature motif; other site 159087003407 active site 159087003408 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 159087003409 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 159087003410 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 159087003411 Cation efflux family; Region: Cation_efflux; cl00316 159087003412 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087003413 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 159087003414 N-terminal plug; other site 159087003415 ligand-binding site [chemical binding]; other site 159087003416 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; cl00284 159087003417 Domain of unknown function DUF302; Region: DUF302; cl01364 159087003418 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 159087003419 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 159087003420 ligand binding site [chemical binding]; other site 159087003421 flexible hinge region; other site 159087003422 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 159087003423 putative switch regulator; other site 159087003424 non-specific DNA interactions [nucleotide binding]; other site 159087003425 DNA binding site [nucleotide binding] 159087003426 sequence specific DNA binding site [nucleotide binding]; other site 159087003427 putative cAMP binding site [chemical binding]; other site 159087003428 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 159087003429 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 159087003430 FeS/SAM binding site; other site 159087003431 HemN C-terminal region; Region: HemN_C; pfam06969 159087003432 LysE type translocator; Region: LysE; cl00565 159087003433 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 159087003434 Ligand Binding Site [chemical binding]; other site 159087003435 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087003436 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 159087003437 metal-binding site [ion binding] 159087003438 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087003439 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087003440 PAS domain S-box; Region: sensory_box; TIGR00229 159087003441 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 159087003442 putative active site [active] 159087003443 heme pocket [chemical binding]; other site 159087003444 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087003445 metal binding site [ion binding]; metal-binding site 159087003446 active site 159087003447 I-site; other site 159087003448 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 159087003449 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 159087003450 metal-binding site [ion binding] 159087003451 selenophosphate synthetase; Provisional; Region: PRK00943 159087003452 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 159087003453 dimerization interface [polypeptide binding]; other site 159087003454 putative ATP binding site [chemical binding]; other site 159087003455 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 159087003456 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 159087003457 N-terminal plug; other site 159087003458 ligand-binding site [chemical binding]; other site 159087003459 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 159087003460 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 159087003461 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 159087003462 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 159087003463 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 159087003464 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 159087003465 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 159087003466 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 159087003467 heme binding site [chemical binding]; other site 159087003468 ferroxidase pore; other site 159087003469 ferroxidase diiron center [ion binding]; other site 159087003470 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 159087003471 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 159087003472 heme binding site [chemical binding]; other site 159087003473 ferroxidase pore; other site 159087003474 ferroxidase diiron center [ion binding]; other site 159087003475 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 159087003476 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087003477 DNA-binding site [nucleotide binding]; DNA binding site 159087003478 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 159087003479 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003480 homodimer interface [polypeptide binding]; other site 159087003481 catalytic residue [active] 159087003482 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 159087003483 Subunit I/III interface [polypeptide binding]; other site 159087003484 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087003485 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087003486 4Fe-4S binding domain; Region: Fer4; cl02805 159087003487 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087003488 FeoA domain; Region: FeoA; cl00838 159087003489 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 159087003490 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 159087003491 G1 box; other site 159087003492 GTP/Mg2+ binding site [chemical binding]; other site 159087003493 Switch I region; other site 159087003494 G2 box; other site 159087003495 G3 box; other site 159087003496 Switch II region; other site 159087003497 G4 box; other site 159087003498 G5 box; other site 159087003499 Nucleoside recognition; Region: Gate; cl00486 159087003500 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 159087003501 Nucleoside recognition; Region: Gate; cl00486 159087003502 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 159087003503 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 159087003504 conserved cys residue [active] 159087003505 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087003506 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087003507 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; cl12031 159087003508 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087003509 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 159087003510 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 159087003511 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 159087003512 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 159087003513 putative NADH binding site [chemical binding]; other site 159087003514 putative active site [active] 159087003515 nudix motif; other site 159087003516 putative metal binding site [ion binding]; other site 159087003517 Membrane protein of unknown function; Region: DUF360; cl00850 159087003518 Uncharacterised ACR, COG2135; Region: DUF159; cl03646 159087003519 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 159087003520 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 159087003521 putative substrate translocation pore; other site 159087003522 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 159087003523 CoenzymeA binding site [chemical binding]; other site 159087003524 subunit interaction site [polypeptide binding]; other site 159087003525 PHB binding site; other site 159087003526 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 159087003527 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003528 active site 159087003529 phosphorylation site [posttranslational modification] 159087003530 intermolecular recognition site; other site 159087003531 dimerization interface [polypeptide binding]; other site 159087003532 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 159087003533 DNA binding site [nucleotide binding] 159087003534 sensor protein KdpD; Provisional; Region: PRK10490 159087003535 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 159087003536 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 159087003537 Ligand Binding Site [chemical binding]; other site 159087003538 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 159087003539 dimer interface [polypeptide binding]; other site 159087003540 phosphorylation site [posttranslational modification] 159087003541 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 159087003542 ATP binding site [chemical binding]; other site 159087003543 Mg2+ binding site [ion binding]; other site 159087003544 G-X-G motif; other site 159087003545 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 159087003546 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 159087003547 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 159087003548 active site 159087003549 phosphorylation site [posttranslational modification] 159087003550 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 159087003551 K+-transporting ATPase, c chain; Region: KdpC; cl00944 159087003552 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 159087003553 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087003554 Potassium-transporting ATPase A subunit; Region: KdpA; cl00903 159087003555 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 159087003556 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087003557 ligand binding site [chemical binding]; other site 159087003558 flexible hinge region; other site 159087003559 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 159087003560 putative switch regulator; other site 159087003561 non-specific DNA interactions [nucleotide binding]; other site 159087003562 DNA binding site [nucleotide binding] 159087003563 sequence specific DNA binding site [nucleotide binding]; other site 159087003564 putative cAMP binding site [chemical binding]; other site 159087003565 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 159087003566 catalytic residues [active] 159087003567 dimer interface [polypeptide binding]; other site 159087003568 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 159087003569 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 159087003570 CoenzymeA binding site [chemical binding]; other site 159087003571 subunit interaction site [polypeptide binding]; other site 159087003572 PHB binding site; other site 159087003573 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087003574 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 159087003575 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 159087003576 putative substrate translocation pore; other site 159087003577 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087003578 Luciferase-like monooxygenase; Region: Bac_luciferase; pfam00296 159087003579 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 159087003580 EamA-like transporter family; Region: EamA; cl01037 159087003581 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 159087003582 EamA-like transporter family; Region: EamA; cl01037 159087003583 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 159087003584 FMN binding site [chemical binding]; other site 159087003585 active site 159087003586 substrate binding site [chemical binding]; other site 159087003587 catalytic residue [active] 159087003588 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087003589 Helix-turn-helix domains; Region: HTH; cl00088 159087003590 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087003591 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087003592 Predicted ATPase [General function prediction only]; Region: COG4637 159087003593 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003594 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 159087003595 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003596 Walker B; other site 159087003597 D-loop; other site 159087003598 H-loop/switch region; other site 159087003599 Nuclease-related domain; Region: NERD; pfam08378 159087003600 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003601 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003602 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 159087003603 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 159087003604 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087003605 Iron permease FTR1 family; Region: FTR1; cl00475 159087003606 Imelysin; Region: Peptidase_M75; cl09159 159087003607 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 159087003608 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 159087003609 Fe2+ transport protein; Region: Iron_transport; cl01377 159087003610 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 159087003611 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 159087003612 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087003613 Hemin uptake protein hemP; Region: hemP; cl10043 159087003614 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 159087003615 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087003616 ATP binding site [chemical binding]; other site 159087003617 Mg++ binding site [ion binding]; other site 159087003618 motif III; other site 159087003619 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 159087003620 nucleotide binding region [chemical binding]; other site 159087003621 ATP-binding site [chemical binding]; other site 159087003622 DbpA RNA binding domain; Region: DbpA; pfam03880 159087003623 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 159087003624 dinuclear metal binding motif [ion binding]; other site 159087003625 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 159087003626 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 159087003627 active site 159087003628 catalytic tetrad [active] 159087003629 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 159087003630 Phosphate transporter family; Region: PHO4; cl00396 159087003631 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 159087003632 domain; Region: GreA_GreB_N; pfam03449 159087003633 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 159087003634 heat shock protein 90; Provisional; Region: PRK05218 159087003635 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 159087003636 ATP binding site [chemical binding]; other site 159087003637 Mg2+ binding site [ion binding]; other site 159087003638 G-X-G motif; other site 159087003639 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 159087003640 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 159087003641 ATP binding site [chemical binding]; other site 159087003642 Mg++ binding site [ion binding]; other site 159087003643 motif III; other site 159087003644 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 159087003645 nucleotide binding region [chemical binding]; other site 159087003646 ATP-binding site [chemical binding]; other site 159087003647 DbpA RNA binding domain; Region: DbpA; pfam03880 159087003648 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; cl15691 159087003649 Flagellin N-methylase; Region: FliB; cl00497 159087003650 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 159087003651 Protein of unknown function DUF45; Region: DUF45; cl00636 159087003652 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 159087003653 putative substrate translocation pore; other site 159087003654 transcriptional activator TtdR; Provisional; Region: PRK09801 159087003655 Helix-turn-helix domains; Region: HTH; cl00088 159087003656 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 159087003657 putative effector binding pocket; other site 159087003658 putative dimerization interface [polypeptide binding]; other site 159087003659 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087003660 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 159087003661 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 159087003662 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087003663 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 159087003664 anti sigma factor interaction site; other site 159087003665 regulatory phosphorylation site [posttranslational modification]; other site 159087003666 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087003667 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 159087003668 putative binding surface; other site 159087003669 active site 159087003670 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087003671 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 159087003672 ATP binding site [chemical binding]; other site 159087003673 Mg2+ binding site [ion binding]; other site 159087003674 G-X-G motif; other site 159087003675 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 159087003676 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 159087003677 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087003678 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 159087003679 dimerization interface [polypeptide binding]; other site 159087003680 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087003681 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087003682 CheD chemotactic sensory transduction; Region: CheD; cl00810 159087003683 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 159087003684 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 159087003685 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; cl12011 159087003686 CheD chemotactic sensory transduction; Region: CheD; cl00810 159087003687 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 159087003688 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003689 active site 159087003690 phosphorylation site [posttranslational modification] 159087003691 intermolecular recognition site; other site 159087003692 dimerization interface [polypeptide binding]; other site 159087003693 CheB methylesterase; Region: CheB_methylest; pfam01339 159087003694 HDOD domain; Region: HDOD; pfam08668 159087003695 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087003696 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 159087003697 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 159087003698 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 159087003699 Walker A motif; other site 159087003700 ATP binding site [chemical binding]; other site 159087003701 Walker B motif; other site 159087003702 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087003703 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 159087003704 FIST C domain; Region: FIST_C; pfam10442 159087003705 endonuclease III; Provisional; Region: PRK10702 159087003706 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 159087003707 minor groove reading motif; other site 159087003708 helix-hairpin-helix signature motif; other site 159087003709 substrate binding pocket [chemical binding]; other site 159087003710 active site 159087003711 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 159087003712 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087003713 PAS fold; Region: PAS_4; pfam08448 159087003714 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087003715 PAS fold; Region: PAS_4; pfam08448 159087003716 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087003717 metal binding site [ion binding]; metal-binding site 159087003718 active site 159087003719 I-site; other site 159087003720 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 159087003721 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 159087003722 FMN-binding domain; Region: FMN_bind; cl01081 159087003723 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 159087003724 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 159087003725 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 159087003726 lipoyl-biotinyl attachment site [posttranslational modification]; other site 159087003727 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 159087003728 SLBB domain; Region: SLBB; pfam10531 159087003729 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 159087003730 electron transport complex protein RnfB; Provisional; Region: PRK05113 159087003731 Putative Fe-S cluster; Region: FeS; pfam04060 159087003732 4Fe-4S binding domain; Region: Fer4; cl02805 159087003733 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 159087003734 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; cl09108 159087003735 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 159087003736 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 159087003737 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087003738 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087003739 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087003740 Walker A/P-loop; other site 159087003741 ATP binding site [chemical binding]; other site 159087003742 Q-loop/lid; other site 159087003743 ABC transporter signature motif; other site 159087003744 Walker B; other site 159087003745 D-loop; other site 159087003746 H-loop/switch region; other site 159087003747 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087003748 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087003749 FtsX-like permease family; Region: FtsX; pfam02687 159087003750 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 159087003751 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 159087003752 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 159087003753 binding surface 159087003754 TPR motif; other site 159087003755 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 159087003756 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087003757 MltA-interacting protein MipA; Region: MipA; cl01504 159087003758 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 159087003759 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 159087003760 dimer interface [polypeptide binding]; other site 159087003761 active site 159087003762 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087003763 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087003764 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 159087003765 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087003766 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087003767 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087003768 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 159087003769 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 159087003770 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003771 active site 159087003772 phosphorylation site [posttranslational modification] 159087003773 intermolecular recognition site; other site 159087003774 dimerization interface [polypeptide binding]; other site 159087003775 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 159087003776 DNA binding site [nucleotide binding] 159087003777 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087003778 sensor protein PhoQ; Provisional; Region: PRK10815 159087003779 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 159087003780 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 159087003781 ATP binding site [chemical binding]; other site 159087003782 Mg2+ binding site [ion binding]; other site 159087003783 G-X-G motif; other site 159087003784 Protein of unknown function, DUF; Region: DUF411; cl01142 159087003785 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 159087003786 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087003787 Amino acid permease; Region: AA_permease; cl00524 159087003788 Acylphosphatase; Region: Acylphosphatase; cl00551 159087003789 Phytochelatin synthase; Region: Phytochelatin; pfam05023 159087003790 Flavin Reductases; Region: FlaRed; cl00801 159087003791 Domain of unknown function (DUF477); Region: DUF477; cl01535 159087003792 Domain of unknown function (DUF477); Region: DUF477; cl01535 159087003793 LemA family; Region: LemA; cl00742 159087003794 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 159087003795 putative active site [active] 159087003796 putative catalytic site [active] 159087003797 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 159087003798 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 159087003799 putative active site [active] 159087003800 putative metal binding site [ion binding]; other site 159087003801 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 159087003802 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 159087003803 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 159087003804 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 159087003805 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 159087003806 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 159087003807 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 159087003808 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 159087003809 Walker A/P-loop; other site 159087003810 ATP binding site [chemical binding]; other site 159087003811 Q-loop/lid; other site 159087003812 ABC transporter signature motif; other site 159087003813 Walker B; other site 159087003814 D-loop; other site 159087003815 H-loop/switch region; other site 159087003816 TOBE domain; Region: TOBE_2; cl01440 159087003817 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 159087003818 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 159087003819 dimer interface [polypeptide binding]; other site 159087003820 conserved gate region; other site 159087003821 putative PBP binding loops; other site 159087003822 ABC-ATPase subunit interface; other site 159087003823 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 159087003824 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087003825 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 159087003826 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 159087003827 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 159087003828 NlpC/P60 family; Region: NLPC_P60; cl11438 159087003829 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 159087003830 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 159087003831 NADP binding site [chemical binding]; other site 159087003832 dimer interface [polypeptide binding]; other site 159087003833 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087003834 active site 159087003835 phosphorylation site [posttranslational modification] 159087003836 intermolecular recognition site; other site 159087003837 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087003838 metal binding site [ion binding]; metal-binding site 159087003839 active site 159087003840 I-site; other site 159087003841 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 159087003842 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 159087003843 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087003844 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 159087003845 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 159087003846 Domain of unknown function DUF140; Region: DUF140; cl00510 159087003847 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 159087003848 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003849 Walker A/P-loop; other site 159087003850 ATP binding site [chemical binding]; other site 159087003851 Q-loop/lid; other site 159087003852 ABC transporter signature motif; other site 159087003853 Walker B; other site 159087003854 D-loop; other site 159087003855 H-loop/switch region; other site 159087003856 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 159087003857 mce related protein; Region: MCE; cl15431 159087003858 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 159087003859 Protein of unknown function (DUF330); Region: DUF330; cl01135 159087003860 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087003861 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087003862 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 159087003863 Ligand binding site [chemical binding]; other site 159087003864 Electron transfer flavoprotein domain; Region: ETF; pfam01012 159087003865 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 159087003866 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 159087003867 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 159087003868 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 159087003869 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 159087003870 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 159087003871 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 159087003872 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087003873 active site 159087003874 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 159087003875 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 159087003876 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 159087003877 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 159087003878 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 159087003879 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 159087003880 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 159087003881 replicative DNA helicase; Region: DnaB; TIGR00665 159087003882 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 159087003883 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 159087003884 Walker A motif; other site 159087003885 ATP binding site [chemical binding]; other site 159087003886 Walker B motif; other site 159087003887 DNA binding loops [nucleotide binding] 159087003888 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087003889 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 159087003890 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 159087003891 putative active site [active] 159087003892 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003893 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 159087003894 catalytic triad [active] 159087003895 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 159087003896 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_18; cd08505 159087003897 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087003898 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 159087003899 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 159087003900 motif II; other site 159087003901 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 159087003902 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 159087003903 S-adenosylmethionine binding site [chemical binding]; other site 159087003904 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087003905 ligand binding site [chemical binding]; other site 159087003906 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 159087003907 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 159087003908 active site 159087003909 putative substrate binding pocket [chemical binding]; other site 159087003910 DNA gyrase subunit A; Validated; Region: PRK05560 159087003911 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 in DNA...; Region: TOP4c; cd00187 159087003912 CAP-like domain; other site 159087003913 active site 159087003914 primary dimer interface [polypeptide binding]; other site 159087003915 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087003916 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087003917 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087003918 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087003919 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087003920 Aminotransferase class-V; Region: Aminotran_5; pfam00266 159087003921 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 159087003922 homodimer interface [polypeptide binding]; other site 159087003923 substrate-cofactor binding pocket; other site 159087003924 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003925 catalytic residue [active] 159087003926 Chorismate mutase type II; Region: CM_2; cl00693 159087003927 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 159087003928 Prephenate dehydratase; Region: PDT; pfam00800 159087003929 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 159087003930 putative L-Phe binding site [chemical binding]; other site 159087003931 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 159087003932 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 159087003933 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003934 homodimer interface [polypeptide binding]; other site 159087003935 catalytic residue [active] 159087003936 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 159087003937 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087003938 DNA ligase; Provisional; Region: PRK09125 159087003939 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 159087003940 DNA binding site [nucleotide binding] 159087003941 active site 159087003942 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 159087003943 DNA binding site [nucleotide binding] 159087003944 UDP-glucose 4-epimerase; Region: PLN02240 159087003945 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 159087003946 NAD binding site [chemical binding]; other site 159087003947 homodimer interface [polypeptide binding]; other site 159087003948 active site 159087003949 substrate binding site [chemical binding]; other site 159087003950 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 159087003951 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 159087003952 NAD binding site [chemical binding]; other site 159087003953 substrate binding site [chemical binding]; other site 159087003954 homodimer interface [polypeptide binding]; other site 159087003955 active site 159087003956 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 159087003957 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 159087003958 substrate binding site; other site 159087003959 tetramer interface; other site 159087003960 Cupin domain; Region: Cupin_2; cl09118 159087003961 Helix-turn-helix domains; Region: HTH; cl00088 159087003962 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 159087003963 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 159087003964 inhibitor-cofactor binding pocket; inhibition site 159087003965 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003966 catalytic residue [active] 159087003967 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087003968 H-loop/switch region; other site 159087003969 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 159087003970 active site 159087003971 catalytic tetrad [active] 159087003972 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 159087003973 ligand binding site; other site 159087003974 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 159087003975 glutamate-1-semialdehyde 2,1-aminomutase; Provisional; Region: PRK06209 159087003976 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087003977 catalytic residue [active] 159087003978 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 159087003979 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087003980 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 159087003981 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_1; cd08821 159087003982 putative active site [active] 159087003983 putative substrate binding site [chemical binding]; other site 159087003984 putative cosubstrate binding site; other site 159087003985 catalytic site [active] 159087003986 pseudaminic acid synthase; Region: PseI; TIGR03586 159087003987 NeuB family; Region: NeuB; cl00496 159087003988 SAF domain; Region: SAF; cl00555 159087003989 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 159087003990 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 159087003991 S-adenosylmethionine binding site [chemical binding]; other site 159087003992 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087003993 UDP-glucose 4-epimerase (G4E), subgroup 5, extended (e) SDRs; Region: UDP_G4E_5_SDR_e; cd05264 159087003994 putative NAD(P) binding site [chemical binding]; other site 159087003995 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 159087003996 active site 159087003997 putative substrate binding site [chemical binding]; other site 159087003998 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 159087003999 substrate binding site; other site 159087004000 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 159087004001 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 159087004002 NAD binding site [chemical binding]; other site 159087004003 homotetramer interface [polypeptide binding]; other site 159087004004 homodimer interface [polypeptide binding]; other site 159087004005 substrate binding site [chemical binding]; other site 159087004006 active site 159087004007 Cupin domain; Region: Cupin_2; cl09118 159087004008 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 159087004009 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004010 NAD(P) binding site [chemical binding]; other site 159087004011 extended (e) SDRs; Region: SDR_e; cd08946 159087004012 NAD(P) binding site [chemical binding]; other site 159087004013 active site 159087004014 active site 159087004015 substrate binding site [chemical binding]; other site 159087004016 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 159087004017 active site 159087004018 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004019 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 159087004020 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087004021 putative glycosyl transferase; Provisional; Region: PRK10307 159087004022 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 159087004023 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 159087004024 NADP binding site [chemical binding]; other site 159087004025 active site 159087004026 putative substrate binding site [chemical binding]; other site 159087004027 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 159087004028 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 159087004029 NAD(P) binding site [chemical binding]; other site 159087004030 homodimer interface [polypeptide binding]; other site 159087004031 substrate binding site [chemical binding]; other site 159087004032 active site 159087004033 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 159087004034 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 159087004035 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 159087004036 active site 159087004037 homodimer interface [polypeptide binding]; other site 159087004038 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004039 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087004040 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 159087004041 Mg++ binding site [ion binding]; other site 159087004042 putative catalytic motif [active] 159087004043 MatE; Region: MatE; cl10513 159087004044 MatE; Region: MatE; cl10513 159087004045 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 159087004046 Probable Catalytic site; other site 159087004047 metal-binding site 159087004048 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004049 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087004050 exosortase 1 system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 159087004051 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 159087004052 active site 159087004053 dimer interface [polypeptide binding]; other site 159087004054 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 159087004055 Ligand Binding Site [chemical binding]; other site 159087004056 Molecular Tunnel; other site 159087004057 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 159087004058 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004059 putative ADP-binding pocket [chemical binding]; other site 159087004060 Bacterial sugar transferase; Region: Bac_transf; cl00939 159087004061 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 159087004062 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 159087004063 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 159087004064 NAD(P) binding site [chemical binding]; other site 159087004065 homodimer interface [polypeptide binding]; other site 159087004066 substrate binding site [chemical binding]; other site 159087004067 active site 159087004068 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 159087004069 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 159087004070 hinge; other site 159087004071 active site 159087004072 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 159087004073 CMP-binding site; other site 159087004074 The sites determining sugar specificity; other site 159087004075 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 159087004076 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 consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 159087004077 RNA binding site [nucleotide binding]; other site 159087004078 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 159087004079 RNA binding site [nucleotide binding]; other site 159087004080 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 of...; Region: S1_RPS1_repeat_ec3; cd05688 159087004081 RNA binding site [nucleotide binding]; other site 159087004082 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec4; cd05689 159087004083 RNA binding site [nucleotide binding]; other site 159087004084 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 159087004085 RNA binding site [nucleotide binding]; other site 159087004086 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 of...; Region: S1_RPS1_repeat_ec6; cd05691 159087004087 RNA binding site [nucleotide binding]; other site 159087004088 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 159087004089 IHF dimer interface [polypeptide binding]; other site 159087004090 IHF - DNA interface [nucleotide binding]; other site 159087004091 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 159087004092 tetratricopeptide repeat protein; Provisional; Region: PRK11788 159087004093 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 159087004094 binding surface 159087004095 TPR motif; other site 159087004096 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087004097 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 159087004098 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004099 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 159087004100 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004101 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 159087004102 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 159087004103 putative ribose interaction site [chemical binding]; other site 159087004104 putative ADP binding site [chemical binding]; other site 159087004105 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 159087004106 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 159087004107 NADP binding site [chemical binding]; other site 159087004108 homopentamer interface [polypeptide binding]; other site 159087004109 substrate binding site [chemical binding]; other site 159087004110 active site 159087004111 cysteine synthase B; Region: cysM; TIGR01138 159087004112 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 159087004113 dimer interface [polypeptide binding]; other site 159087004114 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087004115 catalytic residue [active] 159087004116 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 159087004117 active site 159087004118 catalytic site [active] 159087004119 substrate binding site [chemical binding]; other site 159087004120 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 159087004121 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 159087004122 dimer interface [polypeptide binding]; other site 159087004123 substrate binding site [chemical binding]; other site 159087004124 metal binding sites [ion binding]; metal-binding site 159087004125 NAD synthetase; Provisional; Region: PRK13981 159087004126 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 159087004127 multimer interface [polypeptide binding]; other site 159087004128 active site 159087004129 catalytic triad [active] 159087004130 protein interface 1 [polypeptide binding]; other site 159087004131 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 159087004132 homodimer interface [polypeptide binding]; other site 159087004133 NAD binding pocket [chemical binding]; other site 159087004134 ATP binding pocket [chemical binding]; other site 159087004135 Mg binding site [ion binding]; other site 159087004136 active-site loop [active] 159087004137 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087004138 MutS2 family protein; Region: mutS2; TIGR01069 159087004139 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 159087004140 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004141 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087004142 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 159087004143 ligand binding site [chemical binding]; other site 159087004144 flexible hinge region; other site 159087004145 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004146 DNA translocase FtsK; Provisional; Region: PRK10263 159087004147 type VII secretion protein EccCb; Region: T7SS_EccC_b; TIGR03925 159087004148 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087004149 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 159087004150 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 159087004151 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 159087004152 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 159087004153 putative uracil binding site [chemical binding]; other site 159087004154 putative active site [active] 159087004155 recombination factor protein RarA; Reviewed; Region: PRK13342 159087004156 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 159087004157 Walker A motif; other site 159087004158 ATP binding site [chemical binding]; other site 159087004159 Walker B motif; other site 159087004160 arginine finger; other site 159087004161 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 159087004162 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 159087004163 seryl-tRNA synthetase; Provisional; Region: PRK05431 159087004164 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 159087004165 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 bound...; Region: SerRS_core; cd00770 159087004166 dimer interface [polypeptide binding]; other site 159087004167 active site 159087004168 motif 1; other site 159087004169 motif 2; other site 159087004170 motif 3; other site 159087004171 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 159087004172 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 159087004173 substrate binding pocket [chemical binding]; other site 159087004174 membrane-bound complex binding site; other site 159087004175 hinge residues; other site 159087004176 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 catalyze...; Region: LT_GEWL; cd00254 159087004177 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087004178 catalytic residue [active] 159087004179 Phage integrase family; Region: Phage_integrase; pfam00589 159087004180 INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence...; Region: INT_SG2_C; cd01184 159087004181 Int/Topo IB signature motif; other site 159087004182 HsdM N-terminal domain; Region: HsdM_N; pfam12161 159087004183 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 159087004184 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; cl12011 159087004185 putative transposase OrfB; Reviewed; Region: PHA02517 159087004186 Integrase core domain; Region: rve; cl01316 159087004187 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 159087004188 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 159087004189 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 159087004190 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 159087004191 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 159087004192 ATP binding site [chemical binding]; other site 159087004193 putative Mg++ binding site [ion binding]; other site 159087004194 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 159087004195 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087004196 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 159087004197 non-specific DNA binding site [nucleotide binding]; other site 159087004198 salt bridge; other site 159087004199 sequence-specific DNA binding site [nucleotide binding]; other site 159087004200 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 159087004201 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 159087004202 catalytic residues [active] 159087004203 catalytic nucleophile [active] 159087004204 Presynaptic Site I dimer interface [polypeptide binding]; other site 159087004205 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 159087004206 Synaptic Flat tetramer interface [polypeptide binding]; other site 159087004207 Synaptic Site I dimer interface [polypeptide binding]; other site 159087004208 DNA binding site [nucleotide binding] 159087004209 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 159087004210 DNA-binding interface [nucleotide binding]; DNA binding site 159087004211 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 159087004212 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 159087004213 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 159087004214 dimer interface [polypeptide binding]; other site 159087004215 putative PBP binding loops; other site 159087004216 ABC-ATPase subunit interface; other site 159087004217 antimicrobial peptide ABC transporter permease SapC; Provisional; Region: PRK15111 159087004218 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 159087004219 dimer interface [polypeptide binding]; other site 159087004220 conserved gate region; other site 159087004221 putative PBP binding loops; other site 159087004222 ABC-ATPase subunit interface; other site 159087004223 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 159087004224 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 159087004225 Walker A/P-loop; other site 159087004226 ATP binding site [chemical binding]; other site 159087004227 Q-loop/lid; other site 159087004228 ABC transporter signature motif; other site 159087004229 Walker B; other site 159087004230 D-loop; other site 159087004231 H-loop/switch region; other site 159087004232 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 159087004233 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 159087004234 Walker A/P-loop; other site 159087004235 ATP binding site [chemical binding]; other site 159087004236 Q-loop/lid; other site 159087004237 ABC transporter signature motif; other site 159087004238 Walker B; other site 159087004239 D-loop; other site 159087004240 H-loop/switch region; other site 159087004241 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 159087004242 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 catalyze...; Region: LT_GEWL; cd00254 159087004243 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087004244 catalytic residue [active] 159087004245 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 159087004246 putative peptidoglycan binding site; other site 159087004247 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 159087004248 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 159087004249 active site 159087004250 HIGH motif; other site 159087004251 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 159087004252 active site 159087004253 KMSKS motif; other site 159087004254 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004255 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 159087004256 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 159087004257 Phage integrase family; Region: Phage_integrase; pfam00589 159087004258 DNA binding site [nucleotide binding] 159087004259 Int/Topo IB signature motif; other site 159087004260 active site 159087004261 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087004262 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 159087004263 IHF dimer interface [polypeptide binding]; other site 159087004264 IHF - DNA interface [nucleotide binding]; other site 159087004265 Restriction endonuclease; Region: Mrr_cat; cl00747 159087004266 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004267 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004268 active site 159087004269 phosphorylation site [posttranslational modification] 159087004270 intermolecular recognition site; other site 159087004271 dimerization interface [polypeptide binding]; other site 159087004272 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087004273 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087004274 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004275 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087004276 octamerization interface [polypeptide binding]; other site 159087004277 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087004278 diferric-oxygen binding site [ion binding]; other site 159087004279 Lipocalin-like domain; Region: Lipocalin_5; pfam13924 159087004280 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 159087004281 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 159087004282 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 159087004283 active site 159087004284 Fe binding site [ion binding]; other site 159087004285 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 159087004286 indole acetimide hydrolase; Validated; Region: PRK07488 159087004287 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 159087004288 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 159087004289 putative metal binding site [ion binding]; other site 159087004290 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 159087004291 dimer interface [polypeptide binding]; other site 159087004292 FMN binding site [chemical binding]; other site 159087004293 Domain of unknown function (DUF336); Region: DUF336; cl01249 159087004294 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 159087004295 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 159087004296 Flavin Reductases; Region: FlaRed; cl00801 159087004297 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 159087004298 Cupin domain; Region: Cupin_2; cl09118 159087004299 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 159087004300 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 159087004301 NAD(P) binding site [chemical binding]; other site 159087004302 Ycf48-like protein; Provisional; Region: PRK13684 159087004303 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 159087004304 Ycf48-like protein; Provisional; Region: PRK13684 159087004305 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 159087004306 Protein export membrane protein; Region: SecD_SecF; cl14618 159087004307 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 159087004308 Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate; Region: MhpB_like; cd07365 159087004309 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087004310 putative active site [active] 159087004311 Fe(II) binding site [ion binding]; other site 159087004312 putative dimer interface [polypeptide binding]; other site 159087004313 putative tetramer interface [polypeptide binding]; other site 159087004314 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087004315 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087004316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004317 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087004318 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087004319 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087004320 active site 159087004321 catalytic residues [active] 159087004322 metal binding site [ion binding]; metal-binding site 159087004323 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087004324 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087004325 classical (c) SDRs; Region: SDR_c; cd05233 159087004326 NAD(P) binding site [chemical binding]; other site 159087004327 active site 159087004328 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 159087004329 Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating...; Region: Rieske_RO_Alpha_OMO_CARDO; cd03548 159087004330 iron-sulfur cluster [ion binding]; other site 159087004331 alpha subunit interaction site [polypeptide binding]; other site 159087004332 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 159087004333 alpha subunit interface [polypeptide binding]; other site 159087004334 active site 159087004335 substrate binding site [chemical binding]; other site 159087004336 Fe binding site [ion binding]; other site 159087004337 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087004338 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 159087004339 catalytic loop [active] 159087004340 iron binding site [ion binding]; other site 159087004341 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 159087004342 FAD binding pocket [chemical binding]; other site 159087004343 FAD binding motif [chemical binding]; other site 159087004344 phosphate binding motif [ion binding]; other site 159087004345 beta-alpha-beta structure motif; other site 159087004346 NAD binding pocket [chemical binding]; other site 159087004347 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 159087004348 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 159087004349 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087004350 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087004351 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 159087004352 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 159087004353 putative active site [active] 159087004354 heme pocket [chemical binding]; other site 159087004355 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 159087004356 putative active site [active] 159087004357 heme pocket [chemical binding]; other site 159087004358 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087004359 metal binding site [ion binding]; metal-binding site 159087004360 active site 159087004361 I-site; other site 159087004362 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 159087004363 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 159087004364 PAS fold; Region: PAS_3; pfam08447 159087004365 putative active site [active] 159087004366 heme pocket [chemical binding]; other site 159087004367 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087004368 T5orf172 domain; Region: T5orf172; cl11176 159087004369 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; Region: Sig-70_plancto1; TIGR02984 159087004370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004371 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004372 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 159087004373 NlpC/P60 family; Region: NLPC_P60; cl11438 159087004374 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 159087004375 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 159087004376 Transposase; Region: DEDD_Tnp_IS110; pfam01548 159087004377 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 159087004378 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 159087004379 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087004380 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 159087004381 Int/Topo IB signature motif; other site 159087004382 active site 159087004383 catalytic residues [active] 159087004384 DNA binding site [nucleotide binding] 159087004385 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 159087004386 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 159087004387 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 159087004388 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 159087004389 active site 159087004390 substrate binding site [chemical binding]; other site 159087004391 catalytic site [active] 159087004392 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 159087004393 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 159087004394 putative GSH binding site (G-site) [chemical binding]; other site 159087004395 active site cysteine [active] 159087004396 putative C-terminal domain interface [polypeptide binding]; other site 159087004397 putative dimer interface [polypeptide binding]; other site 159087004398 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 159087004399 putative N-terminal domain interface [polypeptide binding]; other site 159087004400 putative dimer interface [polypeptide binding]; other site 159087004401 putative substrate binding pocket (H-site) [chemical binding]; other site 159087004402 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 159087004403 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087004404 active site 159087004405 Domain of Unknown Function (DUF1520); Region: DUF1520; pfam07480 159087004406 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 protein; Region: CSP_CDS; cd04458 159087004407 DNA-binding site [nucleotide binding]; DNA binding site 159087004408 RNA-binding motif; other site 159087004409 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 159087004410 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 159087004411 active site residue [active] 159087004412 Pirin-related protein [General function prediction only]; Region: COG1741 159087004413 Cupin domain; Region: Cupin_2; cl09118 159087004414 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 159087004415 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087004416 LysR family transcriptional regulator; Provisional; Region: PRK14997 159087004417 Helix-turn-helix domains; Region: HTH; cl00088 159087004418 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 159087004419 putative effector binding pocket; other site 159087004420 dimerization interface [polypeptide binding]; other site 159087004421 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 159087004422 PPIC-type PPIASE domain; Region: Rotamase; cl08278 159087004423 NifZ domain; Region: NifZ; pfam04319 159087004424 Nitrogen fixation protein NifW; Region: NifW; cl03935 159087004425 serine O-acetyltransferase; Region: cysE; TIGR01172 159087004426 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 159087004427 trimer interface [polypeptide binding]; other site 159087004428 active site 159087004429 substrate binding site [chemical binding]; other site 159087004430 CoA binding site [chemical binding]; other site 159087004431 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 159087004432 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 159087004433 active site 159087004434 catalytic residues [active] 159087004435 metal binding site [ion binding]; metal-binding site 159087004436 PAS domain S-box; Region: sensory_box; TIGR00229 159087004437 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087004438 Histidine kinase; Region: HisKA_3; pfam07730 159087004439 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 159087004440 ATP binding site [chemical binding]; other site 159087004441 Mg2+ binding site [ion binding]; other site 159087004442 G-X-G motif; other site 159087004443 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087004444 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004445 active site 159087004446 phosphorylation site [posttranslational modification] 159087004447 intermolecular recognition site; other site 159087004448 dimerization interface [polypeptide binding]; other site 159087004449 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 159087004450 DNA binding residues [nucleotide binding] 159087004451 dimerization interface [polypeptide binding]; other site 159087004452 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 159087004453 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 159087004454 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 159087004455 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 159087004456 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 159087004457 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 159087004458 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; cl10556 159087004459 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 159087004460 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 159087004461 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 159087004462 binding surface 159087004463 TPR motif; other site 159087004464 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087004465 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087004466 octamerization interface [polypeptide binding]; other site 159087004467 diferric-oxygen binding site [ion binding]; other site 159087004468 LRV protein FeS4 cluster; Region: LRV_FeS; pfam05484 159087004469 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 159087004470 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 159087004471 hypothetical protein; Provisional; Region: PRK13795 159087004472 NifT/FixU protein; Region: NifT; cl02351 159087004473 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 159087004474 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 159087004475 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 159087004476 MoFe protein beta/alpha subunit interactions; other site 159087004477 Beta subunit P cluster binding residues; other site 159087004478 MoFe protein beta subunit/Fe protein contacts; other site 159087004479 MoFe protein dimer/ dimer interactions; other site 159087004480 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 159087004481 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 159087004482 MoFe protein alpha/beta subunit interactions; other site 159087004483 Alpha subunit P cluster binding residues; other site 159087004484 FeMoco binding residues [chemical binding]; other site 159087004485 MoFe protein alpha subunit/Fe protein contacts; other site 159087004486 MoFe protein dimer/ dimer interactions; other site 159087004487 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 159087004488 nitrogenase iron protein; Region: nifH; TIGR01287 159087004489 Nucleotide-binding sites [chemical binding]; other site 159087004490 Walker A motif; other site 159087004491 Switch I region of nucleotide binding site; other site 159087004492 Fe4S4 binding sites [ion binding]; other site 159087004493 Switch II region of nucleotide binding site; other site 159087004494 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 159087004495 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 159087004496 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 159087004497 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087004498 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087004499 octamerization interface [polypeptide binding]; other site 159087004500 diferric-oxygen binding site [ion binding]; other site 159087004501 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 159087004502 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 159087004503 NADPH bind site [chemical binding]; other site 159087004504 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 159087004505 putative FMN binding site [chemical binding]; other site 159087004506 NADPH bind site [chemical binding]; other site 159087004507 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 159087004508 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087004509 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087004510 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 159087004511 UreF; Region: UreF; pfam01730 159087004512 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 159087004513 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 159087004514 dimer interface [polypeptide binding]; other site 159087004515 catalytic residues [active] 159087004516 urease subunit alpha; Reviewed; Region: ureC; PRK13207 159087004517 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 159087004518 subunit interactions [polypeptide binding]; other site 159087004519 active site 159087004520 flap region; other site 159087004521 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 159087004522 alpha-beta subunit interface [polypeptide binding]; other site 159087004523 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 159087004524 alpha-gamma subunit interface [polypeptide binding]; other site 159087004525 beta-gamma subunit interface [polypeptide binding]; other site 159087004526 UreD urease accessory protein; Region: UreD; cl00530 159087004527 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087004528 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 159087004529 S-adenosylmethionine binding site [chemical binding]; other site 159087004530 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 159087004531 Integrase core domain; Region: rve; cl01316 159087004532 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 159087004533 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087004534 Walker A/P-loop; other site 159087004535 ATP binding site [chemical binding]; other site 159087004536 Q-loop/lid; other site 159087004537 ABC transporter signature motif; other site 159087004538 Walker B; other site 159087004539 D-loop; other site 159087004540 H-loop/switch region; other site 159087004541 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 159087004542 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087004543 Walker A/P-loop; other site 159087004544 ATP binding site [chemical binding]; other site 159087004545 Q-loop/lid; other site 159087004546 ABC transporter signature motif; other site 159087004547 Walker B; other site 159087004548 D-loop; other site 159087004549 H-loop/switch region; other site 159087004550 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087004551 TM-ABC transporter signature motif; other site 159087004552 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087004553 TM-ABC transporter signature motif; other site 159087004554 Nitrogen fixation protein of unknown function; Region: Nif11; cl06756 159087004555 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087004556 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 159087004557 ligand binding site [chemical binding]; other site 159087004558 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 159087004559 PAS fold; Region: PAS_4; pfam08448 159087004560 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 159087004561 putative active site [active] 159087004562 heme pocket [chemical binding]; other site 159087004563 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 159087004564 dimer interface [polypeptide binding]; other site 159087004565 phosphorylation site [posttranslational modification] 159087004566 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 159087004567 ATP binding site [chemical binding]; other site 159087004568 Mg2+ binding site [ion binding]; other site 159087004569 G-X-G motif; other site 159087004570 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004571 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004572 active site 159087004573 phosphorylation site [posttranslational modification] 159087004574 intermolecular recognition site; other site 159087004575 dimerization interface [polypeptide binding]; other site 159087004576 cyanate hydratase; Validated; Region: PRK02866 159087004577 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 159087004578 oligomer interface [polypeptide binding]; other site 159087004579 active site 159087004580 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087004581 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 159087004582 putative ligand binding site [chemical binding]; other site 159087004583 phosphoglucomutase; Validated; Region: PRK07564 159087004584 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 159087004585 active site 159087004586 substrate binding site [chemical binding]; other site 159087004587 metal binding site [ion binding]; metal-binding site 159087004588 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004589 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004590 active site 159087004591 phosphorylation site [posttranslational modification] 159087004592 intermolecular recognition site; other site 159087004593 dimerization interface [polypeptide binding]; other site 159087004594 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087004595 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 159087004596 DNA binding residues [nucleotide binding] 159087004597 dimerization interface [polypeptide binding]; other site 159087004598 Sodium:solute symporter family; Region: SSF; cl00456 159087004599 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087004600 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 159087004601 dimer interface [polypeptide binding]; other site 159087004602 phosphorylation site [posttranslational modification] 159087004603 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 159087004604 ATP binding site [chemical binding]; other site 159087004605 Mg2+ binding site [ion binding]; other site 159087004606 G-X-G motif; other site 159087004607 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004608 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004609 active site 159087004610 phosphorylation site [posttranslational modification] 159087004611 intermolecular recognition site; other site 159087004612 dimerization interface [polypeptide binding]; other site 159087004613 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 159087004614 NifQ; Region: NifQ; pfam04891 159087004615 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 159087004616 catalytic loop [active] 159087004617 iron binding site [ion binding]; other site 159087004618 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 159087004619 catalytic loop [active] 159087004620 iron binding site [ion binding]; other site 159087004621 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 159087004622 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087004623 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087004624 Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also...; Region: ArsC_15kD; cd03033 159087004625 putative catalytic residues [active] 159087004626 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 159087004627 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 159087004628 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 159087004629 FeS/SAM binding site; other site 159087004630 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 159087004631 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 159087004632 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087004633 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 159087004634 active site residue [active] 159087004635 PEP-CTERM motif; Region: VPEP; cl15443 159087004636 Protein of unknown function (DUF550); Region: DUF550; pfam04447 159087004637 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 159087004638 cytochrome c oxidase assembly protein; Provisional; Region: PTZ00127 159087004639 UbiA prenyltransferase family; Region: UbiA; cl00337 159087004640 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 159087004641 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 159087004642 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 159087004643 Subunit III/VIIa interface [polypeptide binding]; other site 159087004644 Phospholipid binding site [chemical binding]; other site 159087004645 Subunit I/III interface [polypeptide binding]; other site 159087004646 Subunit III/VIb interface [polypeptide binding]; other site 159087004647 Subunit III/VIa interface; other site 159087004648 Subunit III/Vb interface [polypeptide binding]; other site 159087004649 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 159087004650 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 159087004651 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 159087004652 Subunit I/III interface [polypeptide binding]; other site 159087004653 D-pathway; other site 159087004654 Subunit I/VIIc interface [polypeptide binding]; other site 159087004655 Subunit I/IV interface [polypeptide binding]; other site 159087004656 Subunit I/II interface [polypeptide binding]; other site 159087004657 Low-spin heme (heme a) binding site [chemical binding]; other site 159087004658 Subunit I/VIIa interface [polypeptide binding]; other site 159087004659 Subunit I/VIa interface [polypeptide binding]; other site 159087004660 Dimer interface; other site 159087004661 Putative water exit pathway; other site 159087004662 Binuclear center (heme a3/CuB) [ion binding]; other site 159087004663 K-pathway; other site 159087004664 Subunit I/Vb interface [polypeptide binding]; other site 159087004665 Putative proton exit pathway; other site 159087004666 Subunit I/VIb interface; other site 159087004667 Subunit I/VIc interface [polypeptide binding]; other site 159087004668 Electron transfer pathway; other site 159087004669 Subunit I/VIIIb interface [polypeptide binding]; other site 159087004670 Subunit I/VIIb interface [polypeptide binding]; other site 159087004671 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 159087004672 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 159087004673 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 159087004674 Cu(I) binding site [ion binding]; other site 159087004675 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 159087004676 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 159087004677 ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and...; Region: modD_like; cd01573 159087004678 molybdenum transport protein ModD; Provisional; Region: PRK06096 159087004679 dimerization interface [polypeptide binding]; other site 159087004680 active site 159087004681 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 159087004682 Helix-turn-helix domains; Region: HTH; cl00088 159087004683 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 159087004684 TOBE domain; Region: TOBE_2; cl01440 159087004685 TOBE domain; Region: TOBE_2; cl01440 159087004686 TOBE domain; Region: TOBE_2; cl01440 159087004687 TOBE domain; Region: TOBE_2; cl01440 159087004688 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087004689 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087004690 NifZ domain; Region: NifZ; pfam04319 159087004691 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 159087004692 dimer interface [polypeptide binding]; other site 159087004693 [2Fe-2S] cluster binding site [ion binding]; other site 159087004694 Nif-specific regulatory protein; Region: nifA; TIGR01817 159087004695 GAF domain; Region: GAF; cl00853 159087004696 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 159087004697 Walker A motif; other site 159087004698 ATP binding site [chemical binding]; other site 159087004699 Walker B motif; other site 159087004700 arginine finger; other site 159087004701 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004702 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 159087004703 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 159087004704 putative active site [active] 159087004705 heme pocket [chemical binding]; other site 159087004706 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 159087004707 ATP binding site [chemical binding]; other site 159087004708 Mg2+ binding site [ion binding]; other site 159087004709 G-X-G motif; other site 159087004710 FMN-binding domain; Region: FMN_bind; cl01081 159087004711 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 159087004712 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 159087004713 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 159087004714 electron transport complex protein RnfB; Provisional; Region: PRK05113 159087004715 4Fe-4S binding domain; Region: Fer4; cl02805 159087004716 4Fe-4S binding domain; Region: Fer4; cl02805 159087004717 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 159087004718 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 159087004719 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 159087004720 SLBB domain; Region: SLBB; pfam10531 159087004721 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 159087004722 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 159087004723 Ubiquitin-like proteins; Region: UBQ; cl00155 159087004724 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 159087004725 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 159087004726 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004727 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 159087004728 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 159087004729 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 159087004730 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 159087004731 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 159087004732 Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifE_I; cd01968 159087004733 Protein of unknown function, DUF642; Region: DUF642; pfam04862 159087004734 legume lectins; Region: lectin_L-type; cd01951 159087004735 homotetramer interaction site [polypeptide binding]; other site 159087004736 homodimer interaction site [polypeptide binding]; other site 159087004737 carbohydrate binding site [chemical binding]; other site 159087004738 metal binding site [ion binding]; metal-binding site 159087004739 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 159087004740 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 159087004741 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 159087004742 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 159087004743 Protein of unknown function, DUF269; Region: DUF269; cl03973 159087004744 Protein of unknown function (DUF683); Region: DUF683; cl02247 159087004745 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 159087004746 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 159087004747 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 159087004748 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 159087004749 trimerization site [polypeptide binding]; other site 159087004750 active site 159087004751 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 159087004752 NifU-like domain; Region: NifU; cl00484 159087004753 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 159087004754 Aminotransferase class-V; Region: Aminotran_5; pfam00266 159087004755 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087004756 catalytic residue [active] 159087004757 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 159087004758 Moco binding site; other site 159087004759 metal coordination site [ion binding]; other site 159087004760 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 159087004761 RNA polymerase sigma factor; Provisional; Region: PRK12536 159087004762 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087004763 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 159087004764 DNA binding residues [nucleotide binding] 159087004765 Protein of unknown function (DUF1109); Region: DUF1109; cl02071 159087004766 Protein of unknown function (DUF1348); Region: DUF1348; pfam07080 159087004767 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 159087004768 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 159087004769 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 159087004770 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 159087004771 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087004772 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004773 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 159087004774 putative effector binding pocket; other site 159087004775 putative dimerization interface [polypeptide binding]; other site 159087004776 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 159087004777 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 159087004778 NADP binding site [chemical binding]; other site 159087004779 dimer interface [polypeptide binding]; other site 159087004780 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087004781 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004782 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 159087004783 putative substrate binding pocket [chemical binding]; other site 159087004784 putative dimerization interface [polypeptide binding]; other site 159087004785 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 159087004786 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 159087004787 putative substrate translocation pore; other site 159087004788 C-20 methyltransferase BchU; Region: C20_methyl_CrtF; TIGR02716 159087004789 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 159087004790 S-adenosylmethionine binding site [chemical binding]; other site 159087004791 Phasin protein; Region: Phasin_2; cl11491 159087004792 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 159087004793 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 159087004794 FAD binding pocket [chemical binding]; other site 159087004795 FAD binding motif [chemical binding]; other site 159087004796 phosphate binding motif [ion binding]; other site 159087004797 beta-alpha-beta structure motif; other site 159087004798 NAD binding pocket [chemical binding]; other site 159087004799 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 159087004800 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087004801 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 159087004802 putative dimerization interface [polypeptide binding]; other site 159087004803 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 159087004804 active site 159087004805 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 159087004806 folate binding site [chemical binding]; other site 159087004807 NADP+ binding site [chemical binding]; other site 159087004808 PAS fold; Region: PAS_3; pfam08447 159087004809 PAS domain S-box; Region: sensory_box; TIGR00229 159087004810 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 159087004811 putative active site [active] 159087004812 heme pocket [chemical binding]; other site 159087004813 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087004814 metal binding site [ion binding]; metal-binding site 159087004815 active site 159087004816 I-site; other site 159087004817 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 159087004818 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087004819 Helix-turn-helix domains; Region: HTH; cl00088 159087004820 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 159087004821 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087004822 active site 159087004823 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 159087004824 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 159087004825 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 159087004826 dimer interface [polypeptide binding]; other site 159087004827 active site 159087004828 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 159087004829 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 159087004830 substrate binding site [chemical binding]; other site 159087004831 oxyanion hole (OAH) forming residues; other site 159087004832 trimer interface [polypeptide binding]; other site 159087004833 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 159087004834 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; cl12011 159087004835 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087004836 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 159087004837 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 159087004838 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; cl12011 159087004839 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087004840 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 159087004841 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 159087004842 substrate binding site [chemical binding]; other site 159087004843 oxyanion hole (OAH) forming residues; other site 159087004844 trimer interface [polypeptide binding]; other site 159087004845 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 159087004846 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 159087004847 dimer interface [polypeptide binding]; other site 159087004848 active site 159087004849 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 159087004850 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 159087004851 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087004852 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 159087004853 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 159087004854 FMN binding site [chemical binding]; other site 159087004855 substrate binding site [chemical binding]; other site 159087004856 putative catalytic residue [active] 159087004857 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 159087004858 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 159087004859 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087004860 active site 159087004861 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 159087004862 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 159087004863 binding surface 159087004864 TPR motif; other site 159087004865 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 159087004866 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087004867 PAS fold; Region: PAS_4; pfam08448 159087004868 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087004869 Zn2+ binding site [ion binding]; other site 159087004870 Mg2+ binding site [ion binding]; other site 159087004871 Immunity protein Imm3; Region: Imm3; pfam14425 159087004872 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 159087004873 catalytic residues [active] 159087004874 ABC-2 type transporter; Region: ABC2_membrane; cl11417 159087004875 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 159087004876 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 159087004877 Walker A/P-loop; other site 159087004878 ATP binding site [chemical binding]; other site 159087004879 Q-loop/lid; other site 159087004880 ABC transporter signature motif; other site 159087004881 Walker B; other site 159087004882 D-loop; other site 159087004883 H-loop/switch region; other site 159087004884 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 159087004885 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087004886 4Fe-4S binding domain; Region: Fer4; cl02805 159087004887 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 159087004888 4Fe-4S binding domain; Region: Fer4; cl02805 159087004889 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 159087004890 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 159087004891 Periplasmic copper-binding protein (NosD); Region: NosD; pfam05048 159087004892 Cytochrome c; Region: Cytochrom_C; cl11414 159087004893 Cytochrome c; Region: Cytochrom_C; cl11414 159087004894 Cytochrome c; Region: Cytochrom_C; cl11414 159087004895 nitrous-oxide reductase; Validated; Region: PRK02888 159087004896 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 159087004897 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087004898 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004899 active site 159087004900 phosphorylation site [posttranslational modification] 159087004901 intermolecular recognition site; other site 159087004902 dimerization interface [polypeptide binding]; other site 159087004903 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 159087004904 DNA binding residues [nucleotide binding] 159087004905 dimerization interface [polypeptide binding]; other site 159087004906 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004907 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004908 active site 159087004909 phosphorylation site [posttranslational modification] 159087004910 intermolecular recognition site; other site 159087004911 dimerization interface [polypeptide binding]; other site 159087004912 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 159087004913 Histidine kinase; Region: HisKA_3; pfam07730 159087004914 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 159087004915 ATP binding site [chemical binding]; other site 159087004916 Mg2+ binding site [ion binding]; other site 159087004917 G-X-G motif; other site 159087004918 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087004919 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087004920 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 159087004921 putative active site [active] 159087004922 heme pocket [chemical binding]; other site 159087004923 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 159087004924 dimer interface [polypeptide binding]; other site 159087004925 phosphorylation site [posttranslational modification] 159087004926 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 159087004927 ATP binding site [chemical binding]; other site 159087004928 Mg2+ binding site [ion binding]; other site 159087004929 G-X-G motif; other site 159087004930 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004931 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004932 active site 159087004933 phosphorylation site [posttranslational modification] 159087004934 intermolecular recognition site; other site 159087004935 dimerization interface [polypeptide binding]; other site 159087004936 nitrous-oxide reductase; Validated; Region: PRK02888 159087004937 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 159087004938 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 159087004939 Cu(I) binding site [ion binding]; other site 159087004940 Protein of unknown function (DUF461); Region: DUF461; cl01071 159087004941 PAS domain S-box; Region: sensory_box; TIGR00229 159087004942 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 159087004943 putative active site [active] 159087004944 heme pocket [chemical binding]; other site 159087004945 PAS domain S-box; Region: sensory_box; TIGR00229 159087004946 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 159087004947 putative active site [active] 159087004948 heme pocket [chemical binding]; other site 159087004949 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087004950 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 159087004951 putative active site [active] 159087004952 heme pocket [chemical binding]; other site 159087004953 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 159087004954 putative active site [active] 159087004955 heme pocket [chemical binding]; other site 159087004956 PAS domain S-box; Region: sensory_box; TIGR00229 159087004957 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 159087004958 putative active site [active] 159087004959 heme pocket [chemical binding]; other site 159087004960 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087004961 metal binding site [ion binding]; metal-binding site 159087004962 active site 159087004963 I-site; other site 159087004964 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 159087004965 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087004966 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087004967 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 159087004968 dimer interface [polypeptide binding]; other site 159087004969 phosphorylation site [posttranslational modification] 159087004970 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 159087004971 ATP binding site [chemical binding]; other site 159087004972 Mg2+ binding site [ion binding]; other site 159087004973 G-X-G motif; other site 159087004974 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 159087004975 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004976 active site 159087004977 phosphorylation site [posttranslational modification] 159087004978 intermolecular recognition site; other site 159087004979 dimerization interface [polypeptide binding]; other site 159087004980 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 159087004981 DNA binding site [nucleotide binding] 159087004982 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 159087004983 Cytochrome c; Region: Cytochrom_C; cl11414 159087004984 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 159087004985 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087004986 active site 159087004987 phosphorylation site [posttranslational modification] 159087004988 intermolecular recognition site; other site 159087004989 dimerization interface [polypeptide binding]; other site 159087004990 Helix-turn-helix domains; Region: HTH; cl00088 159087004991 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 159087004992 dimer interface [polypeptide binding]; other site 159087004993 phosphorylation site [posttranslational modification] 159087004994 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 159087004995 ATP binding site [chemical binding]; other site 159087004996 Mg2+ binding site [ion binding]; other site 159087004997 G-X-G motif; other site 159087004998 Cytochrome c; Region: Cytochrom_C; cl11414 159087004999 Cytochrome c; Region: Cytochrom_C; cl11414 159087005000 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 159087005001 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 159087005002 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 159087005003 active site 159087005004 metal binding site [ion binding]; metal-binding site 159087005005 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; cl12031 159087005006 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 159087005007 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 159087005008 active site 159087005009 substrate binding site [chemical binding]; other site 159087005010 catalytic site [active] 159087005011 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 159087005012 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087005013 active site 159087005014 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; cl12011 159087005015 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 159087005016 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 159087005017 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087005018 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005019 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005020 active site 159087005021 phosphorylation site [posttranslational modification] 159087005022 intermolecular recognition site; other site 159087005023 dimerization interface [polypeptide binding]; other site 159087005024 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005025 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005026 active site 159087005027 phosphorylation site [posttranslational modification] 159087005028 intermolecular recognition site; other site 159087005029 dimerization interface [polypeptide binding]; other site 159087005030 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005031 metal binding site [ion binding]; metal-binding site 159087005032 active site 159087005033 I-site; other site 159087005034 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 159087005035 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 159087005036 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 159087005037 RmuC family; Region: RmuC; pfam02646 159087005038 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 159087005039 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087005040 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087005041 active site 159087005042 ATP binding site [chemical binding]; other site 159087005043 substrate binding site [chemical binding]; other site 159087005044 activation loop (A-loop); other site 159087005045 HDOD domain; Region: HDOD; pfam08668 159087005046 GAF domain; Region: GAF; cl00853 159087005047 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 159087005048 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 159087005049 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 159087005050 RNA binding surface [nucleotide binding]; other site 159087005051 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 159087005052 active site 159087005053 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 159087005054 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 159087005055 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 159087005056 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 159087005057 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 159087005058 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 159087005059 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 159087005060 NAD(P) binding site [chemical binding]; other site 159087005061 homotetramer interface [polypeptide binding]; other site 159087005062 homodimer interface [polypeptide binding]; other site 159087005063 active site 159087005064 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 159087005065 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 159087005066 NAD(P) binding site [chemical binding]; other site 159087005067 homotetramer interface [polypeptide binding]; other site 159087005068 homodimer interface [polypeptide binding]; other site 159087005069 active site 159087005070 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 159087005071 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 159087005072 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 159087005073 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 159087005074 PAS fold; Region: PAS_4; pfam08448 159087005075 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 159087005076 putative active site [active] 159087005077 heme pocket [chemical binding]; other site 159087005078 PAS fold; Region: PAS_3; pfam08447 159087005079 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 159087005080 dimer interface [polypeptide binding]; other site 159087005081 phosphorylation site [posttranslational modification] 159087005082 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 159087005083 ATP binding site [chemical binding]; other site 159087005084 Mg2+ binding site [ion binding]; other site 159087005085 G-X-G motif; other site 159087005086 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005087 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005088 active site 159087005089 phosphorylation site [posttranslational modification] 159087005090 intermolecular recognition site; other site 159087005091 dimerization interface [polypeptide binding]; other site 159087005092 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 159087005093 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 159087005094 active site 159087005095 dihydroxynaphthoic acid synthetase; Validated; Region: PRK07396 159087005096 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 159087005097 substrate binding site [chemical binding]; other site 159087005098 oxyanion hole (OAH) forming residues; other site 159087005099 trimer interface [polypeptide binding]; other site 159087005100 hypothetical protein; Provisional; Region: PRK00808 159087005101 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087005102 octamerization interface [polypeptide binding]; other site 159087005103 diferric-oxygen binding site [ion binding]; other site 159087005104 PilZ domain; Region: PilZ; cl01260 159087005105 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 159087005106 putative valine binding site [chemical binding]; other site 159087005107 dimer interface [polypeptide binding]; other site 159087005108 acetolactate synthase catalytic subunit; Validated; Region: PRK08155 159087005109 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 159087005110 PYR/PP interface [polypeptide binding]; other site 159087005111 dimer interface [polypeptide binding]; other site 159087005112 TPP binding site [chemical binding]; other site 159087005113 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 159087005114 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 159087005115 TPP-binding site [chemical binding]; other site 159087005116 dimer interface [polypeptide binding]; other site 159087005117 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 159087005118 PAS fold; Region: PAS_3; pfam08447 159087005119 putative active site [active] 159087005120 heme pocket [chemical binding]; other site 159087005121 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 159087005122 dimer interface [polypeptide binding]; other site 159087005123 phosphorylation site [posttranslational modification] 159087005124 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 159087005125 ATP binding site [chemical binding]; other site 159087005126 Mg2+ binding site [ion binding]; other site 159087005127 G-X-G motif; other site 159087005128 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005129 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005130 active site 159087005131 phosphorylation site [posttranslational modification] 159087005132 intermolecular recognition site; other site 159087005133 dimerization interface [polypeptide binding]; other site 159087005134 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005135 metal binding site [ion binding]; metal-binding site 159087005136 active site 159087005137 I-site; other site 159087005138 RasGAP: Ras-GTPase Activating Domain. RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin. Although the Rho (Ras...; Region: RasGAP; cl02569 159087005139 GAP/RAS interaction site [polypeptide binding]; other site 159087005140 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 159087005141 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 159087005142 Fumarase C-terminus; Region: Fumerase_C; cl00795 159087005143 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 159087005144 acetyl-CoA synthetase; Provisional; Region: PRK00174 159087005145 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 159087005146 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087005147 Sodium:solute symporter family; Region: SSF; cl00456 159087005148 Sodium:solute symporter family; Region: SSF; cl00456 159087005149 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 159087005150 dimer interface [polypeptide binding]; other site 159087005151 phosphorylation site [posttranslational modification] 159087005152 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 159087005153 ATP binding site [chemical binding]; other site 159087005154 Mg2+ binding site [ion binding]; other site 159087005155 G-X-G motif; other site 159087005156 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005157 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005158 active site 159087005159 phosphorylation site [posttranslational modification] 159087005160 intermolecular recognition site; other site 159087005161 dimerization interface [polypeptide binding]; other site 159087005162 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 159087005163 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 159087005164 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 159087005165 active site 159087005166 substrate binding site [chemical binding]; other site 159087005167 catalytic site [active] 159087005168 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087005169 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 159087005170 metal binding triad; other site 159087005171 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 159087005172 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 159087005173 ligand binding site [chemical binding]; other site 159087005174 flexible hinge region; other site 159087005175 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 159087005176 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087005177 metal binding triad; other site 159087005178 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 159087005179 catalytic site [active] 159087005180 Sodium:solute symporter family; Region: SSF; cl00456 159087005181 Sodium:solute symporter family; Region: SSF; cl00456 159087005182 Predicted membrane protein [Function unknown]; Region: COG4327; cl01781 159087005183 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 159087005184 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 159087005185 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087005186 The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; Region: PBP2_LysR_opines_like; cd08415 159087005187 putative dimerization interface [polypeptide binding]; other site 159087005188 diaminopimelate decarboxylase; Provisional; Region: PRK11165 159087005189 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 159087005190 active site 159087005191 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087005192 substrate binding site [chemical binding]; other site 159087005193 catalytic residues [active] 159087005194 dimer interface [polypeptide binding]; other site 159087005195 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 159087005196 IHF - DNA interface [nucleotide binding]; other site 159087005197 IHF dimer interface [polypeptide binding]; other site 159087005198 bifunctional HTH-domain containing protein/aminotransferase; Provisional; Region: PRK13355 159087005199 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 159087005200 putative transposase OrfB; Reviewed; Region: PHA02517 159087005201 Integrase core domain; Region: rve; cl01316 159087005202 Domain of unknown function (DUF932); Region: DUF932; cl12129 159087005203 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 159087005204 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 159087005205 IHF dimer interface [polypeptide binding]; other site 159087005206 IHF - DNA interface [nucleotide binding]; other site 159087005207 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087005208 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087005209 octamerization interface [polypeptide binding]; other site 159087005210 diferric-oxygen binding site [ion binding]; other site 159087005211 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005212 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005213 active site 159087005214 phosphorylation site [posttranslational modification] 159087005215 intermolecular recognition site; other site 159087005216 dimerization interface [polypeptide binding]; other site 159087005217 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005218 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005219 active site 159087005220 phosphorylation site [posttranslational modification] 159087005221 intermolecular recognition site; other site 159087005222 dimerization interface [polypeptide binding]; other site 159087005223 PAS fold; Region: PAS_3; pfam08447 159087005224 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087005225 PAS domain S-box; Region: sensory_box; TIGR00229 159087005226 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 159087005227 putative active site [active] 159087005228 heme pocket [chemical binding]; other site 159087005229 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 159087005230 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005231 metal binding site [ion binding]; metal-binding site 159087005232 active site 159087005233 I-site; other site 159087005234 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005235 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005236 active site 159087005237 phosphorylation site [posttranslational modification] 159087005238 intermolecular recognition site; other site 159087005239 dimerization interface [polypeptide binding]; other site 159087005240 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005241 metal binding site [ion binding]; metal-binding site 159087005242 active site 159087005243 I-site; other site 159087005244 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005245 Septum formation initiator; Region: DivIC; cl11433 159087005246 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 159087005247 dimer interface [polypeptide binding]; other site 159087005248 phosphorylation site [posttranslational modification] 159087005249 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 159087005250 ATP binding site [chemical binding]; other site 159087005251 Mg2+ binding site [ion binding]; other site 159087005252 G-X-G motif; other site 159087005253 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087005254 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 159087005255 ligand binding site [chemical binding]; other site 159087005256 flexible hinge region; other site 159087005257 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087005258 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087005259 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087005260 octamerization interface [polypeptide binding]; other site 159087005261 diferric-oxygen binding site [ion binding]; other site 159087005262 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087005263 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087005264 Walker A/P-loop; other site 159087005265 ATP binding site [chemical binding]; other site 159087005266 Q-loop/lid; other site 159087005267 ABC transporter signature motif; other site 159087005268 Walker B; other site 159087005269 D-loop; other site 159087005270 H-loop/switch region; other site 159087005271 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087005272 FtsX-like permease family; Region: FtsX; pfam02687 159087005273 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087005274 putative membrane fusion protein; Region: TIGR02828 159087005275 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087005276 Helix-turn-helix domains; Region: HTH; cl00088 159087005277 integrase; Provisional; Region: PRK09692 159087005278 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 159087005279 active site 159087005280 Int/Topo IB signature motif; other site 159087005281 PAS fold; Region: PAS_4; pfam08448 159087005282 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 159087005283 putative active site [active] 159087005284 heme pocket [chemical binding]; other site 159087005285 PAS domain S-box; Region: sensory_box; TIGR00229 159087005286 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 159087005287 putative active site [active] 159087005288 heme pocket [chemical binding]; other site 159087005289 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005290 metal binding site [ion binding]; metal-binding site 159087005291 active site 159087005292 I-site; other site 159087005293 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 159087005294 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 159087005295 Domain of unknown function (DUF336); Region: DUF336; cl01249 159087005296 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 159087005297 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 159087005298 inhibitor-cofactor binding pocket; inhibition site 159087005299 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087005300 catalytic residue [active] 159087005301 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005302 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005303 active site 159087005304 phosphorylation site [posttranslational modification] 159087005305 intermolecular recognition site; other site 159087005306 dimerization interface [polypeptide binding]; other site 159087005307 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 159087005308 active site 159087005309 dimerization interface [polypeptide binding]; other site 159087005310 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 159087005311 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 159087005312 HDOD domain; Region: HDOD; pfam08668 159087005313 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087005314 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087005315 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 159087005316 N-terminal plug; other site 159087005317 ligand-binding site [chemical binding]; other site 159087005318 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087005319 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 159087005320 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 159087005321 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 159087005322 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087005323 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087005324 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 159087005325 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 159087005326 S-adenosylmethionine binding site [chemical binding]; other site 159087005327 CbiD; Region: CbiD; cl00828 159087005328 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 159087005329 Precorrin-8X methylmutase; Region: CbiC; pfam02570 159087005330 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 159087005331 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 159087005332 putative active site [active] 159087005333 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 159087005334 putative active site [active] 159087005335 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087005336 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13636 159087005337 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 159087005338 Walker A/P-loop; other site 159087005339 ATP binding site [chemical binding]; other site 159087005340 Q-loop/lid; other site 159087005341 ABC transporter signature motif; other site 159087005342 Walker B; other site 159087005343 D-loop; other site 159087005344 H-loop/switch region; other site 159087005345 Cobalt transport protein; Region: CbiQ; cl00463 159087005346 Cobalt transport protein component CbiN; Region: CbiN; cl00842 159087005347 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 159087005348 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 159087005349 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087005350 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 159087005351 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 159087005352 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 159087005353 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 159087005354 FeS/SAM binding site; other site 159087005355 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; cl14869 159087005356 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 159087005357 GtrA-like protein; Region: GtrA; cl00971 159087005358 hypothetical protein; Provisional; Region: PRK07233 159087005359 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005360 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 159087005361 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005362 NAD(P) binding site [chemical binding]; other site 159087005363 active site 159087005364 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 159087005365 classical (c) SDRs; Region: SDR_c; cd05233 159087005366 NAD(P) binding site [chemical binding]; other site 159087005367 active site 159087005368 FAD binding domain; Region: FAD_binding_4; pfam01565 159087005369 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087005370 hypothetical protein; Validated; Region: PRK08238 159087005371 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087005372 UbiA prenyltransferase family; Region: UbiA; cl00337 159087005373 putative transposase OrfB; Reviewed; Region: PHA02517 159087005374 Integrase core domain; Region: rve; cl01316 159087005375 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 159087005376 IHF dimer interface [polypeptide binding]; other site 159087005377 IHF - DNA interface [nucleotide binding]; other site 159087005378 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 159087005379 Found in ATP-dependent protease La (LON); Region: LON; smart00464 159087005380 Found in ATP-dependent protease La (LON); Region: LON; smart00464 159087005381 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 159087005382 Walker A motif; other site 159087005383 ATP binding site [chemical binding]; other site 159087005384 Walker B motif; other site 159087005385 arginine finger; other site 159087005386 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 159087005387 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 159087005388 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 159087005389 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 159087005390 Walker A motif; other site 159087005391 ATP binding site [chemical binding]; other site 159087005392 Walker B motif; other site 159087005393 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 159087005394 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 159087005395 oligomer interface [polypeptide binding]; other site 159087005396 active site residues [active] 159087005397 trigger factor; Region: tig; TIGR00115 159087005398 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 159087005399 metal binding site [ion binding]; metal-binding site 159087005400 dimer interface [polypeptide binding]; other site 159087005401 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; cl12011 159087005402 HemK family putative methylases; Region: hemK_fam; TIGR00536 159087005403 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 159087005404 S-adenosylmethionine binding site [chemical binding]; other site 159087005405 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 159087005406 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 159087005407 metal binding site [ion binding]; metal-binding site 159087005408 dimer interface [polypeptide binding]; other site 159087005409 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 159087005410 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087005411 Walker A motif; other site 159087005412 ATP binding site [chemical binding]; other site 159087005413 Walker B motif; other site 159087005414 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 159087005415 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 159087005416 trimer interface [polypeptide binding]; other site 159087005417 active site 159087005418 substrate binding site [chemical binding]; other site 159087005419 CoA binding site [chemical binding]; other site 159087005420 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 159087005421 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 159087005422 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087005423 homodimer interface [polypeptide binding]; other site 159087005424 catalytic residue [active] 159087005425 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087005426 Zn2+ binding site [ion binding]; other site 159087005427 Mg2+ binding site [ion binding]; other site 159087005428 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 159087005429 nucleoside/Zn binding site; other site 159087005430 dimer interface [polypeptide binding]; other site 159087005431 catalytic motif [active] 159087005432 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 159087005433 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 159087005434 Walker A/P-loop; other site 159087005435 ATP binding site [chemical binding]; other site 159087005436 Q-loop/lid; other site 159087005437 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 159087005438 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 159087005439 ABC transporter signature motif; other site 159087005440 Walker B; other site 159087005441 D-loop; other site 159087005442 H-loop/switch region; other site 159087005443 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 159087005444 FtsZ protein binding site [polypeptide binding]; other site 159087005445 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 159087005446 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 159087005447 nucleotide binding pocket [chemical binding]; other site 159087005448 K-X-D-G motif; other site 159087005449 catalytic site [active] 159087005450 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 159087005451 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 159087005452 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 159087005453 Dimer interface [polypeptide binding]; other site 159087005454 BRCT sequence motif; other site 159087005455 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 159087005456 active site 159087005457 tetramer interface; other site 159087005458 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087005459 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; cl12011 159087005460 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 159087005461 PII uridylyl-transferase; Provisional; Region: PRK03059 159087005462 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087005463 metal binding triad; other site 159087005464 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 159087005465 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087005466 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 159087005467 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 159087005468 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 159087005469 active site 159087005470 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 159087005471 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 159087005472 NADP binding site [chemical binding]; other site 159087005473 active site 159087005474 putative substrate binding site [chemical binding]; other site 159087005475 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 159087005476 rRNA interaction site [nucleotide binding]; other site 159087005477 S8 interaction site; other site 159087005478 putative laminin-1 binding site; other site 159087005479 elongation factor Ts; Provisional; Region: tsf; PRK09377 159087005480 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 159087005481 Elongation factor TS; Region: EF_TS; pfam00889 159087005482 Elongation factor TS; Region: EF_TS; pfam00889 159087005483 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 159087005484 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 round of...; Region: RRF; cd00520 159087005485 hinge region; other site 159087005486 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 159087005487 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 159087005488 catalytic residue [active] 159087005489 putative FPP diphosphate binding site; other site 159087005490 putative FPP binding hydrophobic cleft; other site 159087005491 dimer interface [polypeptide binding]; other site 159087005492 putative IPP diphosphate binding site; other site 159087005493 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 159087005494 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 159087005495 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 159087005496 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 159087005497 zinc metallopeptidase RseP; Provisional; Region: PRK10779 159087005498 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 159087005499 active site 159087005500 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 159087005501 protein binding site [polypeptide binding]; other site 159087005502 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 159087005503 protein binding site [polypeptide binding]; other site 159087005504 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 159087005505 putative substrate binding region [chemical binding]; other site 159087005506 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 159087005507 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 159087005508 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 159087005509 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 159087005510 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 159087005511 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 159087005512 Surface antigen; Region: Bac_surface_Ag; cl03097 159087005513 periplasmic chaperone; Provisional; Region: PRK10780 159087005514 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 159087005515 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 159087005516 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 159087005517 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 159087005518 trimer interface [polypeptide binding]; other site 159087005519 active site 159087005520 UDP-GlcNAc binding site [chemical binding]; other site 159087005521 lipid binding site [chemical binding]; lipid-binding site 159087005522 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 159087005523 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 159087005524 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 159087005525 active site 159087005526 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 159087005527 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 159087005528 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 159087005529 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087005530 active site 159087005531 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 159087005532 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 159087005533 Domain of unknown function (DUF299); Region: DUF299; cl00780 159087005534 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 159087005535 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 159087005536 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 159087005537 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 159087005538 Ligand Binding Site [chemical binding]; other site 159087005539 glycolate transporter; Provisional; Region: PRK09695 159087005540 L-lactate permease; Region: Lactate_perm; cl00701 159087005541 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087005542 FAD binding domain; Region: FAD_binding_4; pfam01565 159087005543 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 159087005544 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087005545 iron-sulfur cluster-binding protein; Region: TIGR00273 159087005546 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 159087005547 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087005548 Cysteine-rich domain; Region: CCG; pfam02754 159087005549 Cysteine-rich domain; Region: CCG; pfam02754 159087005550 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 159087005551 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087005552 DNA-binding site [nucleotide binding]; DNA binding site 159087005553 FCD domain; Region: FCD; cl11656 159087005554 phosphoenolpyruvate synthase; Validated; Region: PRK06464 159087005555 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 159087005556 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 159087005557 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; cl09155 159087005558 Cache domain; Region: Cache_2; cl07034 159087005559 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 159087005560 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 159087005561 PEP-CTERM motif; Region: VPEP; cl15443 159087005562 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005563 active site 159087005564 Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]; Region: PleD; COG3706 159087005565 phosphorylation site [posttranslational modification] 159087005566 intermolecular recognition site; other site 159087005567 dimerization interface [polypeptide binding]; other site 159087005568 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 159087005569 putative active site [active] 159087005570 heme pocket [chemical binding]; other site 159087005571 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005572 metal binding site [ion binding]; metal-binding site 159087005573 active site 159087005574 I-site; other site 159087005575 PAS fold; Region: PAS_4; pfam08448 159087005576 PAS domain S-box; Region: sensory_box; TIGR00229 159087005577 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 159087005578 putative active site [active] 159087005579 heme pocket [chemical binding]; other site 159087005580 PAS fold; Region: PAS_3; pfam08447 159087005581 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087005582 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087005583 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 159087005584 dimer interface [polypeptide binding]; other site 159087005585 phosphorylation site [posttranslational modification] 159087005586 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 159087005587 ATP binding site [chemical binding]; other site 159087005588 Mg2+ binding site [ion binding]; other site 159087005589 G-X-G motif; other site 159087005590 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005591 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005592 active site 159087005593 phosphorylation site [posttranslational modification] 159087005594 intermolecular recognition site; other site 159087005595 dimerization interface [polypeptide binding]; other site 159087005596 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 159087005597 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 159087005598 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 159087005599 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 159087005600 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005601 domain; Region: Succ_DH_flav_C; pfam02910 159087005602 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 159087005603 Iron-sulfur protein interface; other site 159087005604 proximal heme binding site [chemical binding]; other site 159087005605 distal heme binding site [chemical binding]; other site 159087005606 dimer interface [polypeptide binding]; other site 159087005607 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 159087005608 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087005609 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087005610 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087005611 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 159087005612 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 159087005613 Walker A motif; other site 159087005614 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 159087005615 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 159087005616 dimer interface [polypeptide binding]; other site 159087005617 putative functional site; other site 159087005618 putative MPT binding site; other site 159087005619 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 159087005620 MoaE interaction surface [polypeptide binding]; other site 159087005621 MoeB interaction surface [polypeptide binding]; other site 159087005622 thiocarboxylated glycine; other site 159087005623 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 159087005624 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The...; Region: YlqF; cd01856 159087005625 GTP/Mg2+ binding site [chemical binding]; other site 159087005626 G4 box; other site 159087005627 G5 box; other site 159087005628 G1 box; other site 159087005629 Switch I region; other site 159087005630 G2 box; other site 159087005631 G3 box; other site 159087005632 Switch II region; other site 159087005633 HDOD domain; Region: HDOD; pfam08668 159087005634 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087005635 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 159087005636 active site residue [active] 159087005637 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 159087005638 YaeQ protein; Region: YaeQ; cl01913 159087005639 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087005640 ligand binding site [chemical binding]; other site 159087005641 FOG: CBS domain [General function prediction only]; Region: COG0517 159087005642 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 159087005643 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 159087005644 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 159087005645 Peptidase family U32; Region: Peptidase_U32; cl03113 159087005646 Collagenase; Region: DUF3656; pfam12392 159087005647 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005648 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 159087005649 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087005650 Walker A/P-loop; other site 159087005651 ATP binding site [chemical binding]; other site 159087005652 Q-loop/lid; other site 159087005653 ABC transporter signature motif; other site 159087005654 Walker B; other site 159087005655 D-loop; other site 159087005656 H-loop/switch region; other site 159087005657 ABC transporter; Region: ABC_tran_2; pfam12848 159087005658 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 159087005659 hypothetical protein; Provisional; Region: PRK14852 159087005660 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 159087005661 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 159087005662 dimer interface [polypeptide binding]; other site 159087005663 phosphorylation site [posttranslational modification] 159087005664 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 159087005665 ATP binding site [chemical binding]; other site 159087005666 Mg2+ binding site [ion binding]; other site 159087005667 G-X-G motif; other site 159087005668 response regulator GlrR; Provisional; Region: PRK15115 159087005669 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005670 active site 159087005671 phosphorylation site [posttranslational modification] 159087005672 intermolecular recognition site; other site 159087005673 dimerization interface [polypeptide binding]; other site 159087005674 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 159087005675 Walker A motif; other site 159087005676 ATP binding site [chemical binding]; other site 159087005677 Walker B motif; other site 159087005678 arginine finger; other site 159087005679 BON domain; Region: BON; cl02771 159087005680 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087005681 DsrE/DsrF-like family; Region: DrsE; cl00672 159087005682 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 159087005683 lipoyl attachment site [posttranslational modification]; other site 159087005684 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 159087005685 SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB...; Region: SelB; cd04171 159087005686 G1 box; other site 159087005687 putative GEF interaction site [polypeptide binding]; other site 159087005688 GTP/Mg2+ binding site [chemical binding]; other site 159087005689 Switch I region; other site 159087005690 G2 box; other site 159087005691 G3 box; other site 159087005692 Switch II region; other site 159087005693 G4 box; other site 159087005694 G5 box; other site 159087005695 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 159087005696 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 159087005697 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 159087005698 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 159087005699 MOSC domain; Region: MOSC; pfam03473 159087005700 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087005701 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 159087005702 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005703 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 159087005704 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 159087005705 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 159087005706 formate dehydrogenase accessory protein FdhE; Provisional; Region: PRK03564; cl11689 159087005707 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 159087005708 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 159087005709 4Fe-4S binding domain; Region: Fer4; cl02805 159087005710 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 159087005711 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 159087005712 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 159087005713 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 159087005714 molybdopterin cofactor binding site; other site 159087005715 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 159087005716 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 159087005717 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087005718 ATP binding site [chemical binding]; other site 159087005719 Mg++ binding site [ion binding]; other site 159087005720 motif III; other site 159087005721 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 159087005722 nucleotide binding region [chemical binding]; other site 159087005723 ATP-binding site [chemical binding]; other site 159087005724 DsrE/DsrF-like family; Region: DrsE; cl00672 159087005725 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 159087005726 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; cl12011 159087005727 tRNA (uracil-5-)-methyltransferase; Region: trmA_only; TIGR02143 159087005728 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 159087005729 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 159087005730 dimer interface [polypeptide binding]; other site 159087005731 conserved gate region; other site 159087005732 putative PBP binding loops; other site 159087005733 ABC-ATPase subunit interface; other site 159087005734 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 159087005735 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 159087005736 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 159087005737 Walker A/P-loop; other site 159087005738 ATP binding site [chemical binding]; other site 159087005739 Q-loop/lid; other site 159087005740 ABC transporter signature motif; other site 159087005741 Walker B; other site 159087005742 D-loop; other site 159087005743 H-loop/switch region; other site 159087005744 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087005745 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087005746 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087005747 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005748 active site 159087005749 phosphorylation site [posttranslational modification] 159087005750 intermolecular recognition site; other site 159087005751 dimerization interface [polypeptide binding]; other site 159087005752 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 159087005753 Walker A motif; other site 159087005754 ATP binding site [chemical binding]; other site 159087005755 Walker B motif; other site 159087005756 arginine finger; other site 159087005757 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087005758 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 159087005759 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 159087005760 dimer interface [polypeptide binding]; other site 159087005761 phosphorylation site [posttranslational modification] 159087005762 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 159087005763 ATP binding site [chemical binding]; other site 159087005764 Mg2+ binding site [ion binding]; other site 159087005765 G-X-G motif; other site 159087005766 NosL; Region: NosL; cl01769 159087005767 LysE type translocator; Region: LysE; cl00565 159087005768 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 159087005769 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087005770 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 159087005771 DNA binding residues [nucleotide binding] 159087005772 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 159087005773 FecR protein; Region: FecR; pfam04773 159087005774 Secretin and TonB N terminus short domain; Region: STN; cl06624 159087005775 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 159087005776 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 159087005777 N-terminal plug; other site 159087005778 ligand-binding site [chemical binding]; other site 159087005779 NosL; Region: NosL; cl01769 159087005780 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087005781 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 159087005782 metal-binding site [ion binding] 159087005783 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087005784 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087005785 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087005786 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087005787 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087005788 Walker A/P-loop; other site 159087005789 ATP binding site [chemical binding]; other site 159087005790 Q-loop/lid; other site 159087005791 ABC transporter signature motif; other site 159087005792 Walker B; other site 159087005793 D-loop; other site 159087005794 H-loop/switch region; other site 159087005795 FtsX-like permease family; Region: FtsX; pfam02687 159087005796 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 159087005797 Cu(I) binding site [ion binding]; other site 159087005798 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 159087005799 NAD-dependent deacetylase; Provisional; Region: PRK14138 159087005800 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 159087005801 NAD+ binding site [chemical binding]; other site 159087005802 substrate binding site [chemical binding]; other site 159087005803 Zn binding site [ion binding]; other site 159087005804 Phasin protein; Region: Phasin_2; cl11491 159087005805 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 159087005806 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 in DNA...; Region: TOP4c; cd00187 159087005807 CAP-like domain; other site 159087005808 active site 159087005809 primary dimer interface [polypeptide binding]; other site 159087005810 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 159087005811 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 159087005812 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087005813 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087005814 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087005815 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 159087005816 Domain of unknown function (DUF3597); Region: DUF3597; pfam12200 159087005817 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 159087005818 Protein tyrosine kinase; Region: Pkinase_Tyr; pfam07714 159087005819 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087005820 active site 159087005821 ATP binding site [chemical binding]; other site 159087005822 substrate binding site [chemical binding]; other site 159087005823 activation loop (A-loop); other site 159087005824 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 159087005825 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 159087005826 B12 binding site [chemical binding]; other site 159087005827 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 159087005828 S-adenosylmethionine binding site [chemical binding]; other site 159087005829 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087005830 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 159087005831 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 159087005832 active site 159087005833 nucleophile elbow; other site 159087005834 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 159087005835 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087005836 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087005837 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087005838 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087005839 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form; Region: argC_other; TIGR01851 159087005840 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 159087005841 nucleophile elbow; other site 159087005842 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 159087005843 ATP binding site [chemical binding]; other site 159087005844 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 159087005845 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 159087005846 ATP binding site [chemical binding]; other site 159087005847 Mg2+ binding site [ion binding]; other site 159087005848 G-X-G motif; other site 159087005849 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 159087005850 anchoring element; other site 159087005851 dimer interface [polypeptide binding]; other site 159087005852 ATP binding site [chemical binding]; other site 159087005853 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 159087005854 active site 159087005855 putative metal-binding site [ion binding]; other site 159087005856 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 159087005857 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 159087005858 dimer interface [polypeptide binding]; other site 159087005859 FMN binding site [chemical binding]; other site 159087005860 Protein of unknown function (DUF808); Region: DUF808; cl01002 159087005861 chromosome segregation protein; Provisional; Region: PRK02224 159087005862 Double zinc ribbon; Region: DZR; pfam12773 159087005863 OpgC protein; Region: OpgC_C; cl00792 159087005864 Acyltransferase family; Region: Acyl_transf_3; pfam01757 159087005865 Domain of Unknown Function (DUF1520); Region: DUF1520; pfam07480 159087005866 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; cl14780 159087005867 hypothetical protein; Reviewed; Region: PRK09588 159087005868 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 159087005869 hydrophobic ligand binding site; other site 159087005870 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087005871 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087005872 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087005873 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 159087005874 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005875 active site 159087005876 phosphorylation site [posttranslational modification] 159087005877 intermolecular recognition site; other site 159087005878 dimerization interface [polypeptide binding]; other site 159087005879 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 159087005880 DNA binding site [nucleotide binding] 159087005881 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087005882 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 159087005883 dimer interface [polypeptide binding]; other site 159087005884 phosphorylation site [posttranslational modification] 159087005885 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 159087005886 ATP binding site [chemical binding]; other site 159087005887 Mg2+ binding site [ion binding]; other site 159087005888 G-X-G motif; other site 159087005889 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 159087005890 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; cl00083 159087005891 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 159087005892 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 159087005893 active site 159087005894 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 159087005895 Radical SAM superfamily; Region: Radical_SAM; pfam04055 159087005896 FeS/SAM binding site; other site 159087005897 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 159087005898 putative substrate translocation pore; other site 159087005899 Cupin domain; Region: Cupin_2; cl09118 159087005900 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087005901 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 159087005902 AAA domain; Region: AAA_21; pfam13304 159087005903 SelR domain; Region: SelR; cl00369 159087005904 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 159087005905 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087005906 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087005907 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 159087005908 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 159087005909 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 159087005910 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 159087005911 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 159087005912 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 159087005913 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 159087005914 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 159087005915 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 159087005916 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 159087005917 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 159087005918 Ligand binding site; other site 159087005919 metal-binding site 159087005920 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 159087005921 SEC-C motif; Region: SEC-C; pfam02810 159087005922 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 159087005923 PAS fold; Region: PAS_4; pfam08448 159087005924 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 159087005925 putative active site [active] 159087005926 heme pocket [chemical binding]; other site 159087005927 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 159087005928 PAS fold; Region: PAS_3; pfam08447 159087005929 putative active site [active] 159087005930 heme pocket [chemical binding]; other site 159087005931 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 159087005932 dimer interface [polypeptide binding]; other site 159087005933 phosphorylation site [posttranslational modification] 159087005934 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 159087005935 ATP binding site [chemical binding]; other site 159087005936 Mg2+ binding site [ion binding]; other site 159087005937 G-X-G motif; other site 159087005938 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005939 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087005940 active site 159087005941 phosphorylation site [posttranslational modification] 159087005942 intermolecular recognition site; other site 159087005943 dimerization interface [polypeptide binding]; other site 159087005944 CHASE2 domain; Region: CHASE2; cl01732 159087005945 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087005946 Zn2+ binding site [ion binding]; other site 159087005947 Mg2+ binding site [ion binding]; other site 159087005948 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087005949 ligand binding site [chemical binding]; other site 159087005950 FecR protein; Region: FecR; pfam04773 159087005951 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 159087005952 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 159087005953 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 159087005954 protein binding site [polypeptide binding]; other site 159087005955 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 159087005956 protein binding site [polypeptide binding]; other site 159087005957 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087005958 dimer interface [polypeptide binding]; other site 159087005959 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 159087005960 putative CheW interface [polypeptide binding]; other site 159087005961 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; cl01450 159087005962 Cupin domain; Region: Cupin_2; cl09118 159087005963 CreA protein; Region: CreA; pfam05981 159087005964 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 159087005965 active site 159087005966 nucleophile elbow; other site 159087005967 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 159087005968 active site 159087005969 catalytic site [active] 159087005970 substrate binding site [chemical binding]; other site 159087005971 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 159087005972 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 159087005973 GIY-YIG motif/motif A; other site 159087005974 active site 159087005975 catalytic site [active] 159087005976 putative DNA binding site [nucleotide binding]; other site 159087005977 metal binding site [ion binding]; metal-binding site 159087005978 PAS fold; Region: PAS_4; pfam08448 159087005979 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 159087005980 putative active site [active] 159087005981 heme pocket [chemical binding]; other site 159087005982 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 159087005983 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087005984 putative active site [active] 159087005985 heme pocket [chemical binding]; other site 159087005986 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005987 metal binding site [ion binding]; metal-binding site 159087005988 active site 159087005989 I-site; other site 159087005990 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 159087005991 Cupin domain; Region: Cupin_2; cl09118 159087005992 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087005993 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087005994 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 159087005995 putative catalytic residues [active] 159087005996 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 159087005997 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005998 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 159087005999 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087006000 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; cl01740 159087006001 exonuclease SbcC; Region: sbcc; TIGR00618 159087006002 exonuclease SbcC; Region: sbcc; TIGR00618 159087006003 exonuclease SbcC; Region: sbcc; TIGR00618 159087006004 exonuclease subunit SbcD; Provisional; Region: PRK10966 159087006005 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 159087006006 active site 159087006007 metal binding site [ion binding]; metal-binding site 159087006008 DNA binding site [nucleotide binding] 159087006009 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 159087006010 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 159087006011 glycerol kinase; Provisional; Region: glpK; PRK00047 159087006012 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 159087006013 N- and C-terminal domain interface [polypeptide binding]; other site 159087006014 active site 159087006015 MgATP binding site [chemical binding]; other site 159087006016 catalytic site [active] 159087006017 metal binding site [ion binding]; metal-binding site 159087006018 glycerol binding site [chemical binding]; other site 159087006019 homotetramer interface [polypeptide binding]; other site 159087006020 homodimer interface [polypeptide binding]; other site 159087006021 FBP binding site [chemical binding]; other site 159087006022 protein IIAGlc interface [polypeptide binding]; other site 159087006023 Uncharacterized conserved protein (DUF2164); Region: DUF2164; cl02278 159087006024 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 159087006025 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 159087006026 dimerization interface [polypeptide binding]; other site 159087006027 ATP binding site [chemical binding]; other site 159087006028 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 159087006029 dimerization interface [polypeptide binding]; other site 159087006030 ATP binding site [chemical binding]; other site 159087006031 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 159087006032 putative active site [active] 159087006033 catalytic triad [active] 159087006034 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 159087006035 oligomer interface [polypeptide binding]; other site 159087006036 active site residues [active] 159087006037 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 159087006038 Macro domain, Appr-1'-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 159087006039 putative ADP-ribose binding site [chemical binding]; other site 159087006040 putative active site [active] 159087006041 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 159087006042 active site residue [active] 159087006043 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 159087006044 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 159087006045 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087006046 DNA-binding site [nucleotide binding]; DNA binding site 159087006047 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 159087006048 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087006049 homodimer interface [polypeptide binding]; other site 159087006050 catalytic residue [active] 159087006051 periplasmic folding chaperone; Provisional; Region: PRK10788 159087006052 SurA N-terminal domain; Region: SurA_N; pfam09312 159087006053 PPIC-type PPIASE domain; Region: Rotamase; cl08278 159087006054 PAS domain S-box; Region: sensory_box; TIGR00229 159087006055 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 159087006056 putative active site [active] 159087006057 heme pocket [chemical binding]; other site 159087006058 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 159087006059 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087006060 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 159087006061 dimer interface [polypeptide binding]; other site 159087006062 phosphorylation site [posttranslational modification] 159087006063 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 159087006064 ATP binding site [chemical binding]; other site 159087006065 Mg2+ binding site [ion binding]; other site 159087006066 G-X-G motif; other site 159087006067 Response regulator receiver domain; Region: Response_reg; pfam00072 159087006068 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006069 active site 159087006070 phosphorylation site [posttranslational modification] 159087006071 intermolecular recognition site; other site 159087006072 dimerization interface [polypeptide binding]; other site 159087006073 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 159087006074 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 159087006075 NAD binding site [chemical binding]; other site 159087006076 homotetramer interface [polypeptide binding]; other site 159087006077 homodimer interface [polypeptide binding]; other site 159087006078 substrate binding site [chemical binding]; other site 159087006079 active site 159087006080 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 159087006081 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087006082 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 159087006083 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 159087006084 active site 159087006085 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087006086 LexA repressor; Validated; Region: PRK00215 159087006087 Helix-turn-helix domains; Region: HTH; cl00088 159087006088 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 159087006089 Catalytic site [active] 159087006090 Cell division inhibitor SulA; Region: SulA; cl01880 159087006091 DNA Polymerase Y-family; Region: PolY_like; cd03468 159087006092 active site 159087006093 DNA binding site [nucleotide binding] 159087006094 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 159087006095 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 159087006096 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 159087006097 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 159087006098 generic binding surface II; other site 159087006099 generic binding surface I; other site 159087006100 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087006101 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 159087006102 binding surface 159087006103 TPR motif; other site 159087006104 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 159087006105 binding surface 159087006106 TPR motif; other site 159087006107 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 159087006108 TPR motif; other site 159087006109 binding surface 159087006110 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 159087006111 TPR motif; other site 159087006112 binding surface 159087006113 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 159087006114 binding surface 159087006115 TPR motif; other site 159087006116 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087006117 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 159087006118 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087006119 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 159087006120 serine O-acetyltransferase; Region: cysE; TIGR01172 159087006121 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 159087006122 trimer interface [polypeptide binding]; other site 159087006123 active site 159087006124 substrate binding site [chemical binding]; other site 159087006125 CoA binding site [chemical binding]; other site 159087006126 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087006127 Rrf2 family protein; Region: rrf2_super; TIGR00738 159087006128 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 159087006129 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 159087006130 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087006131 catalytic residue [active] 159087006132 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 159087006133 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 159087006134 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087006135 catalytic residue [active] 159087006136 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 159087006137 trimerization site [polypeptide binding]; other site 159087006138 active site 159087006139 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 159087006140 co-chaperone HscB; Provisional; Region: hscB; PRK03578 159087006141 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; cl02542 159087006142 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 159087006143 chaperone protein HscA; Provisional; Region: hscA; PRK05183 159087006144 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 159087006145 Protein of unknown function (DUF528); Region: DUF528; cl01123 159087006146 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; cl01467 159087006147 Flagellin N-methylase; Region: FliB; cl00497 159087006148 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 159087006149 phosphoserine phosphatase; Provisional; Region: serB; PRK11133 159087006150 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 159087006151 motif II; other site 159087006152 NeuB family; Region: NeuB; cl00496 159087006153 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 159087006154 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 159087006155 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 159087006156 ATP binding site [chemical binding]; other site 159087006157 putative Mg++ binding site [ion binding]; other site 159087006158 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 159087006159 nucleotide binding region [chemical binding]; other site 159087006160 ATP-binding site [chemical binding]; other site 159087006161 TRCF domain; Region: TRCF; cl04088 159087006162 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 159087006163 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 159087006164 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087006165 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 159087006166 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 159087006167 FeS/SAM binding site; other site 159087006168 AMMECR1; Region: AMMECR1; cl00911 159087006169 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 159087006170 putative ligand binding pocket/active site [active] 159087006171 putative metal binding site [ion binding]; other site 159087006172 MgtC family; Region: MgtC; cl12207 159087006173 Predicted membrane protein [Function unknown]; Region: COG3174 159087006174 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 159087006175 substrate binding site; other site 159087006176 dimer interface; other site 159087006177 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 159087006178 homotrimer interaction site [polypeptide binding]; other site 159087006179 zinc binding site [ion binding]; other site 159087006180 CDP-binding sites; other site 159087006181 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 159087006182 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 159087006183 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 159087006184 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006185 active site 159087006186 phosphorylation site [posttranslational modification] 159087006187 intermolecular recognition site; other site 159087006188 dimerization interface [polypeptide binding]; other site 159087006189 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 159087006190 PAS fold; Region: PAS_3; pfam08447 159087006191 putative active site [active] 159087006192 heme pocket [chemical binding]; other site 159087006193 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006194 metal binding site [ion binding]; metal-binding site 159087006195 active site 159087006196 I-site; other site 159087006197 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 159087006198 HDOD domain; Region: HDOD; pfam08668 159087006199 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087006200 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087006201 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 159087006202 dimerization interface [polypeptide binding]; other site 159087006203 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 159087006204 dimer interface [polypeptide binding]; other site 159087006205 phosphorylation site [posttranslational modification] 159087006206 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 159087006207 ATP binding site [chemical binding]; other site 159087006208 Mg2+ binding site [ion binding]; other site 159087006209 G-X-G motif; other site 159087006210 osmolarity response regulator; Provisional; Region: ompR; PRK09468 159087006211 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006212 active site 159087006213 phosphorylation site [posttranslational modification] 159087006214 intermolecular recognition site; other site 159087006215 dimerization interface [polypeptide binding]; other site 159087006216 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 159087006217 DNA binding site [nucleotide binding] 159087006218 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 159087006219 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 159087006220 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087006221 Coenzyme A binding pocket [chemical binding]; other site 159087006222 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 159087006223 Fe-S cluster binding site [ion binding]; other site 159087006224 active site 159087006225 LysR transcriptional regulator; Provisional; Region: rbcR; CHL00180 159087006226 Helix-turn-helix domains; Region: HTH; cl00088 159087006227 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 159087006228 putative dimerization interface [polypeptide binding]; other site 159087006229 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 159087006230 alanine racemase; Reviewed; Region: dadX; PRK03646 159087006231 active site 159087006232 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087006233 substrate binding site [chemical binding]; other site 159087006234 catalytic residues [active] 159087006235 dimer interface [polypeptide binding]; other site 159087006236 DNA repair protein RadA; Provisional; Region: PRK11823 159087006237 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 159087006238 Walker A motif/ATP binding site; other site 159087006239 ATP binding site [chemical binding]; other site 159087006240 Walker B motif; other site 159087006241 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 159087006242 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087006243 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006244 metal binding site [ion binding]; metal-binding site 159087006245 active site 159087006246 I-site; other site 159087006247 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 159087006248 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 159087006249 FtsX-like permease family; Region: FtsX; pfam02687 159087006250 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; cl00075 159087006251 FecR protein; Region: FecR; pfam04773 159087006252 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006253 ligand binding site [chemical binding]; other site 159087006254 CHASE2 domain; Region: CHASE2; cl01732 159087006255 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 159087006256 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087006257 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 159087006258 anti sigma factor interaction site; other site 159087006259 regulatory phosphorylation site [posttranslational modification]; other site 159087006260 hypothetical protein; Provisional; Region: PRK01254 159087006261 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 159087006262 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 159087006263 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 159087006264 apolar tunnel; other site 159087006265 heme binding site [chemical binding]; other site 159087006266 dimerization interface [polypeptide binding]; other site 159087006267 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 159087006268 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 159087006269 G1 box; other site 159087006270 putative GEF interaction site [polypeptide binding]; other site 159087006271 GTP/Mg2+ binding site [chemical binding]; other site 159087006272 Switch I region; other site 159087006273 G2 box; other site 159087006274 G3 box; other site 159087006275 Switch II region; other site 159087006276 G4 box; other site 159087006277 G5 box; other site 159087006278 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 159087006279 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 159087006280 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 159087006281 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 159087006282 FeS/SAM binding site; other site 159087006283 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 159087006284 AsmA-like C-terminal region; Region: AsmA_2; cl15864 159087006285 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 159087006286 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 159087006287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087006288 homodimer interface [polypeptide binding]; other site 159087006289 catalytic residue [active] 159087006290 excinuclease ABC subunit B; Provisional; Region: PRK05298 159087006291 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 159087006292 ATP binding site [chemical binding]; other site 159087006293 putative Mg++ binding site [ion binding]; other site 159087006294 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 159087006295 nucleotide binding region [chemical binding]; other site 159087006296 ATP-binding site [chemical binding]; other site 159087006297 Ultra-violet resistance protein B; Region: UvrB; pfam12344 159087006298 Low molecular weight phosphatase family; Region: LMWPc; cd00115 159087006299 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 159087006300 active site 159087006301 ribonuclease E; Reviewed; Region: rne; PRK10811 159087006302 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 159087006303 homodimer interface [polypeptide binding]; other site 159087006304 oligonucleotide binding site [chemical binding]; other site 159087006305 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 159087006306 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 159087006307 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 159087006308 active site 159087006309 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 159087006310 iron-sulfur cluster [ion binding]; other site 159087006311 [2Fe-2S] cluster binding site [ion binding]; other site 159087006312 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 159087006313 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 159087006314 tandem repeat interface [polypeptide binding]; other site 159087006315 oligomer interface [polypeptide binding]; other site 159087006316 active site residues [active] 159087006317 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087006318 Maf-like protein; Region: Maf; pfam02545 159087006319 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 159087006320 active site 159087006321 dimer interface [polypeptide binding]; other site 159087006322 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 159087006323 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 159087006324 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 159087006325 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 159087006326 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 159087006327 dimer interface [polypeptide binding]; other site 159087006328 active site 159087006329 CoA binding pocket [chemical binding]; other site 159087006330 Acyl transferase domain; Region: Acyl_transf_1; cl08282 159087006331 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 159087006332 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 159087006333 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 159087006334 NAD(P) binding site [chemical binding]; other site 159087006335 homotetramer interface [polypeptide binding]; other site 159087006336 homodimer interface [polypeptide binding]; other site 159087006337 active site 159087006338 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087006339 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 159087006340 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 159087006341 dimer interface [polypeptide binding]; other site 159087006342 active site 159087006343 L-aspartate oxidase; Provisional; Region: PRK09077 159087006344 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087006345 domain; Region: Succ_DH_flav_C; pfam02910 159087006346 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 159087006347 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087006348 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 159087006349 DNA binding residues [nucleotide binding] 159087006350 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 159087006351 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 159087006352 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 159087006353 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 159087006354 protein binding site [polypeptide binding]; other site 159087006355 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 159087006356 protein binding site [polypeptide binding]; other site 159087006357 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087006358 GTP-binding protein LepA; Provisional; Region: PRK05433 159087006359 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 159087006360 G1 box; other site 159087006361 putative GEF interaction site [polypeptide binding]; other site 159087006362 GTP/Mg2+ binding site [chemical binding]; other site 159087006363 Switch I region; other site 159087006364 G2 box; other site 159087006365 G3 box; other site 159087006366 Switch II region; other site 159087006367 G4 box; other site 159087006368 G5 box; other site 159087006369 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 159087006370 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 159087006371 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 159087006372 signal peptidase I; Provisional; Region: PRK10861 159087006373 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 159087006374 Catalytic site [active] 159087006375 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 159087006376 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 159087006377 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 159087006378 dimerization interface [polypeptide binding]; other site 159087006379 active site 159087006380 metal binding site [ion binding]; metal-binding site 159087006381 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 159087006382 dsRNA binding site [nucleotide binding]; other site 159087006383 GTPase Era; Reviewed; Region: era; PRK00089 159087006384 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly...; Region: Era; cd04163 159087006385 G1 box; other site 159087006386 GTP/Mg2+ binding site [chemical binding]; other site 159087006387 Switch I region; other site 159087006388 G2 box; other site 159087006389 Switch II region; other site 159087006390 G3 box; other site 159087006391 G4 box; other site 159087006392 G5 box; other site 159087006393 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 159087006394 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 159087006395 Recombination protein O N terminal; Region: RecO_N; pfam11967 159087006396 Recombination protein O C terminal; Region: RecO_C; pfam02565 159087006397 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 the...; Region: PNPsynthase; cd00003 159087006398 active site 159087006399 hydrophilic channel; other site 159087006400 dimerization interface [polypeptide binding]; other site 159087006401 catalytic residues [active] 159087006402 active site lid [active] 159087006403 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 159087006404 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 159087006405 elongation factor P; Validated; Region: PRK00529 159087006406 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 159087006407 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 159087006408 RNA binding site [nucleotide binding]; other site 159087006409 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 159087006410 RNA binding site [nucleotide binding]; other site 159087006411 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 159087006412 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 159087006413 Fe-S cluster binding site [ion binding]; other site 159087006414 DNA binding site [nucleotide binding] 159087006415 active site 159087006416 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 159087006417 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 159087006418 GIY-YIG motif/motif A; other site 159087006419 active site 159087006420 catalytic site [active] 159087006421 putative DNA binding site [nucleotide binding]; other site 159087006422 metal binding site [ion binding]; metal-binding site 159087006423 UvrB/uvrC motif; Region: UVR; pfam02151 159087006424 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 159087006425 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 159087006426 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 159087006427 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 159087006428 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 159087006429 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 159087006430 Transposase; Region: DEDD_Tnp_IS110; pfam01548 159087006431 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 159087006432 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087006433 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 159087006434 ligand binding site [chemical binding]; other site 159087006435 flexible hinge region; other site 159087006436 Helix-turn-helix domains; Region: HTH; cl00088 159087006437 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 159087006438 CheB methylesterase; Region: CheB_methylest; pfam01339 159087006439 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 159087006440 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 159087006441 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; cl12011 159087006442 transcription factor, RsfA family; Region: DNA_bind_RsfA; TIGR02894 159087006443 PAS fold; Region: PAS_4; pfam08448 159087006444 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 159087006445 Uncharacterized protein conserved in bacteria (DUF2329); Region: DUF2329; pfam10091 159087006446 Putative carbohydrate binding domain; Region: CBM_X; cl05621 159087006447 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 159087006448 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 159087006449 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 159087006450 Putative carbohydrate binding domain; Region: CBM_X; cl05621 159087006451 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 159087006452 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 159087006453 BON domain; Region: BON; cl02771 159087006454 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087006455 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006456 active site 159087006457 phosphorylation site [posttranslational modification] 159087006458 intermolecular recognition site; other site 159087006459 PAS domain S-box; Region: sensory_box; TIGR00229 159087006460 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 159087006461 putative active site [active] 159087006462 heme pocket [chemical binding]; other site 159087006463 PAS fold; Region: PAS; pfam00989 159087006464 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 159087006465 putative active site [active] 159087006466 heme pocket [chemical binding]; other site 159087006467 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006468 metal binding site [ion binding]; metal-binding site 159087006469 active site 159087006470 I-site; other site 159087006471 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 159087006472 Uncharacterized conserved protein [Function unknown]; Region: COG3461 159087006473 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 159087006474 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 159087006475 periplasmic protein; Provisional; Region: PRK10568 159087006476 BON domain; Region: BON; cl02771 159087006477 transcription termination factor Rho; Provisional; Region: PRK12678 159087006478 Family of unknown function (DUF500); Region: DUF500; cl01109 159087006479 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 159087006480 HSP70 interaction site [polypeptide binding]; other site 159087006481 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; cl12031 159087006482 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 159087006483 CsbD-like; Region: CsbD; cl01888 159087006484 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 159087006485 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 159087006486 putative active site [active] 159087006487 transaldolase; Provisional; Region: PRK03903 159087006488 catalytic residue [active] 159087006489 putative phosphoketolase; Provisional; Region: PRK05261 159087006490 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 159087006491 TPP-binding site; other site 159087006492 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 159087006493 XFP C-terminal domain; Region: XFP_C; pfam09363 159087006494 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 159087006495 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 159087006496 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 159087006497 HSP70 interaction site [polypeptide binding]; other site 159087006498 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 159087006499 substrate binding site [polypeptide binding]; other site 159087006500 dimer interface [polypeptide binding]; other site 159087006501 CHRD domain; Region: CHRD; cl06473 159087006502 OsmC-like protein; Region: OsmC; cl00767 159087006503 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 159087006504 tetrameric interface [polypeptide binding]; other site 159087006505 activator binding site; other site 159087006506 NADP binding site [chemical binding]; other site 159087006507 substrate binding site [chemical binding]; other site 159087006508 catalytic residues [active] 159087006509 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087006510 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 159087006511 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 159087006512 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 159087006513 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 159087006514 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 159087006515 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 159087006516 putative active site [active] 159087006517 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087006518 na(+)/h(+) antiporter; Region: c_cpa1; TIGR00844 159087006519 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 159087006520 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087006521 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_6; cd07824 159087006522 putative hydrophobic ligand binding site [chemical binding]; other site 159087006523 Cupin domain; Region: Cupin_2; cl09118 159087006524 BON domain; Region: BON; cl02771 159087006525 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 159087006526 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 159087006527 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087006528 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087006529 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 159087006530 cyclase homology domain; Region: CHD; cd07302 159087006531 nucleotidyl binding site; other site 159087006532 metal binding site [ion binding]; metal-binding site 159087006533 dimer interface [polypeptide binding]; other site 159087006534 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 159087006535 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 159087006536 putative active site [active] 159087006537 catalytic site [active] 159087006538 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 159087006539 putative active site [active] 159087006540 catalytic site [active] 159087006541 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 159087006542 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 159087006543 dimerization interface [polypeptide binding]; other site 159087006544 substrate binding site [chemical binding]; other site 159087006545 active site 159087006546 calcium binding site [ion binding]; other site 159087006547 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; cl00391 159087006548 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 159087006549 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 159087006550 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006551 active site 159087006552 phosphorylation site [posttranslational modification] 159087006553 intermolecular recognition site; other site 159087006554 dimerization interface [polypeptide binding]; other site 159087006555 LytTr DNA-binding domain; Region: LytTR; cl04498 159087006556 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 159087006557 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 159087006558 Histidine kinase; Region: His_kinase; pfam06580 159087006559 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; cl00075 159087006560 Carbon starvation protein CstA; Region: CstA; pfam02554 159087006561 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 159087006562 Pyruvate formate lyase 1; Region: PFL1; cd01678 159087006563 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 159087006564 coenzyme A binding site [chemical binding]; other site 159087006565 active site 159087006566 catalytic residues [active] 159087006567 glycine loop; other site 159087006568 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 159087006569 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 159087006570 FeS/SAM binding site; other site 159087006571 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 159087006572 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 159087006573 dimer interaction site [polypeptide binding]; other site 159087006574 substrate-binding tunnel; other site 159087006575 active site 159087006576 catalytic site [active] 159087006577 substrate binding site [chemical binding]; other site 159087006578 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 159087006579 Acetokinase family; Region: Acetate_kinase; cl01029 159087006580 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 159087006581 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 159087006582 Domain of unknown function (DUF802); Region: DUF802; pfam05650 159087006583 Domain of unknown function (DUF802); Region: DUF802; pfam05650 159087006584 hypothetical protein; Provisional; Region: PRK09040 159087006585 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006586 ligand binding site [chemical binding]; other site 159087006587 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 159087006588 PAS fold; Region: PAS_4; pfam08448 159087006589 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087006590 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 159087006591 dimer interface [polypeptide binding]; other site 159087006592 phosphorylation site [posttranslational modification] 159087006593 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 159087006594 ATP binding site [chemical binding]; other site 159087006595 Mg2+ binding site [ion binding]; other site 159087006596 G-X-G motif; other site 159087006597 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006598 Response regulator receiver domain; Region: Response_reg; pfam00072 159087006599 active site 159087006600 phosphorylation site [posttranslational modification] 159087006601 intermolecular recognition site; other site 159087006602 dimerization interface [polypeptide binding]; other site 159087006603 Response regulator receiver domain; Region: Response_reg; pfam00072 159087006604 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006605 active site 159087006606 phosphorylation site [posttranslational modification] 159087006607 intermolecular recognition site; other site 159087006608 dimerization interface [polypeptide binding]; other site 159087006609 haemagglutination activity domain; Region: Haemagg_act; cl05436 159087006610 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 159087006611 Surface antigen; Region: Bac_surface_Ag; cl03097 159087006612 Transposase domain (DUF772); Region: DUF772; cl12084 159087006613 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 159087006614 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006615 ligand binding site [chemical binding]; other site 159087006616 Transcriptional regulators [Transcription]; Region: MarR; COG1846 159087006617 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087006618 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 159087006619 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087006620 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 159087006621 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087006622 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 159087006623 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 159087006624 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087006625 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087006626 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087006627 pyruvate kinase; Provisional; Region: PRK06247 159087006628 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; cl09155 159087006629 domain interfaces; other site 159087006630 active site 159087006631 MOFRL family; Region: MOFRL; cl01013 159087006632 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 159087006633 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 159087006634 putative substrate translocation pore; other site 159087006635 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 159087006636 DNA polymerase IV; Provisional; Region: PRK14133 159087006637 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 159087006638 active site 159087006639 DNA binding site [nucleotide binding] 159087006640 RNA polymerase sigma factor; Provisional; Region: PRK11922 159087006641 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087006642 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 159087006643 DNA binding residues [nucleotide binding] 159087006644 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 159087006645 dinuclear metal binding motif [ion binding]; other site 159087006646 Cytochrome c; Region: Cytochrom_C; cl11414 159087006647 PAS domain S-box; Region: sensory_box; TIGR00229 159087006648 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 159087006649 putative active site [active] 159087006650 heme pocket [chemical binding]; other site 159087006651 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006652 metal binding site [ion binding]; metal-binding site 159087006653 active site 159087006654 I-site; other site 159087006655 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 159087006656 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 159087006657 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; cl12031 159087006658 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 159087006659 Helix-turn-helix domains; Region: HTH; cl00088 159087006660 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 159087006661 substrate binding site [chemical binding]; other site 159087006662 dimerization interface [polypeptide binding]; other site 159087006663 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 159087006664 active site 159087006665 catalytic residues [active] 159087006666 metal binding site [ion binding]; metal-binding site 159087006667 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 159087006668 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; cl12031 159087006669 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 159087006670 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 159087006671 dimerization interface [polypeptide binding]; other site 159087006672 putative DNA binding site [nucleotide binding]; other site 159087006673 putative Zn2+ binding site [ion binding]; other site 159087006674 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 159087006675 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 159087006676 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 159087006677 dimer interface [polypeptide binding]; other site 159087006678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087006679 catalytic residue [active] 159087006680 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 159087006681 active site residue [active] 159087006682 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4782 159087006683 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 159087006684 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 159087006685 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 159087006686 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087006687 carboxy-terminal protease; Provisional; Region: PRK11186 159087006688 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 159087006689 protein binding site [polypeptide binding]; other site 159087006690 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 159087006691 Catalytic dyad [active] 159087006692 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 159087006693 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; cl12031 159087006694 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087006695 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087006696 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006697 active site 159087006698 phosphorylation site [posttranslational modification] 159087006699 intermolecular recognition site; other site 159087006700 dimerization interface [polypeptide binding]; other site 159087006701 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 159087006702 Walker A motif; other site 159087006703 ATP binding site [chemical binding]; other site 159087006704 Walker B motif; other site 159087006705 arginine finger; other site 159087006706 Helix-turn-helix domains; Region: HTH; cl00088 159087006707 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 159087006708 putative substrate binding pocket [chemical binding]; other site 159087006709 trimer interface [polypeptide binding]; other site 159087006710 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087006711 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 159087006712 dimer interface [polypeptide binding]; other site 159087006713 phosphorylation site [posttranslational modification] 159087006714 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 159087006715 ATP binding site [chemical binding]; other site 159087006716 Mg2+ binding site [ion binding]; other site 159087006717 G-X-G motif; other site 159087006718 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 159087006719 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 159087006720 Walker A/P-loop; other site 159087006721 ATP binding site [chemical binding]; other site 159087006722 Q-loop/lid; other site 159087006723 ABC transporter signature motif; other site 159087006724 Walker B; other site 159087006725 D-loop; other site 159087006726 H-loop/switch region; other site 159087006727 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 159087006728 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 159087006729 dimer interface [polypeptide binding]; other site 159087006730 conserved gate region; other site 159087006731 putative PBP binding loops; other site 159087006732 ABC-ATPase subunit interface; other site 159087006733 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 159087006734 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 159087006735 substrate binding pocket [chemical binding]; other site 159087006736 membrane-bound complex binding site; other site 159087006737 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; cl02542 159087006738 Bacterial protein of unknown function (DUF898); Region: DUF898; cl01738 159087006739 Peptidase family M48; Region: Peptidase_M48; cl12018 159087006740 Domain of unknown function DUF302; Region: DUF302; cl01364 159087006741 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 159087006742 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 159087006743 dimer interface [polypeptide binding]; other site 159087006744 active site 159087006745 metal binding site [ion binding]; metal-binding site 159087006746 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087006747 Helix-turn-helix domains; Region: HTH; cl00088 159087006748 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 159087006749 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 159087006750 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 159087006751 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 159087006752 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 159087006753 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 159087006754 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 159087006755 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 159087006756 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 159087006757 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087006758 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 159087006759 Domain of unknown function (DUF4285); Region: DUF4285; pfam14113 159087006760 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 159087006761 Clp amino terminal domain; Region: Clp_N; pfam02861 159087006762 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 159087006763 Walker A motif; other site 159087006764 ATP binding site [chemical binding]; other site 159087006765 Walker B motif; other site 159087006766 arginine finger; other site 159087006767 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 159087006768 Walker A motif; other site 159087006769 ATP binding site [chemical binding]; other site 159087006770 Walker B motif; other site 159087006771 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 159087006772 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 159087006773 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 159087006774 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 159087006775 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 159087006776 Protein of unknown function (DUF796); Region: DUF796; cl01226 159087006777 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 159087006778 Protein of unknown function (DUF877); Region: DUF877; pfam05943 159087006779 Protein of unknown function (DUF770); Region: DUF770; cl01402 159087006780 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 159087006781 TPR motif; other site 159087006782 binding surface 159087006783 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 159087006784 Bacterial protein of unknown function (DUF876); Region: DUF876; cl01406 159087006785 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 159087006786 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 159087006787 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087006788 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 159087006789 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 159087006790 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 159087006791 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006792 ligand binding site [chemical binding]; other site 159087006793 Uncharacterized protein conserved in bacteria (DUF2094); Region: DUF2094; cl01611 159087006794 Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]; Region: IcmF; COG3523 159087006795 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 159087006796 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 159087006797 Uncharacterized conserved protein [Function unknown]; Region: COG4104 159087006798 PAAR motif; Region: PAAR_motif; pfam05488 159087006799 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 159087006800 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087006801 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 159087006802 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087006803 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 159087006804 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 159087006805 active site 159087006806 PilZ domain; Region: PilZ; cl01260 159087006807 DNA polymerase III subunit delta'; Validated; Region: PRK06964 159087006808 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006809 thymidylate kinase; Validated; Region: tmk; PRK00698 159087006810 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 159087006811 TMP-binding site; other site 159087006812 ATP-binding site [chemical binding]; other site 159087006813 YceG-like family; Region: YceG; pfam02618 159087006814 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 159087006815 dimerization interface [polypeptide binding]; other site 159087006816 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 159087006817 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 159087006818 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 159087006819 Protein of unknown function (DUF833); Region: DUF833; cl01315 159087006820 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 159087006821 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 159087006822 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 159087006823 nucleoside/Zn binding site; other site 159087006824 dimer interface [polypeptide binding]; other site 159087006825 catalytic motif [active] 159087006826 TIR domain; Region: TIR; cl02060 159087006827 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 159087006828 active site 159087006829 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 159087006830 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 159087006831 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4861 159087006832 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 159087006833 PRTRC system protein D; Region: PRTRC_D; TIGR03739 159087006834 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 159087006835 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 159087006836 ParB-like nuclease domain; Region: ParBc; cl02129 159087006837 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 159087006838 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006839 metal binding site [ion binding]; metal-binding site 159087006840 active site 159087006841 I-site; other site 159087006842 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 159087006843 S-adenosylmethionine binding site [chemical binding]; other site 159087006844 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; cl12011 159087006845 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006846 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087006847 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006848 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006849 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 159087006850 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 159087006851 Uncharacterised ACR, COG2135; Region: DUF159; cl03646 159087006852 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 159087006853 MPN+ (JAMM) motif; other site 159087006854 Zinc-binding site [ion binding]; other site 159087006855 Competence protein CoiA-like family; Region: CoiA; cl11541 159087006856 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 159087006857 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 159087006858 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006859 Walker A/P-loop; other site 159087006860 ATP binding site [chemical binding]; other site 159087006861 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 159087006862 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006863 ABC transporter signature motif; other site 159087006864 Walker B; other site 159087006865 D-loop; other site 159087006866 H-loop/switch region; other site 159087006867 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 159087006868 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 159087006869 active site 159087006870 metal binding site [ion binding]; metal-binding site 159087006871 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3972 159087006872 AAA-like domain; Region: AAA_10; pfam12846 159087006873 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087006874 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 159087006875 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 159087006876 Int/Topo IB signature motif; other site 159087006877 active site 159087006878 catalytic residues [active] 159087006879 DNA binding site [nucleotide binding] 159087006880 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 159087006881 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 159087006882 non-specific DNA binding site [nucleotide binding]; other site 159087006883 salt bridge; other site 159087006884 sequence-specific DNA binding site [nucleotide binding]; other site 159087006885 Predicted membrane protein [Function unknown]; Region: COG2119 159087006886 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087006887 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087006888 EamA-like transporter family; Region: EamA; cl01037 159087006889 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 159087006890 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 159087006891 putative active site [active] 159087006892 putative NTP binding site [chemical binding]; other site 159087006893 putative nucleic acid binding site [nucleotide binding]; other site 159087006894 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 159087006895 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087006896 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087006897 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087006898 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 159087006899 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087006900 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 159087006901 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 159087006902 DNA binding residues [nucleotide binding] 159087006903 dimer interface [polypeptide binding]; other site 159087006904 putative metal binding site [ion binding]; other site 159087006905 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087006906 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; cl00207 159087006907 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087006908 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087006909 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 159087006910 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 159087006911 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 159087006912 dimer interface [polypeptide binding]; other site 159087006913 phosphorylation site [posttranslational modification] 159087006914 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 159087006915 ATP binding site [chemical binding]; other site 159087006916 Mg2+ binding site [ion binding]; other site 159087006917 G-X-G motif; other site 159087006918 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 159087006919 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006920 active site 159087006921 phosphorylation site [posttranslational modification] 159087006922 intermolecular recognition site; other site 159087006923 dimerization interface [polypeptide binding]; other site 159087006924 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 159087006925 DNA binding site [nucleotide binding] 159087006926 putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional; Region: PRK14486 159087006927 Protein of unknown function, DUF; Region: DUF411; cl01142 159087006928 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 159087006929 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087006930 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 159087006931 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 159087006932 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087006933 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 159087006934 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087006935 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087006936 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087006937 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087006938 octamerization interface [polypeptide binding]; other site 159087006939 diferric-oxygen binding site [ion binding]; other site 159087006940 Flagellar basal body protein [Cell motility and secretion]; Region: FlgB; COG1815 159087006941 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 159087006942 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087006943 Zn2+ binding site [ion binding]; other site 159087006944 Mg2+ binding site [ion binding]; other site 159087006945 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 159087006946 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 159087006947 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 159087006948 LysE type translocator; Region: LysE; cl00565 159087006949 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 159087006950 catalytic residues [active] 159087006951 tetrahydromethanopterin S-methyltransferase subunit A; Provisional; Region: PRK00964 159087006952 Tetrahydromethanopterin S-methyltransferase, subunit A; Region: MtrA; cl04449 159087006953 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 159087006954 dimerization interface [polypeptide binding]; other site 159087006955 putative DNA binding site [nucleotide binding]; other site 159087006956 putative Zn2+ binding site [ion binding]; other site 159087006957 Copper resistance protein K; Region: CopK; pfam11525 159087006958 putative transposase OrfB; Reviewed; Region: PHA02517 159087006959 Integrase core domain; Region: rve; cl01316 159087006960 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; cl00075 159087006961 heat shock protein 90; Provisional; Region: PRK05218 159087006962 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 159087006963 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087006964 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087006965 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 159087006966 active site 159087006967 metal binding site [ion binding]; metal-binding site 159087006968 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006969 metal binding site [ion binding]; metal-binding site 159087006970 active site 159087006971 I-site; other site 159087006972 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 159087006973 non-specific DNA binding site [nucleotide binding]; other site 159087006974 salt bridge; other site 159087006975 sequence-specific DNA binding site [nucleotide binding]; other site 159087006976 EamA-like transporter family; Region: EamA; cl01037 159087006977 sensor protein QseC; Provisional; Region: PRK10337 159087006978 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 159087006979 dimer interface [polypeptide binding]; other site 159087006980 phosphorylation site [posttranslational modification] 159087006981 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 159087006982 ATP binding site [chemical binding]; other site 159087006983 Mg2+ binding site [ion binding]; other site 159087006984 G-X-G motif; other site 159087006985 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 159087006986 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087006987 active site 159087006988 phosphorylation site [posttranslational modification] 159087006989 intermolecular recognition site; other site 159087006990 dimerization interface [polypeptide binding]; other site 159087006991 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 159087006992 DNA binding site [nucleotide binding] 159087006993 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087006994 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087006995 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087006996 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 159087006997 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087006998 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087006999 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007000 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007001 PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from...; Region: PAP2_BcrC_like; cd03385 159087007002 active site 159087007003 Peptidase propeptide and YPEB domain; Region: PepSY; cl15480 159087007004 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 159087007005 Putative helicase; Region: TraI_2; pfam07514 159087007006 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 159087007007 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 159087007008 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007009 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007010 Walker B motif; other site 159087007011 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 159087007012 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 catalyze...; Region: LT_GEWL; cd00254 159087007013 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087007014 catalytic residue [active] 159087007015 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087007016 ligand binding site [chemical binding]; other site 159087007017 TraL protein; Region: TraL; cl06278 159087007018 TraE protein; Region: TraE; cl05060 159087007019 TraK protein; Region: TraK; pfam06586 159087007020 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 159087007021 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 159087007022 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 159087007023 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 159087007024 dimerization domain [polypeptide binding]; other site 159087007025 dimer interface [polypeptide binding]; other site 159087007026 catalytic residues [active] 159087007027 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 159087007028 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 159087007029 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 159087007030 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 159087007031 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007032 Walker A motif; other site 159087007033 ATP binding site [chemical binding]; other site 159087007034 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 159087007035 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 159087007036 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 159087007037 TraU protein; Region: TraU; cl06067 159087007038 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 159087007039 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 159087007040 Mating pair stabilisation protein TraN; Region: TraN; cl15453 159087007041 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087007042 Conjugative relaxosome accessory transposon protein; Region: TraH; cl05580 159087007043 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 159087007044 conjugal transfer mating pair stabilization protein TraG; Provisional; Region: PRK13735 159087007045 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 159087007046 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 159087007047 integrase; Provisional; Region: PRK09692 159087007048 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 159087007049 active site 159087007050 Int/Topo IB signature motif; other site 159087007051 GMP synthase; Reviewed; Region: guaA; PRK00074 159087007052 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 159087007053 AMP/PPi binding site [chemical binding]; other site 159087007054 candidate oxyanion hole; other site 159087007055 catalytic triad [active] 159087007056 potential glutamine specificity residues [chemical binding]; other site 159087007057 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 159087007058 ATP Binding subdomain [chemical binding]; other site 159087007059 Ligand Binding sites [chemical binding]; other site 159087007060 Dimerization subdomain; other site 159087007061 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 159087007062 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; cl09108 159087007063 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 key...; Region: CBS_pair_IMPDH; cd04601 159087007064 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 the guanine...; Region: IMPDH; cd00381 159087007065 active site 159087007066 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087007067 Ubiquitin-like proteins; Region: UBQ; cl00155 159087007068 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 159087007069 putative coenzyme Q binding site [chemical binding]; other site 159087007070 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 159087007071 SmpB-tmRNA interface; other site 159087007072 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087007073 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007074 active site 159087007075 phosphorylation site [posttranslational modification] 159087007076 intermolecular recognition site; other site 159087007077 dimerization interface [polypeptide binding]; other site 159087007078 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 159087007079 DNA binding residues [nucleotide binding] 159087007080 dimerization interface [polypeptide binding]; other site 159087007081 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 159087007082 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 159087007083 dimer interface [polypeptide binding]; other site 159087007084 tetramer interface [polypeptide binding]; other site 159087007085 PYR/PP interface [polypeptide binding]; other site 159087007086 TPP binding site [chemical binding]; other site 159087007087 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 159087007088 TPP-binding site; other site 159087007089 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 159087007090 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 159087007091 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 159087007092 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 159087007093 MutS domain I; Region: MutS_I; pfam01624 159087007094 MutS domain II; Region: MutS_II; pfam05188 159087007095 MutS family domain IV; Region: MutS_IV; pfam05190 159087007096 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 159087007097 Walker A/P-loop; other site 159087007098 ATP binding site [chemical binding]; other site 159087007099 Q-loop/lid; other site 159087007100 ABC transporter signature motif; other site 159087007101 Walker B; other site 159087007102 D-loop; other site 159087007103 H-loop/switch region; other site 159087007104 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087007105 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 159087007106 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 159087007107 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 159087007108 substrate binding site [chemical binding]; other site 159087007109 oxyanion hole (OAH) forming residues; other site 159087007110 trimer interface [polypeptide binding]; other site 159087007111 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; cl12011 159087007112 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087007113 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087007114 acyl-CoA synthetase; Validated; Region: PRK08316 159087007115 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087007116 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 159087007117 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 159087007118 dimer interface [polypeptide binding]; other site 159087007119 active site 159087007120 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087007121 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087007122 active site 159087007123 enoyl-CoA hydratase; Provisional; Region: PRK06688 159087007124 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 159087007125 substrate binding site [chemical binding]; other site 159087007126 oxyanion hole (OAH) forming residues; other site 159087007127 trimer interface [polypeptide binding]; other site 159087007128 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 159087007129 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087007130 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087007131 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087007132 Walker A/P-loop; other site 159087007133 ATP binding site [chemical binding]; other site 159087007134 Q-loop/lid; other site 159087007135 ABC transporter signature motif; other site 159087007136 Walker B; other site 159087007137 D-loop; other site 159087007138 H-loop/switch region; other site 159087007139 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 159087007140 Receptor family ligand binding region; Region: ANF_receptor; pfam01094 159087007141 putative ligand binding site [chemical binding]; other site 159087007142 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087007143 TM-ABC transporter signature motif; other site 159087007144 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087007145 TM-ABC transporter signature motif; other site 159087007146 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 159087007147 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087007148 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087007149 Walker A/P-loop; other site 159087007150 ATP binding site [chemical binding]; other site 159087007151 Q-loop/lid; other site 159087007152 ABC transporter signature motif; other site 159087007153 Walker B; other site 159087007154 D-loop; other site 159087007155 H-loop/switch region; other site 159087007156 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 159087007157 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 159087007158 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087007159 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 159087007160 catalytic triad [active] 159087007161 Septum formation initiator; Region: DivIC; cl11433 159087007162 enolase; Provisional; Region: eno; PRK00077 159087007163 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 159087007164 dimer interface [polypeptide binding]; other site 159087007165 metal binding site [ion binding]; metal-binding site 159087007166 substrate binding pocket [chemical binding]; other site 159087007167 NeuB family; Region: NeuB; cl00496 159087007168 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 159087007169 CTP synthetase; Validated; Region: pyrG; PRK05380 159087007170 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 159087007171 Catalytic site [active] 159087007172 active site 159087007173 UTP binding site [chemical binding]; other site 159087007174 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 159087007175 active site 159087007176 putative oxyanion hole; other site 159087007177 catalytic triad [active] 159087007178 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 159087007179 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 159087007180 dimer interface [polypeptide binding]; other site 159087007181 active site 159087007182 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 159087007183 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 159087007184 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007185 Walker A/P-loop; other site 159087007186 ATP binding site [chemical binding]; other site 159087007187 Q-loop/lid; other site 159087007188 ABC transporter signature motif; other site 159087007189 Walker B; other site 159087007190 D-loop; other site 159087007191 H-loop/switch region; other site 159087007192 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 159087007193 ABC-2 type transporter; Region: ABC2_membrane; cl11417 159087007194 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087007195 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 159087007196 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 159087007197 active site 159087007198 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 159087007199 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 159087007200 catalytic residues [active] 159087007201 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 159087007202 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 159087007203 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 159087007204 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 159087007205 putative active site [active] 159087007206 heme pocket [chemical binding]; other site 159087007207 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 159087007208 dimer interface [polypeptide binding]; other site 159087007209 phosphorylation site [posttranslational modification] 159087007210 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 159087007211 ATP binding site [chemical binding]; other site 159087007212 G-X-G motif; other site 159087007213 Response regulator receiver domain; Region: Response_reg; pfam00072 159087007214 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007215 active site 159087007216 phosphorylation site [posttranslational modification] 159087007217 intermolecular recognition site; other site 159087007218 dimerization interface [polypeptide binding]; other site 159087007219 putative carbohydrate kinase; Provisional; Region: PRK10565 159087007220 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 159087007221 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 159087007222 putative substrate binding site [chemical binding]; other site 159087007223 putative ATP binding site [chemical binding]; other site 159087007224 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 159087007225 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 159087007226 dimerization interface [polypeptide binding]; other site 159087007227 active site 159087007228 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 159087007229 S-adenosylmethionine binding site [chemical binding]; other site 159087007230 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 159087007231 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 159087007232 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007233 catalytic residue [active] 159087007234 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; cl00436 159087007235 Rhomboid family; Region: Rhomboid; cl11446 159087007236 homoserine dehydrogenase; Provisional; Region: PRK06349 159087007237 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087007238 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 159087007239 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 159087007240 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 159087007241 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 159087007242 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007243 homodimer interface [polypeptide binding]; other site 159087007244 catalytic residue [active] 159087007245 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 159087007246 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 159087007247 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 159087007248 Substrate binding site; other site 159087007249 Cupin domain; Region: Cupin_2; cl09118 159087007250 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087007251 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087007252 Walker A/P-loop; other site 159087007253 ATP binding site [chemical binding]; other site 159087007254 Q-loop/lid; other site 159087007255 ABC transporter signature motif; other site 159087007256 Walker B; other site 159087007257 D-loop; other site 159087007258 H-loop/switch region; other site 159087007259 PEP-CTERM motif; Region: VPEP; cl15443 159087007260 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 159087007261 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087007262 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087007263 FtsX-like permease family; Region: FtsX; pfam02687 159087007264 hypothetical protein; Validated; Region: PRK08223 159087007265 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 159087007266 ATP binding site [chemical binding]; other site 159087007267 substrate interface [chemical binding]; other site 159087007268 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 159087007269 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 159087007270 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 159087007271 Chain length determinant protein; Region: Wzz; cl01623 159087007272 exopolysaccharide/PEPCTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 159087007273 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007274 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 159087007275 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007276 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 159087007277 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 159087007278 active site 159087007279 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 159087007280 homodimer interface [polypeptide binding]; other site 159087007281 polysaccharide deactylase family protein, PEP-CTERM locus subfamily; Region: pepcterm_polyde; TIGR03006 159087007282 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 159087007283 Domain of unknown function (DUF3473); Region: DUF3473; pfam11959 159087007284 FemAB family; Region: FemAB; cl11444 159087007285 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087007286 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 159087007287 eight transmembrane protein EpsH (proposed exosortase); Region: 8TM_EpsH; cl10495 159087007288 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 159087007289 Protein of unknown function (DUF3485); Region: DUF3485; cl11827 159087007290 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 159087007291 This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis; Region: GT1_WbnK_like; cd03807 159087007292 putative ADP-binding pocket [chemical binding]; other site 159087007293 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 159087007294 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 159087007295 active site 159087007296 dimer interface [polypeptide binding]; other site 159087007297 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 159087007298 Ligand Binding Site [chemical binding]; other site 159087007299 Molecular Tunnel; other site 159087007300 PEP-CTERM/exosortase 1-associated glycosyltransferase, Daro_2409 family; Region: stp3; TIGR04063 159087007301 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087007302 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087007303 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087007304 O-Antigen ligase; Region: Wzy_C; cl04850 159087007305 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 159087007306 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 159087007307 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 159087007308 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 159087007309 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 159087007310 active site 159087007311 MatE; Region: MatE; cl10513 159087007312 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087007313 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 159087007314 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 159087007315 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 159087007316 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087007317 OpgC protein; Region: OpgC_C; cl00792 159087007318 MBOAT family; Region: MBOAT; cl00738 159087007319 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 159087007320 TPR motif; other site 159087007321 binding surface 159087007322 Helix-turn-helix domains; Region: HTH; cl00088 159087007323 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 159087007324 Integrase core domain; Region: rve; cl01316 159087007325 OpgC protein; Region: OpgC_C; cl00792 159087007326 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 159087007327 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 159087007328 Ligand Binding Site [chemical binding]; other site 159087007329 Molecular Tunnel; other site 159087007330 VanZ like family; Region: VanZ; cl01971 159087007331 hydrolase, ortholog 1, exosortase system type 1 associated; Region: hydr1_PEP; TIGR03100 159087007332 hydrolase, ortholog 2, exosortase system type 1 associated; Region: hydr2_PEP; TIGR03101 159087007333 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; cl12031 159087007334 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087007335 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 159087007336 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 159087007337 pyridoxal-dependent decarboxylase, exosortase system type 1 associated; Region: dCO2ase_PEP1; TIGR03099 159087007338 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase; Region: PLPDE_III_Btrk_like; cd06839 159087007339 dimer interface [polypeptide binding]; other site 159087007340 active site 159087007341 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087007342 catalytic residues [active] 159087007343 substrate binding site [chemical binding]; other site 159087007344 sugar transferase, PEP-CTERM system associated; Region: EpsB_2; TIGR03013 159087007345 Bacterial sugar transferase; Region: Bac_transf; cl00939 159087007346 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 159087007347 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 159087007348 dimer interface [polypeptide binding]; other site 159087007349 phosphorylation site [posttranslational modification] 159087007350 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 159087007351 ATP binding site [chemical binding]; other site 159087007352 Mg2+ binding site [ion binding]; other site 159087007353 G-X-G motif; other site 159087007354 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 159087007355 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007356 active site 159087007357 phosphorylation site [posttranslational modification] 159087007358 intermolecular recognition site; other site 159087007359 dimerization interface [polypeptide binding]; other site 159087007360 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 159087007361 Walker A motif; other site 159087007362 ATP binding site [chemical binding]; other site 159087007363 Walker B motif; other site 159087007364 arginine finger; other site 159087007365 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087007366 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 159087007367 binding surface 159087007368 TPR motif; other site 159087007369 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 159087007370 binding surface 159087007371 TPR motif; other site 159087007372 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 159087007373 binding surface 159087007374 TPR motif; other site 159087007375 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 159087007376 TPR motif; other site 159087007377 binding surface 159087007378 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 159087007379 binding surface 159087007380 TPR motif; other site 159087007381 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 159087007382 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 159087007383 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087007384 Sel1 repeat; Region: Sel1; cl02723 159087007385 Sel1 repeat; Region: Sel1; cl02723 159087007386 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 catalyze...; Region: LT_GEWL; cd00254 159087007387 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087007388 catalytic residue [active] 159087007389 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 159087007390 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_HprK; cl00270 159087007391 active site 159087007392 metal-binding site [ion binding] 159087007393 nucleotide-binding site [chemical binding]; other site 159087007394 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 159087007395 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 159087007396 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 159087007397 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 159087007398 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 159087007399 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 159087007400 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 159087007401 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 159087007402 putative nucleic acid binding region [nucleotide binding]; other site 159087007403 G-X-X-G motif; other site 159087007404 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 159087007405 RNA binding site [nucleotide binding]; other site 159087007406 domain interface; other site 159087007407 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 159087007408 16S/18S rRNA binding site [nucleotide binding]; other site 159087007409 S13e-L30e interaction site [polypeptide binding]; other site 159087007410 25S rRNA binding site [nucleotide binding]; other site 159087007411 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 159087007412 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 159087007413 RNA binding site [nucleotide binding]; other site 159087007414 active site 159087007415 Ribosome-binding factor A; Region: RBFA; cl00542 159087007416 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 159087007417 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 159087007418 translation initiation factor IF-2; Region: IF-2; TIGR00487 159087007419 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 159087007420 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases; Region: IF2_eIF5B; cd01887 159087007421 G1 box; other site 159087007422 putative GEF interaction site [polypeptide binding]; other site 159087007423 GTP/Mg2+ binding site [chemical binding]; other site 159087007424 Switch I region; other site 159087007425 G2 box; other site 159087007426 G3 box; other site 159087007427 Switch II region; other site 159087007428 G4 box; other site 159087007429 G5 box; other site 159087007430 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 159087007431 Translation-initiation factor 2; Region: IF-2; pfam11987 159087007432 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 159087007433 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 159087007434 NusA N-terminal domain; Region: NusA_N; pfam08529 159087007435 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 159087007436 RNA binding site [nucleotide binding]; other site 159087007437 homodimer interface [polypeptide binding]; other site 159087007438 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 159087007439 G-X-X-G motif; other site 159087007440 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 159087007441 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 159087007442 ribosome maturation protein RimP; Reviewed; Region: PRK00092 159087007443 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 159087007444 Sm1 motif; other site 159087007445 predicted subunit interaction site [polypeptide binding]; other site 159087007446 RNA binding pocket [nucleotide binding]; other site 159087007447 Sm2 motif; other site 159087007448 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 159087007449 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 159087007450 RNA binding surface [nucleotide binding]; other site 159087007451 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 159087007452 probable active site [active] 159087007453 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 159087007454 ScpA/B protein; Region: ScpA_ScpB; cl00598 159087007455 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 159087007456 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 159087007457 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 159087007458 active site 159087007459 HIGH motif; other site 159087007460 dimer interface [polypeptide binding]; other site 159087007461 KMSKS motif; other site 159087007462 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 159087007463 active site 159087007464 putative substrate binding region [chemical binding]; other site 159087007465 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 159087007466 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 159087007467 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 159087007468 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 159087007469 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 159087007470 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 159087007471 lipoyl attachment site [posttranslational modification]; other site 159087007472 glycine dehydrogenase; Provisional; Region: PRK05367 159087007473 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 159087007474 tetramer interface [polypeptide binding]; other site 159087007475 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007476 catalytic residue [active] 159087007477 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 159087007478 tetramer interface [polypeptide binding]; other site 159087007479 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007480 catalytic residue [active] 159087007481 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 159087007482 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 159087007483 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 159087007484 HSP70 interaction site [polypeptide binding]; other site 159087007485 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 159087007486 substrate binding site [polypeptide binding]; other site 159087007487 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 159087007488 Zn binding sites [ion binding]; other site 159087007489 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 159087007490 dimer interface [polypeptide binding]; other site 159087007491 Arginase family; Region: Arginase; cl00306 159087007492 Protein of unknown function, DUF480; Region: DUF480; cl01209 159087007493 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 159087007494 putative active site [active] 159087007495 catalytic site [active] 159087007496 putative substrate binding site [chemical binding]; other site 159087007497 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 159087007498 GIY-YIG motif/motif A; other site 159087007499 putative active site [active] 159087007500 putative metal binding site [ion binding]; other site 159087007501 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 159087007502 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 159087007503 dimerization interface [polypeptide binding]; other site 159087007504 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 159087007505 dimer interface [polypeptide binding]; other site 159087007506 phosphorylation site [posttranslational modification] 159087007507 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 159087007508 ATP binding site [chemical binding]; other site 159087007509 Mg2+ binding site [ion binding]; other site 159087007510 G-X-G motif; other site 159087007511 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 159087007512 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007513 active site 159087007514 phosphorylation site [posttranslational modification] 159087007515 intermolecular recognition site; other site 159087007516 dimerization interface [polypeptide binding]; other site 159087007517 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 159087007518 DNA binding site [nucleotide binding] 159087007519 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; cl01544 159087007520 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 159087007521 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087007522 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 159087007523 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 159087007524 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087007525 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 159087007526 active site 159087007527 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 159087007528 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 159087007529 Transposase domain (DUF772); Region: DUF772; cl12084 159087007530 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087007531 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 159087007532 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 159087007533 dimer interface [polypeptide binding]; other site 159087007534 phosphorylation site [posttranslational modification] 159087007535 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 159087007536 ATP binding site [chemical binding]; other site 159087007537 Mg2+ binding site [ion binding]; other site 159087007538 G-X-G motif; other site 159087007539 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087007540 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007541 active site 159087007542 phosphorylation site [posttranslational modification] 159087007543 intermolecular recognition site; other site 159087007544 dimerization interface [polypeptide binding]; other site 159087007545 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 159087007546 DNA binding residues [nucleotide binding] 159087007547 dimerization interface [polypeptide binding]; other site 159087007548 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087007549 Cytochrome c; Region: Cytochrom_C; cl11414 159087007550 Cytochrome c [Energy production and conversion]; Region: COG3258 159087007551 Cytochrome c; Region: Cytochrom_C; cl11414 159087007552 DsrE/DsrF-like family; Region: DrsE; cl00672 159087007553 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 159087007554 Helix-turn-helix domains; Region: HTH; cl00088 159087007555 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 159087007556 putative dimerization interface [polypeptide binding]; other site 159087007557 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 159087007558 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087007559 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 159087007560 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 159087007561 DNA binding site [nucleotide binding] 159087007562 Int/Topo IB signature motif; other site 159087007563 active site 159087007564 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 159087007565 catalytic residues [active] 159087007566 catalytic nucleophile [active] 159087007567 bZIP transcription factor; Region: bZIP_1; cl02576 159087007568 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 159087007569 BRO family, N-terminal domain; Region: Bro-N; cl10591 159087007570 KilA-N domain; Region: KilA-N; pfam04383 159087007571 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 159087007572 BRO family, N-terminal domain; Region: Bro-N; cl10591 159087007573 aspartate kinase; Reviewed; Region: PRK06635 159087007574 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 159087007575 putative nucleotide binding site [chemical binding]; other site 159087007576 putative catalytic residues [active] 159087007577 putative Mg ion binding site [ion binding]; other site 159087007578 putative aspartate binding site [chemical binding]; other site 159087007579 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 159087007580 putative allosteric regulatory site; other site 159087007581 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 159087007582 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 159087007583 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 159087007584 MoxR-like ATPases [General function prediction only]; Region: COG0714 159087007585 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 159087007586 Walker A motif; other site 159087007587 ATP binding site [chemical binding]; other site 159087007588 Walker B motif; other site 159087007589 arginine finger; other site 159087007590 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 159087007591 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 159087007592 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 159087007593 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087007594 lytic murein transglycosylase; Region: MltB_2; TIGR02283 159087007595 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 catalyze...; Region: LT_GEWL; cd00254 159087007596 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087007597 catalytic residue [active] 159087007598 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 159087007599 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 159087007600 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087007601 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 159087007602 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 159087007603 DNA binding residues [nucleotide binding] 159087007604 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 159087007605 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 159087007606 putative peptidoglycan binding site; other site 159087007607 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 159087007608 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 159087007609 S-adenosylmethionine binding site [chemical binding]; other site 159087007610 Survival protein SurE; Region: SurE; cl00448 159087007611 H-NS histone family; Region: Histone_HNS; pfam00816 159087007612 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 159087007613 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 159087007614 Phage integrase family; Region: Phage_integrase; pfam00589 159087007615 active site 159087007616 Int/Topo IB signature motif; other site 159087007617 PRTRC system protein D; Region: PRTRC_D; TIGR03739 159087007618 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 159087007619 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 159087007620 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 159087007621 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 159087007622 oligomeric interface; other site 159087007623 putative active site [active] 159087007624 homodimer interface [polypeptide binding]; other site 159087007625 Phd_YefM; Region: PhdYeFM; cl09153 159087007626 PRTRC system ThiF family protein; Region: PRTRC_ThiF; TIGR03736 159087007627 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087007628 ATP binding site [chemical binding]; other site 159087007629 substrate interface [chemical binding]; other site 159087007630 Domain of unknown function (DUF2016); Region: DUF2016; cl09677 159087007631 PRTRC system protein B; Region: PRTRC_B; TIGR03737 159087007632 PRTRC system protein F; Region: PRTRC_F; TIGR03742 159087007633 PRTRC system protein C; Region: PRTRC_C; TIGR03738 159087007634 PRTRC system protein E; Region: PRTRC_E; TIGR03741 159087007635 ParB-like nuclease domain; Region: ParBc; cl02129 159087007636 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 159087007637 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; cl12011 159087007638 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007639 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087007640 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007641 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007642 acyl-CoA thioesterase II; Provisional; Region: PRK10526 159087007643 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 159087007644 substrate pocket [chemical binding]; other site 159087007645 active site 159087007646 proteolytic cleavage site; other site 159087007647 dimer interface [polypeptide binding]; other site 159087007648 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 159087007649 MPN+ (JAMM) motif; other site 159087007650 Zinc-binding site [ion binding]; other site 159087007651 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 159087007652 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007653 Walker A/P-loop; other site 159087007654 ATP binding site [chemical binding]; other site 159087007655 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 159087007656 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 159087007657 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 159087007658 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 159087007659 putative active site [active] 159087007660 putative metal-binding site [ion binding]; other site 159087007661 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007662 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007663 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 159087007664 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 159087007665 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 159087007666 active site 159087007667 metal binding site [ion binding]; metal-binding site 159087007668 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 159087007669 IHF dimer interface [polypeptide binding]; other site 159087007670 IHF - DNA interface [nucleotide binding]; other site 159087007671 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 159087007672 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 159087007673 Int/Topo IB signature motif; other site 159087007674 active site 159087007675 DNA binding site [nucleotide binding] 159087007676 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 159087007677 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 159087007678 non-specific DNA binding site [nucleotide binding]; other site 159087007679 salt bridge; other site 159087007680 sequence-specific DNA binding site [nucleotide binding]; other site 159087007681 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 159087007682 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087007683 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087007684 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 159087007685 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 159087007686 FeS/SAM binding site; other site 159087007687 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 159087007688 Domon-like ligand-binding domains; Region: DOMON_like; cl14783 159087007689 putative ligand binding site [chemical binding]; other site 159087007690 Domon-like ligand-binding domains; Region: DOMON_like; cl14783 159087007691 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 159087007692 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 159087007693 Chlorite dismutase; Region: Chlor_dismutase; cl01280 159087007694 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 159087007695 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 159087007696 DMSO reductase family type II enzyme, iron-sulfur subunit; Region: DMSO_red_II_bet; TIGR03478 159087007697 DMSO reductase family type II enzyme, molybdopterin subunit; Region: DMSO_red_II_alp; TIGR03479 159087007698 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 159087007699 [4Fe-4S] binding site [ion binding]; other site 159087007700 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 159087007701 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 159087007702 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 159087007703 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 159087007704 molybdopterin cofactor binding site; other site 159087007705 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087007706 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007707 active site 159087007708 phosphorylation site [posttranslational modification] 159087007709 intermolecular recognition site; other site 159087007710 dimerization interface [polypeptide binding]; other site 159087007711 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 159087007712 Walker A motif; other site 159087007713 ATP binding site [chemical binding]; other site 159087007714 Walker B motif; other site 159087007715 arginine finger; other site 159087007716 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087007717 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087007718 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 159087007719 dimerization interface [polypeptide binding]; other site 159087007720 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 159087007721 dimer interface [polypeptide binding]; other site 159087007722 phosphorylation site [posttranslational modification] 159087007723 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 159087007724 ATP binding site [chemical binding]; other site 159087007725 Mg2+ binding site [ion binding]; other site 159087007726 G-X-G motif; other site 159087007727 PAS fold; Region: PAS_4; pfam08448 159087007728 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087007729 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087007730 PAS domain S-box; Region: sensory_box; TIGR00229 159087007731 Cupin domain; Region: Cupin_2; cl09118 159087007732 Protein of unknown function (DUF1109); Region: DUF1109; cl02071 159087007733 RNA polymerase sigma factor; Provisional; Region: PRK12536 159087007734 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 159087007735 DNA binding residues [nucleotide binding] 159087007736 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 159087007737 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 159087007738 Moco binding site; other site 159087007739 metal coordination site [ion binding]; other site 159087007740 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 159087007741 Putative helicase; Region: TraI_2; pfam07514 159087007742 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 159087007743 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 159087007744 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007745 Walker A motif; other site 159087007746 ATP binding site [chemical binding]; other site 159087007747 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007748 Walker B motif; other site 159087007749 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 159087007750 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087007751 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087007752 active site 159087007753 phosphorylation site [posttranslational modification] 159087007754 intermolecular recognition site; other site 159087007755 dimerization interface [polypeptide binding]; other site 159087007756 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 159087007757 Walker A motif; other site 159087007758 ATP binding site [chemical binding]; other site 159087007759 Walker B motif; other site 159087007760 arginine finger; other site 159087007761 Helix-turn-helix domains; Region: HTH; cl00088 159087007762 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 159087007763 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 159087007764 dimer interface [polypeptide binding]; other site 159087007765 phosphorylation site [posttranslational modification] 159087007766 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 159087007767 ATP binding site [chemical binding]; other site 159087007768 G-X-G motif; other site 159087007769 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087007770 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087007771 tetrathionate reductase subunit B; Provisional; Region: PRK14993 159087007772 4Fe-4S binding domain; Region: Fer4; cl02805 159087007773 Polysulphide reductase, NrfD; Region: NrfD; cl01295 159087007774 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 159087007775 This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_Arsenate-R; cd02757 159087007776 putative [Fe4-S4] binding site [ion binding]; other site 159087007777 putative molybdopterin cofactor binding site [chemical binding]; other site 159087007778 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 159087007779 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 159087007780 putative molybdopterin cofactor binding site; other site 159087007781 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 159087007782 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 159087007783 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; cl09108 159087007784 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 159087007785 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087007786 hydrogenase 4 subunit H; Validated; Region: PRK08222 159087007787 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 159087007788 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 159087007789 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 159087007790 FeS/SAM binding site; other site 159087007791 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 159087007792 Protein of unknown function (DUF2703); Region: DUF2703; pfam10865 159087007793 Membrane transport protein; Region: Mem_trans; cl09117 159087007794 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087007795 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087007796 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087007797 Protein of unknown function, DUF; Region: DUF411; cl01142 159087007798 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 159087007799 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 159087007800 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087007801 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087007802 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087007803 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087007804 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 159087007805 lipoprotein signal peptidase; Provisional; Region: PRK14787 159087007806 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; cl00207 159087007807 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087007808 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087007809 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087007810 Uncharacterised BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 159087007811 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 159087007812 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 159087007813 DNA binding residues [nucleotide binding] 159087007814 dimer interface [polypeptide binding]; other site 159087007815 putative metal binding site [ion binding]; other site 159087007816 RNA polymerase sigma factor, SigZ family; Region: SigZ; TIGR02959 159087007817 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087007818 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 159087007819 DNA binding residues [nucleotide binding] 159087007820 OsmC-like protein; Region: OsmC; cl00767 159087007821 Membrane transport protein; Region: Mem_trans; cl09117 159087007822 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 159087007823 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 159087007824 P loop; other site 159087007825 Nucleotide binding site [chemical binding]; other site 159087007826 DTAP/Switch II; other site 159087007827 Switch I; other site 159087007828 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 159087007829 arsenite-activated ATPase ArsA; Region: arsA; TIGR00345 159087007830 DTAP/Switch II; other site 159087007831 Switch I; other site 159087007832 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 159087007833 Low molecular weight phosphatase family; Region: LMWPc; cl00105 159087007834 Low molecular weight phosphatase family; Region: LMWPc; cd00115 159087007835 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 159087007836 active site 159087007837 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 159087007838 putative DNA binding site [nucleotide binding]; other site 159087007839 putative Zn2+ binding site [ion binding]; other site 159087007840 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 catalyze...; Region: LT_GEWL; cd00254 159087007841 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087007842 catalytic residue [active] 159087007843 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087007844 ligand binding site [chemical binding]; other site 159087007845 TraL protein; Region: TraL; cl06278 159087007846 TraE protein; Region: TraE; cl05060 159087007847 TraK protein; Region: TraK; pfam06586 159087007848 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 159087007849 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 159087007850 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 159087007851 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 159087007852 dimerization domain [polypeptide binding]; other site 159087007853 dimer interface [polypeptide binding]; other site 159087007854 catalytic residues [active] 159087007855 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 159087007856 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 159087007857 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 159087007858 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087007859 Walker A motif; other site 159087007860 ATP binding site [chemical binding]; other site 159087007861 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 159087007862 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 159087007863 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 159087007864 TraU protein; Region: TraU; cl06067 159087007865 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 159087007866 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 159087007867 Mating pair stabilisation protein TraN; Region: TraN; cl15453 159087007868 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087007869 Conjugative relaxosome accessory transposon protein; Region: TraH; cl05580 159087007870 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 159087007871 Fic/DOC family; Region: Fic; cl00960 159087007872 chromosome segregation protein; Provisional; Region: PRK02224 159087007873 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 159087007874 DNA binding residues [nucleotide binding] 159087007875 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 159087007876 IHF - DNA interface [nucleotide binding]; other site 159087007877 IHF dimer interface [polypeptide binding]; other site 159087007878 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 159087007879 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 159087007880 putative tRNA-binding site [nucleotide binding]; other site 159087007881 B3/4 domain; Region: B3_4; cl11458 159087007882 tRNA synthetase B5 domain; Region: B5; cl08394 159087007883 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 159087007884 dimer interface [polypeptide binding]; other site 159087007885 motif 1; other site 159087007886 motif 3; other site 159087007887 motif 2; other site 159087007888 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 159087007889 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 159087007890 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 159087007891 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 159087007892 dimer interface [polypeptide binding]; other site 159087007893 motif 1; other site 159087007894 active site 159087007895 motif 2; other site 159087007896 motif 3; other site 159087007897 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 159087007898 23S rRNA binding site [nucleotide binding]; other site 159087007899 L21 binding site [polypeptide binding]; other site 159087007900 L13 binding site [polypeptide binding]; other site 159087007901 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 159087007902 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 159087007903 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 159087007904 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 159087007905 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 159087007906 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 159087007907 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 159087007908 active site 159087007909 dimer interface [polypeptide binding]; other site 159087007910 motif 1; other site 159087007911 motif 2; other site 159087007912 motif 3; other site 159087007913 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 159087007914 anticodon binding site; other site 159087007915 SlyX; Region: SlyX; cl01090 159087007916 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 159087007917 DHHA1 domain; Region: DHHA1; pfam02272 159087007918 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087007919 PEP-CTERM motif; Region: VPEP; cl15443 159087007920 Uncharacterised ACR, COG2135; Region: DUF159; cl03646 159087007921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 159087007922 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087007923 CHC2 zinc finger; Region: zf-CHC2; cl15369 159087007924 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 159087007925 ATP binding site [chemical binding]; other site 159087007926 putative Mg++ binding site [ion binding]; other site 159087007927 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 159087007928 nucleotide binding region [chemical binding]; other site 159087007929 ATP-binding site [chemical binding]; other site 159087007930 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 159087007931 Helix-turn-helix domain; Region: HTH_39; pfam14090 159087007932 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 159087007933 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 159087007934 integrase; Provisional; Region: PRK09692 159087007935 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 159087007936 active site 159087007937 Int/Topo IB signature motif; other site 159087007938 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 159087007939 active site lid residues [active] 159087007940 substrate binding pocket [chemical binding]; other site 159087007941 catalytic residues [active] 159087007942 substrate-Mg2+ binding site; other site 159087007943 aspartate-rich region 1; other site 159087007944 aspartate-rich region 2; other site 159087007945 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 159087007946 active site lid residues [active] 159087007947 substrate binding pocket [chemical binding]; other site 159087007948 catalytic residues [active] 159087007949 substrate-Mg2+ binding site; other site 159087007950 aspartate-rich region 1; other site 159087007951 aspartate-rich region 2; other site 159087007952 Uncharacterized conserved protein [Function unknown]; Region: COG3349 159087007953 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087007954 acetyl-CoA synthetase; Provisional; Region: PRK04319 159087007955 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 159087007956 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087007957 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087007958 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087007959 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087007960 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_2; cd06335 159087007961 putative ligand binding site [chemical binding]; other site 159087007962 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 159087007963 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087007964 Walker A/P-loop; other site 159087007965 ATP binding site [chemical binding]; other site 159087007966 Q-loop/lid; other site 159087007967 ABC transporter signature motif; other site 159087007968 Walker B; other site 159087007969 D-loop; other site 159087007970 H-loop/switch region; other site 159087007971 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 159087007972 active site 159087007973 catalytic triad [active] 159087007974 oxyanion hole [active] 159087007975 switch loop; other site 159087007976 tRNA 2-selenouridine synthase; Region: tRNA_sel_U_synt; TIGR03167 159087007977 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 159087007978 active site residue [active] 159087007979 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; cl12011 159087007980 OsmC-like protein; Region: OsmC; cl00767 159087007981 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 159087007982 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087007983 CoA-ligase; Region: Ligase_CoA; pfam00549 159087007984 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 159087007985 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087007986 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 159087007987 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 159087007988 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 159087007989 G1 box; other site 159087007990 GTP/Mg2+ binding site [chemical binding]; other site 159087007991 Switch I region; other site 159087007992 G2 box; other site 159087007993 G3 box; other site 159087007994 Switch II region; other site 159087007995 G4 box; other site 159087007996 G5 box; other site 159087007997 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 159087007998 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 159087007999 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 159087008000 NAD(P) binding site [chemical binding]; other site 159087008001 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 159087008002 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 159087008003 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087008004 catalytic residue [active] 159087008005 Protein of unknown function (DUF1684); Region: DUF1684; cl01327 159087008006 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_1; cd08894 159087008007 putative hydrophobic ligand binding site [chemical binding]; other site 159087008008 Protein of unknown function (DUF2502); Region: DUF2502; pfam10697 159087008009 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 159087008010 Clp amino terminal domain; Region: Clp_N; pfam02861 159087008011 Clp amino terminal domain; Region: Clp_N; pfam02861 159087008012 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 159087008013 Walker A motif; other site 159087008014 ATP binding site [chemical binding]; other site 159087008015 Walker B motif; other site 159087008016 arginine finger; other site 159087008017 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 159087008018 Walker A motif; other site 159087008019 ATP binding site [chemical binding]; other site 159087008020 Walker B motif; other site 159087008021 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 159087008022 Cache domain; Region: Cache_2; cl07034 159087008023 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 159087008024 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087008025 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087008026 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 159087008027 MoaE homodimer interface [polypeptide binding]; other site 159087008028 MoaD interaction [polypeptide binding]; other site 159087008029 active site residues [active] 159087008030 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 159087008031 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 159087008032 G1 box; other site 159087008033 putative GEF interaction site [polypeptide binding]; other site 159087008034 GTP/Mg2+ binding site [chemical binding]; other site 159087008035 Switch I region; other site 159087008036 G2 box; other site 159087008037 G3 box; other site 159087008038 Switch II region; other site 159087008039 G4 box; other site 159087008040 G5 box; other site 159087008041 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 159087008042 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 159087008043 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 159087008044 active site 159087008045 phosphate binding residues; other site 159087008046 catalytic residues [active] 159087008047 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 159087008048 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 159087008049 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 159087008050 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 159087008051 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 159087008052 trimer interface [polypeptide binding]; other site 159087008053 putative metal binding site [ion binding]; other site 159087008054 A new structural DNA glycosylase containing HEAT-like repeats; Region: AlkD_like_1; cd07064 159087008055 active site 159087008056 FliW protein; Region: FliW; cl00740 159087008057 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 159087008058 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 159087008059 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 includes...; Region: RuvC_resolvase; cl00243 159087008060 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 159087008061 RNA binding site [nucleotide binding]; other site 159087008062 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 159087008063 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 159087008064 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 159087008065 FAD binding pocket [chemical binding]; other site 159087008066 FAD binding motif [chemical binding]; other site 159087008067 phosphate binding motif [ion binding]; other site 159087008068 beta-alpha-beta structure motif; other site 159087008069 NAD binding pocket [chemical binding]; other site 159087008070 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 159087008071 ArsC family; Region: ArsC; pfam03960 159087008072 putative catalytic residues [active] 159087008073 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 159087008074 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 159087008075 dimerization interface [polypeptide binding]; other site 159087008076 domain crossover interface; other site 159087008077 redox-dependent activation switch; other site 159087008078 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087008079 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 159087008080 dimer interface [polypeptide binding]; other site 159087008081 phosphorylation site [posttranslational modification] 159087008082 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 159087008083 ATP binding site [chemical binding]; other site 159087008084 Mg2+ binding site [ion binding]; other site 159087008085 G-X-G motif; other site 159087008086 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087008087 FAD binding domain; Region: FAD_binding_4; pfam01565 159087008088 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 159087008089 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 159087008090 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 159087008091 FeS/SAM binding site; other site 159087008092 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087008093 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087008094 Zn2+ binding site [ion binding]; other site 159087008095 Mg2+ binding site [ion binding]; other site 159087008096 potassium/proton antiporter; Reviewed; Region: PRK05326 159087008097 PAS domain S-box; Region: sensory_box; TIGR00229 159087008098 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087008099 PAS fold; Region: PAS_7; pfam12860 159087008100 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087008101 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 159087008102 putative active site [active] 159087008103 heme pocket [chemical binding]; other site 159087008104 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 159087008105 dimer interface [polypeptide binding]; other site 159087008106 phosphorylation site [posttranslational modification] 159087008107 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 159087008108 ATP binding site [chemical binding]; other site 159087008109 Mg2+ binding site [ion binding]; other site 159087008110 G-X-G motif; other site 159087008111 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008112 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008113 active site 159087008114 phosphorylation site [posttranslational modification] 159087008115 intermolecular recognition site; other site 159087008116 dimerization interface [polypeptide binding]; other site 159087008117 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008118 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008119 active site 159087008120 phosphorylation site [posttranslational modification] 159087008121 intermolecular recognition site; other site 159087008122 dimerization interface [polypeptide binding]; other site 159087008123 Mechanosensitive ion channel; Region: MS_channel; pfam00924 159087008124 YdjC-like protein; Region: YdjC; cl01344 159087008125 GtrA-like protein; Region: GtrA; cl00971 159087008126 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl15364 159087008127 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 159087008128 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 159087008129 Ligand binding site; other site 159087008130 Putative Catalytic site; other site 159087008131 DXD motif; other site 159087008132 Permease family; Region: Xan_ur_permease; cl00967 159087008133 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 159087008134 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 159087008135 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 159087008136 active site 159087008137 catalytic tetrad [active] 159087008138 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087008139 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087008140 octamerization interface [polypeptide binding]; other site 159087008141 diferric-oxygen binding site [ion binding]; other site 159087008142 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087008143 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087008144 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087008145 putative ligand binding site [chemical binding]; other site 159087008146 EamA-like transporter family; Region: EamA; cl01037 159087008147 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 159087008148 EamA-like transporter family; Region: EamA; cl01037 159087008149 Uncharacterized conserved protein [Function unknown]; Region: COG3945 159087008150 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087008151 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087008152 Walker A/P-loop; other site 159087008153 ATP binding site [chemical binding]; other site 159087008154 Q-loop/lid; other site 159087008155 ABC transporter signature motif; other site 159087008156 Walker B; other site 159087008157 D-loop; other site 159087008158 H-loop/switch region; other site 159087008159 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087008160 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087008161 Walker A/P-loop; other site 159087008162 ATP binding site [chemical binding]; other site 159087008163 Q-loop/lid; other site 159087008164 ABC transporter signature motif; other site 159087008165 Walker B; other site 159087008166 D-loop; other site 159087008167 H-loop/switch region; other site 159087008168 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087008169 TM-ABC transporter signature motif; other site 159087008170 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087008171 TM-ABC transporter signature motif; other site 159087008172 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087008173 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 159087008174 putative ligand binding site [chemical binding]; other site 159087008175 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087008176 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087008177 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 159087008178 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 159087008179 NAD binding site [chemical binding]; other site 159087008180 catalytic residues [active] 159087008181 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 159087008182 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 159087008183 tetramer interface [polypeptide binding]; other site 159087008184 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 159087008185 tetramer interface [polypeptide binding]; other site 159087008186 active site 159087008187 Fe binding site [ion binding]; other site 159087008188 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 159087008189 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087008190 dimer interface [polypeptide binding]; other site 159087008191 PYR/PP interface [polypeptide binding]; other site 159087008192 TPP binding site [chemical binding]; other site 159087008193 substrate binding site [chemical binding]; other site 159087008194 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 159087008195 TPP-binding site; other site 159087008196 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 159087008197 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 159087008198 Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to...; Region: Rieske_RO_Alpha_HBDO; cd03542 159087008199 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 159087008200 putative alpha subunit interface [polypeptide binding]; other site 159087008201 putative active site [active] 159087008202 putative substrate binding site [chemical binding]; other site 159087008203 Fe binding site [ion binding]; other site 159087008204 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 159087008205 inter-subunit interface; other site 159087008206 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 159087008207 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 159087008208 catalytic loop [active] 159087008209 iron binding site [ion binding]; other site 159087008210 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 159087008211 FAD binding pocket [chemical binding]; other site 159087008212 FAD binding motif [chemical binding]; other site 159087008213 phosphate binding motif [ion binding]; other site 159087008214 beta-alpha-beta structure motif; other site 159087008215 NAD binding pocket [chemical binding]; other site 159087008216 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 159087008217 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087008218 putative NAD(P) binding site [chemical binding]; other site 159087008219 active site 159087008220 Cupin domain; Region: Cupin_2; cl09118 159087008221 Helix-turn-helix domain; Region: HTH_18; pfam12833 159087008222 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087008223 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 159087008224 putative PBP binding loops; other site 159087008225 dimer interface [polypeptide binding]; other site 159087008226 ABC-ATPase subunit interface; other site 159087008227 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087008228 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 159087008229 Walker A/P-loop; other site 159087008230 ATP binding site [chemical binding]; other site 159087008231 Q-loop/lid; other site 159087008232 ABC transporter signature motif; other site 159087008233 Walker B; other site 159087008234 D-loop; other site 159087008235 H-loop/switch region; other site 159087008236 TOBE domain; Region: TOBE_2; cl01440 159087008237 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 159087008238 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 159087008239 N-terminal plug; other site 159087008240 ligand-binding site [chemical binding]; other site 159087008241 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 159087008242 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 159087008243 dimerization interface [polypeptide binding]; other site 159087008244 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 159087008245 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 159087008246 dimer interface [polypeptide binding]; other site 159087008247 phosphorylation site [posttranslational modification] 159087008248 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 159087008249 ATP binding site [chemical binding]; other site 159087008250 Mg2+ binding site [ion binding]; other site 159087008251 G-X-G motif; other site 159087008252 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008253 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008254 active site 159087008255 phosphorylation site [posttranslational modification] 159087008256 intermolecular recognition site; other site 159087008257 dimerization interface [polypeptide binding]; other site 159087008258 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 159087008259 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008260 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008261 active site 159087008262 phosphorylation site [posttranslational modification] 159087008263 intermolecular recognition site; other site 159087008264 dimerization interface [polypeptide binding]; other site 159087008265 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 159087008266 putative active site [active] 159087008267 heme pocket [chemical binding]; other site 159087008268 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087008269 metal binding site [ion binding]; metal-binding site 159087008270 active site 159087008271 I-site; other site 159087008272 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 159087008273 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 159087008274 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 159087008275 N-terminal plug; other site 159087008276 ligand-binding site [chemical binding]; other site 159087008277 Protein of unknown function (DUF541); Region: SIMPL; cl01077 159087008278 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 159087008279 LysR family transcriptional regulator; Provisional; Region: PRK14997 159087008280 Helix-turn-helix domains; Region: HTH; cl00088 159087008281 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 159087008282 putative effector binding pocket; other site 159087008283 dimerization interface [polypeptide binding]; other site 159087008284 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 159087008285 putative active site [active] 159087008286 metal binding site [ion binding]; metal-binding site 159087008287 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 159087008288 YceI-like domain; Region: YceI; cl01001 159087008289 YceI-like domain; Region: YceI; cl01001 159087008290 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087008291 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008292 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008293 active site 159087008294 phosphorylation site [posttranslational modification] 159087008295 intermolecular recognition site; other site 159087008296 dimerization interface [polypeptide binding]; other site 159087008297 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008298 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008299 active site 159087008300 phosphorylation site [posttranslational modification] 159087008301 intermolecular recognition site; other site 159087008302 dimerization interface [polypeptide binding]; other site 159087008303 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087008304 Zn2+ binding site [ion binding]; other site 159087008305 Mg2+ binding site [ion binding]; other site 159087008306 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 159087008307 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 159087008308 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087008309 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087008310 Outer membrane efflux protein; Region: OEP; pfam02321 159087008311 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 159087008312 RES domain; Region: RES; cl02411 159087008313 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 159087008314 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 159087008315 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 159087008316 Helix-turn-helix domains; Region: HTH; cl00088 159087008317 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 159087008318 dimerization interface [polypeptide binding]; other site 159087008319 substrate binding pocket [chemical binding]; other site 159087008320 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087008321 GAF domain; Region: GAF; cl00853 159087008322 PAS domain S-box; Region: sensory_box; TIGR00229 159087008323 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 159087008324 putative active site [active] 159087008325 heme pocket [chemical binding]; other site 159087008326 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 159087008327 dimer interface [polypeptide binding]; other site 159087008328 phosphorylation site [posttranslational modification] 159087008329 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 159087008330 ATP binding site [chemical binding]; other site 159087008331 Mg2+ binding site [ion binding]; other site 159087008332 G-X-G motif; other site 159087008333 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008334 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008335 active site 159087008336 phosphorylation site [posttranslational modification] 159087008337 intermolecular recognition site; other site 159087008338 dimerization interface [polypeptide binding]; other site 159087008339 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 159087008340 Dihaem cytochrome c; Region: DHC; pfam09626 159087008341 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 159087008342 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 159087008343 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008344 active site 159087008345 phosphorylation site [posttranslational modification] 159087008346 intermolecular recognition site; other site 159087008347 dimerization interface [polypeptide binding]; other site 159087008348 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 159087008349 DNA binding site [nucleotide binding] 159087008350 sensor protein QseC; Provisional; Region: PRK10337 159087008351 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 159087008352 dimer interface [polypeptide binding]; other site 159087008353 phosphorylation site [posttranslational modification] 159087008354 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 159087008355 ATP binding site [chemical binding]; other site 159087008356 Mg2+ binding site [ion binding]; other site 159087008357 G-X-G motif; other site 159087008358 H+ Antiporter protein; Region: 2A0121; TIGR00900 159087008359 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 159087008360 putative substrate translocation pore; other site 159087008361 acyl-CoA synthetase; Validated; Region: PRK09088 159087008362 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087008363 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 159087008364 chorismate binding enzyme; Region: Chorismate_bind; cl10555 159087008365 polyphosphate kinase; Provisional; Region: PRK05443 159087008366 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 159087008367 putative domain interface [polypeptide binding]; other site 159087008368 putative active site [active] 159087008369 catalytic site [active] 159087008370 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 159087008371 putative domain interface [polypeptide binding]; other site 159087008372 putative active site [active] 159087008373 catalytic site [active] 159087008374 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008375 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008376 active site 159087008377 phosphorylation site [posttranslational modification] 159087008378 intermolecular recognition site; other site 159087008379 dimerization interface [polypeptide binding]; other site 159087008380 PAS domain S-box; Region: sensory_box; TIGR00229 159087008381 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 159087008382 putative active site [active] 159087008383 heme pocket [chemical binding]; other site 159087008384 PAS fold; Region: PAS_4; pfam08448 159087008385 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 159087008386 putative active site [active] 159087008387 heme pocket [chemical binding]; other site 159087008388 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087008389 metal binding site [ion binding]; metal-binding site 159087008390 active site 159087008391 I-site; other site 159087008392 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 159087008393 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 159087008394 synthetase active site [active] 159087008395 NTP binding site [chemical binding]; other site 159087008396 metal binding site [ion binding]; metal-binding site 159087008397 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 159087008398 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 159087008399 EamA-like transporter family; Region: EamA; cl01037 159087008400 EamA-like transporter family; Region: EamA; cl01037 159087008401 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 159087008402 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; cl12031 159087008403 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087008404 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; cl12031 159087008405 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087008406 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087008407 ComEC family competence protein; Provisional; Region: PRK11539 159087008408 Competence protein; Region: Competence; cl00471 159087008409 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087008410 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 159087008411 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 159087008412 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087008413 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 159087008414 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087008415 Walker A/P-loop; other site 159087008416 ATP binding site [chemical binding]; other site 159087008417 Q-loop/lid; other site 159087008418 ABC transporter signature motif; other site 159087008419 Walker B; other site 159087008420 D-loop; other site 159087008421 H-loop/switch region; other site 159087008422 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 159087008423 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087008424 FtsX-like permease family; Region: FtsX; pfam02687 159087008425 Sulfatase; Region: Sulfatase; cl10460 159087008426 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 159087008427 DHH family; Region: DHH; pfam01368 159087008428 DHHA1 domain; Region: DHHA1; pfam02272 159087008429 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK07565 159087008430 Dihydroorotate dehydrogenase (DHOD) like proteins. 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...; Region: DHOD_like; cd04739 159087008431 putative active site [active] 159087008432 putative FMN binding site [chemical binding]; other site 159087008433 putative substrate binding site [chemical binding]; other site 159087008434 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 159087008435 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087008436 dimer interface [polypeptide binding]; other site 159087008437 PYR/PP interface [polypeptide binding]; other site 159087008438 TPP binding site [chemical binding]; other site 159087008439 substrate binding site [chemical binding]; other site 159087008440 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 159087008441 Domain of unknown function; Region: EKR; cl11037 159087008442 4Fe-4S binding domain; Region: Fer4; cl02805 159087008443 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 159087008444 TPP-binding site [chemical binding]; other site 159087008445 dimer interface [polypeptide binding]; other site 159087008446 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087008447 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 159087008448 putative active site [active] 159087008449 heme pocket [chemical binding]; other site 159087008450 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 159087008451 putative active site [active] 159087008452 heme pocket [chemical binding]; other site 159087008453 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087008454 metal binding site [ion binding]; metal-binding site 159087008455 active site 159087008456 I-site; other site 159087008457 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 159087008458 Protein of unknown function (DUF2665); Region: DUF2665; pfam11654 159087008459 Nitrate and nitrite sensing; Region: NIT; pfam08376 159087008460 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087008461 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087008462 peptide chain release factor 2; Provisional; Region: PRK07342 159087008463 RF-1 domain; Region: RF-1; cl02875 159087008464 RF-1 domain; Region: RF-1; cl02875 159087008465 Predicted periplasmic lipoprotein (DUF2279); Region: DUF2279; cl11574 159087008466 Cupin domain; Region: Cupin_2; cl09118 159087008467 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008468 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008469 active site 159087008470 phosphorylation site [posttranslational modification] 159087008471 intermolecular recognition site; other site 159087008472 dimerization interface [polypeptide binding]; other site 159087008473 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008474 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008475 active site 159087008476 phosphorylation site [posttranslational modification] 159087008477 intermolecular recognition site; other site 159087008478 dimerization interface [polypeptide binding]; other site 159087008479 PAS domain S-box; Region: sensory_box; TIGR00229 159087008480 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 159087008481 dimer interface [polypeptide binding]; other site 159087008482 phosphorylation site [posttranslational modification] 159087008483 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 159087008484 ATP binding site [chemical binding]; other site 159087008485 Mg2+ binding site [ion binding]; other site 159087008486 G-X-G motif; other site 159087008487 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008488 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008489 active site 159087008490 phosphorylation site [posttranslational modification] 159087008491 intermolecular recognition site; other site 159087008492 dimerization interface [polypeptide binding]; other site 159087008493 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 159087008494 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 159087008495 dimer interface [polypeptide binding]; other site 159087008496 putative anticodon binding site; other site 159087008497 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 159087008498 motif 1; other site 159087008499 active site 159087008500 motif 2; other site 159087008501 motif 3; other site 159087008502 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 159087008503 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; cl12011 159087008504 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087008505 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 159087008506 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 159087008507 homodimer interface [polypeptide binding]; other site 159087008508 substrate-cofactor binding pocket; other site 159087008509 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087008510 catalytic residue [active] 159087008511 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 159087008512 catalytic residue [active] 159087008513 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 159087008514 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087008515 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087008516 Zn2+ binding site [ion binding]; other site 159087008517 Mg2+ binding site [ion binding]; other site 159087008518 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087008519 Zn2+ binding site [ion binding]; other site 159087008520 Mg2+ binding site [ion binding]; other site 159087008521 Predicted ATPase [General function prediction only]; Region: COG1485 159087008522 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 159087008523 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087008524 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 159087008525 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 159087008526 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 159087008527 E3 interaction surface; other site 159087008528 lipoyl attachment site [posttranslational modification]; other site 159087008529 e3 binding domain; Region: E3_binding; pfam02817 159087008530 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 159087008531 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 159087008532 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 159087008533 TPP-binding site [chemical binding]; other site 159087008534 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 159087008535 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 159087008536 dimer interface [polypeptide binding]; other site 159087008537 Citrate synthase; Region: Citrate_synt; pfam00285 159087008538 active site 159087008539 citrylCoA binding site [chemical binding]; other site 159087008540 NADH binding [chemical binding]; other site 159087008541 cationic pore residues; other site 159087008542 oxalacetate/citrate binding site [chemical binding]; other site 159087008543 coenzyme A binding site [chemical binding]; other site 159087008544 catalytic triad [active] 159087008545 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 159087008546 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 159087008547 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 159087008548 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087008549 domain; Region: Succ_DH_flav_C; pfam02910 159087008550 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 159087008551 SdhC subunit interface [polypeptide binding]; other site 159087008552 proximal heme binding site [chemical binding]; other site 159087008553 cardiolipin binding site; other site 159087008554 Iron-sulfur protein interface; other site 159087008555 proximal quinone binding site [chemical binding]; other site 159087008556 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 159087008557 Iron-sulfur protein interface; other site 159087008558 proximal quinone binding site [chemical binding]; other site 159087008559 SdhD (CybS) interface [polypeptide binding]; other site 159087008560 proximal heme binding site [chemical binding]; other site 159087008561 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 159087008562 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087008563 DNA-binding site [nucleotide binding]; DNA binding site 159087008564 UTRA domain; Region: UTRA; cl01230 159087008565 malate dehydrogenase; Provisional; Region: PRK05442 159087008566 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 159087008567 NAD(P) binding site [chemical binding]; other site 159087008568 dimer interface [polypeptide binding]; other site 159087008569 malate binding site [chemical binding]; other site 159087008570 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; cl09155 159087008571 tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not...; Region: PseudoU_synth_TruC; cd02563 159087008572 probable active site [active] 159087008573 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 159087008574 FOG: CBS domain [General function prediction only]; Region: COG0517 159087008575 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 159087008576 FMN binding site [chemical binding]; other site 159087008577 substrate binding site [chemical binding]; other site 159087008578 putative catalytic residue [active] 159087008579 NnrS protein; Region: NnrS; cl01258 159087008580 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 159087008581 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 159087008582 S-adenosylmethionine binding site [chemical binding]; other site 159087008583 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 159087008584 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087008585 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 159087008586 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 159087008587 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087008588 metal binding site [ion binding]; metal-binding site 159087008589 active site 159087008590 I-site; other site 159087008591 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_13; cd06324 159087008592 putative ligand binding site [chemical binding]; other site 159087008593 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 159087008594 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 159087008595 substrate binding site [chemical binding]; other site 159087008596 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 159087008597 substrate binding site [chemical binding]; other site 159087008598 ligand binding site [chemical binding]; other site 159087008599 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 159087008600 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087008601 Flagellin N-methylase; Region: FliB; cl00497 159087008602 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; cl12011 159087008603 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 159087008604 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 159087008605 FMN binding site [chemical binding]; other site 159087008606 active site 159087008607 catalytic residues [active] 159087008608 substrate binding site [chemical binding]; other site 159087008609 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 159087008610 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 159087008611 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087008612 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 159087008613 Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing...; Region: H2MP; cd00518 159087008614 nickel binding site [ion binding]; other site 159087008615 sensory histidine kinase AtoS; Provisional; Region: PRK11360 159087008616 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 159087008617 dimer interface [polypeptide binding]; other site 159087008618 phosphorylation site [posttranslational modification] 159087008619 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 159087008620 ATP binding site [chemical binding]; other site 159087008621 Mg2+ binding site [ion binding]; other site 159087008622 G-X-G motif; other site 159087008623 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008624 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 159087008625 active site 159087008626 phosphorylation site [posttranslational modification] 159087008627 intermolecular recognition site; other site 159087008628 dimerization interface [polypeptide binding]; other site 159087008629 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008630 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008631 active site 159087008632 phosphorylation site [posttranslational modification] 159087008633 intermolecular recognition site; other site 159087008634 dimerization interface [polypeptide binding]; other site 159087008635 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 159087008636 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087008637 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 159087008638 dimer interface [polypeptide binding]; other site 159087008639 phosphorylation site [posttranslational modification] 159087008640 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 159087008641 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 159087008642 ATP binding site [chemical binding]; other site 159087008643 Mg2+ binding site [ion binding]; other site 159087008644 G-X-G motif; other site 159087008645 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008646 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008647 active site 159087008648 phosphorylation site [posttranslational modification] 159087008649 intermolecular recognition site; other site 159087008650 dimerization interface [polypeptide binding]; other site 159087008651 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008652 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008653 active site 159087008654 phosphorylation site [posttranslational modification] 159087008655 intermolecular recognition site; other site 159087008656 dimerization interface [polypeptide binding]; other site 159087008657 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 159087008658 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 159087008659 active site residue [active] 159087008660 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 159087008661 active site residue [active] 159087008662 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 159087008663 active site residue [active] 159087008664 Protein of unknown function (DUF328); Region: DUF328; cl01143 159087008665 Protein of unknown function (DUF2863); Region: DUF2863; pfam11062 159087008666 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 159087008667 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 159087008668 inhibitor-cofactor binding pocket; inhibition site 159087008669 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087008670 catalytic residue [active] 159087008671 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087008672 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087008673 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 159087008674 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 159087008675 substrate-cofactor binding pocket; other site 159087008676 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087008677 catalytic residue [active] 159087008678 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 159087008679 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087008680 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 159087008681 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 159087008682 S-adenosylmethionine binding site [chemical binding]; other site 159087008683 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; cl12011 159087008684 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087008685 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 159087008686 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087008687 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 159087008688 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087008689 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008690 active site 159087008691 phosphorylation site [posttranslational modification] 159087008692 intermolecular recognition site; other site 159087008693 dimerization interface [polypeptide binding]; other site 159087008694 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087008695 Zn2+ binding site [ion binding]; other site 159087008696 Mg2+ binding site [ion binding]; other site 159087008697 Intracellular septation protein A; Region: IspA; cl01098 159087008698 YCII-related domain; Region: YCII; cl00999 159087008699 BolA-like protein; Region: BolA; cl00386 159087008700 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 159087008701 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 159087008702 PPIC-type PPIASE domain; Region: Rotamase; cl08278 159087008703 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 159087008704 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 159087008705 HDOD domain; Region: HDOD; pfam08668 159087008706 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 159087008707 Helix-turn-helix domains; Region: HTH; cl00088 159087008708 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 159087008709 substrate binding site [chemical binding]; other site 159087008710 dimerization interface [polypeptide binding]; other site 159087008711 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087008712 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087008713 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 159087008714 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 159087008715 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 159087008716 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 159087008717 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 159087008718 Active Sites [active] 159087008719 Domain of unknown function DUF37; Region: DUF37; cl00506 159087008720 Helix-turn-helix domains; Region: HTH; cl00088 159087008721 Rrf2 family protein; Region: rrf2_super; TIGR00738 159087008722 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087008723 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087008724 4Fe-4S binding domain; Region: Fer4; cl02805 159087008725 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087008726 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 159087008727 Transglycosylase; Region: Transgly; cl07896 159087008728 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087008729 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 159087008730 ligand binding site [chemical binding]; other site 159087008731 flexible hinge region; other site 159087008732 Acetokinase family; Region: Acetate_kinase; cl01029 159087008733 Propanediol utilisation protein PduL; Region: PduL; pfam06130 159087008734 Propanediol utilisation protein PduL; Region: PduL; pfam06130 159087008735 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087008736 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087008737 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008738 active site 159087008739 phosphorylation site [posttranslational modification] 159087008740 intermolecular recognition site; other site 159087008741 dimerization interface [polypeptide binding]; other site 159087008742 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 159087008743 Walker A motif; other site 159087008744 ATP binding site [chemical binding]; other site 159087008745 Walker B motif; other site 159087008746 arginine finger; other site 159087008747 Helix-turn-helix domains; Region: HTH; cl00088 159087008748 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087008749 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 159087008750 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 159087008751 dimer interface [polypeptide binding]; other site 159087008752 phosphorylation site [posttranslational modification] 159087008753 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 159087008754 ATP binding site [chemical binding]; other site 159087008755 Mg2+ binding site [ion binding]; other site 159087008756 G-X-G motif; other site 159087008757 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087008758 ligand binding site [chemical binding]; other site 159087008759 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087008760 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 159087008761 ligand binding site [chemical binding]; other site 159087008762 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 159087008763 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087008764 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 159087008765 YcaO-like family; Region: YcaO; cl09146 159087008766 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 159087008767 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 159087008768 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087008769 CHASE domain; Region: CHASE; cl01369 159087008770 PAS domain S-box; Region: sensory_box; TIGR00229 159087008771 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 159087008772 putative active site [active] 159087008773 heme pocket [chemical binding]; other site 159087008774 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087008775 PAS fold; Region: PAS_4; pfam08448 159087008776 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 159087008777 dimer interface [polypeptide binding]; other site 159087008778 phosphorylation site [posttranslational modification] 159087008779 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 159087008780 ATP binding site [chemical binding]; other site 159087008781 Mg2+ binding site [ion binding]; other site 159087008782 G-X-G motif; other site 159087008783 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008784 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008785 active site 159087008786 phosphorylation site [posttranslational modification] 159087008787 intermolecular recognition site; other site 159087008788 dimerization interface [polypeptide binding]; other site 159087008789 fumarate hydratase; Reviewed; Region: fumC; PRK00485 159087008790 Class II fumarases; Region: Fumarase_classII; cd01362 159087008791 active site 159087008792 tetramer interface [polypeptide binding]; other site 159087008793 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 159087008794 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 159087008795 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087008796 Cytochrome c; Region: Cytochrom_C; cl11414 159087008797 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 159087008798 TIR domain; Region: TIR; cl02060 159087008799 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087008800 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087008801 ligand binding site [chemical binding]; other site 159087008802 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 159087008803 E-class dimer interface [polypeptide binding]; other site 159087008804 P-class dimer interface [polypeptide binding]; other site 159087008805 active site 159087008806 Cu2+ binding site [ion binding]; other site 159087008807 Zn2+ binding site [ion binding]; other site 159087008808 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 159087008809 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 159087008810 Active Sites [active] 159087008811 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 159087008812 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 159087008813 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 159087008814 CysD dimerization site [polypeptide binding]; other site 159087008815 G1 box; other site 159087008816 putative GEF interaction site [polypeptide binding]; other site 159087008817 GTP/Mg2+ binding site [chemical binding]; other site 159087008818 Switch I region; other site 159087008819 G2 box; other site 159087008820 G3 box; other site 159087008821 Switch II region; other site 159087008822 G4 box; other site 159087008823 G5 box; other site 159087008824 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 159087008825 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 159087008826 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 159087008827 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087008828 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 159087008829 dimer interface [polypeptide binding]; other site 159087008830 phosphorylation site [posttranslational modification] 159087008831 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 159087008832 ATP binding site [chemical binding]; other site 159087008833 Mg2+ binding site [ion binding]; other site 159087008834 G-X-G motif; other site 159087008835 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008836 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008837 active site 159087008838 phosphorylation site [posttranslational modification] 159087008839 intermolecular recognition site; other site 159087008840 dimerization interface [polypeptide binding]; other site 159087008841 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087008842 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 159087008843 ligand binding site [chemical binding]; other site 159087008844 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 159087008845 Predicted permease; Region: DUF318; cl00487 159087008846 RNA polymerase sigma factor, SigZ family; Region: SigZ; TIGR02959 159087008847 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087008848 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 159087008849 DNA binding residues [nucleotide binding] 159087008850 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 159087008851 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 159087008852 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 159087008853 N-terminal plug; other site 159087008854 ligand-binding site [chemical binding]; other site 159087008855 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 159087008856 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 159087008857 N-terminal plug; other site 159087008858 ligand-binding site [chemical binding]; other site 159087008859 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 159087008860 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087008861 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 159087008862 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 159087008863 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087008864 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 159087008865 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087008866 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008867 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087008868 active site 159087008869 phosphorylation site [posttranslational modification] 159087008870 intermolecular recognition site; other site 159087008871 dimerization interface [polypeptide binding]; other site 159087008872 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 159087008873 interface (dimer of trimers) [polypeptide binding]; other site 159087008874 Substrate-binding/catalytic site; other site 159087008875 Zn-binding sites [ion binding]; other site 159087008876 Isochorismatase family; Region: Isochorismatase; pfam00857 159087008877 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 159087008878 catalytic triad [active] 159087008879 conserved cis-peptide bond; other site 159087008880 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 159087008881 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087008882 metal binding site [ion binding]; metal-binding site 159087008883 active site 159087008884 I-site; other site 159087008885 Protein of unknown function, DUF599; Region: DUF599; cl01575 159087008886 Predicted permeases [General function prediction only]; Region: RarD; COG2962 159087008887 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 159087008888 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 159087008889 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 159087008890 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087008891 octamerization interface [polypeptide binding]; other site 159087008892 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087008893 diferric-oxygen binding site [ion binding]; other site 159087008894 ribonuclease R; Region: RNase_R; TIGR02063 159087008895 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 159087008896 RNB domain; Region: RNB; pfam00773 159087008897 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 play an important...; Region: S1_RNase_R; cd04471 159087008898 RNA binding site [nucleotide binding]; other site 159087008899 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 159087008900 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 159087008901 GDP-binding site [chemical binding]; other site 159087008902 ACT binding site; other site 159087008903 IMP binding site; other site 159087008904 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 159087008905 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 ATP-dependent...; Region: HisRS-like_core; cd00773 159087008906 dimer interface [polypeptide binding]; other site 159087008907 motif 1; other site 159087008908 active site 159087008909 motif 2; other site 159087008910 motif 3; other site 159087008911 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 159087008912 FtsH protease regulator HflC; Provisional; Region: PRK11029 159087008913 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 159087008914 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 159087008915 HflK protein; Region: hflK; TIGR01933 159087008916 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 159087008917 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 159087008918 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 159087008919 G1 box; other site 159087008920 GTP/Mg2+ binding site [chemical binding]; other site 159087008921 Switch I region; other site 159087008922 G2 box; other site 159087008923 G3 box; other site 159087008924 Switch II region; other site 159087008925 G4 box; other site 159087008926 G5 box; other site 159087008927 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 159087008928 Sm1 motif; other site 159087008929 intra - hexamer interaction site; other site 159087008930 inter - hexamer interaction site [polypeptide binding]; other site 159087008931 nucleotide binding pocket [chemical binding]; other site 159087008932 Sm2 motif; other site 159087008933 GTP-binding protein Der; Reviewed; Region: PRK00093 159087008934 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA1; cd01894 159087008935 G1 box; other site 159087008936 GTP/Mg2+ binding site [chemical binding]; other site 159087008937 Switch I region; other site 159087008938 G2 box; other site 159087008939 Switch II region; other site 159087008940 G3 box; other site 159087008941 G4 box; other site 159087008942 G5 box; other site 159087008943 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA2; cd01895 159087008944 G1 box; other site 159087008945 GTP/Mg2+ binding site [chemical binding]; other site 159087008946 Switch I region; other site 159087008947 G2 box; other site 159087008948 G3 box; other site 159087008949 Switch II region; other site 159087008950 G4 box; other site 159087008951 G5 box; other site 159087008952 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 159087008953 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 159087008954 Trp docking motif [polypeptide binding]; other site 159087008955 active site 159087008956 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 159087008957 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 159087008958 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 159087008959 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 ATP-dependent...; Region: HisRS-like_core; cd00773 159087008960 dimer interface [polypeptide binding]; other site 159087008961 motif 1; other site 159087008962 active site 159087008963 motif 2; other site 159087008964 motif 3; other site 159087008965 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 159087008966 anticodon binding site; other site 159087008967 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 159087008968 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694; cl15446 159087008969 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 159087008970 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 159087008971 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 159087008972 binding surface 159087008973 TPR motif; other site 159087008974 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 159087008975 binding surface 159087008976 TPR motif; other site 159087008977 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 159087008978 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 159087008979 FeS/SAM binding site; other site 159087008980 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 159087008981 active site 159087008982 multimer interface [polypeptide binding]; other site 159087008983 DctM-like transporters; Region: DctM; pfam06808 159087008984 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 159087008985 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 159087008986 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087008987 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087008988 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 159087008989 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 159087008990 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 159087008991 putative active site [active] 159087008992 heme pocket [chemical binding]; other site 159087008993 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 159087008994 dimer interface [polypeptide binding]; other site 159087008995 phosphorylation site [posttranslational modification] 159087008996 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 159087008997 ATP binding site [chemical binding]; other site 159087008998 Mg2+ binding site [ion binding]; other site 159087008999 G-X-G motif; other site 159087009000 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087009001 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009002 active site 159087009003 phosphorylation site [posttranslational modification] 159087009004 intermolecular recognition site; other site 159087009005 dimerization interface [polypeptide binding]; other site 159087009006 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 159087009007 DNA binding residues [nucleotide binding] 159087009008 dimerization interface [polypeptide binding]; other site 159087009009 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 159087009010 catalytic residues [active] 159087009011 transcription termination factor Rho; Provisional; Region: rho; PRK09376 159087009012 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 159087009013 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 159087009014 RNA binding site [nucleotide binding]; other site 159087009015 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 159087009016 multimer interface [polypeptide binding]; other site 159087009017 Walker A motif; other site 159087009018 ATP binding site [chemical binding]; other site 159087009019 Walker B motif; other site 159087009020 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 159087009021 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087009022 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 159087009023 putative active site [active] 159087009024 putative substrate binding site [chemical binding]; other site 159087009025 catalytic site [active] 159087009026 dimer interface [polypeptide binding]; other site 159087009027 Peptidase family M48; Region: Peptidase_M48; cl12018 159087009028 GTPase RsgA; Reviewed; Region: PRK00098 159087009029 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs...; Region: YjeQ_engC; cd01854 159087009030 GTPase/OB domain interface [polypeptide binding]; other site 159087009031 GTPase/Zn-binding domain interface [polypeptide binding]; other site 159087009032 GTP/Mg2+ binding site [chemical binding]; other site 159087009033 G4 box; other site 159087009034 G5 box; other site 159087009035 G1 box; other site 159087009036 Switch I region; other site 159087009037 G2 box; other site 159087009038 G3 box; other site 159087009039 Switch II region; other site 159087009040 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087009041 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009042 active site 159087009043 phosphorylation site [posttranslational modification] 159087009044 intermolecular recognition site; other site 159087009045 dimerization interface [polypeptide binding]; other site 159087009046 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009047 Zn2+ binding site [ion binding]; other site 159087009048 Mg2+ binding site [ion binding]; other site 159087009049 FOG: CBS domain [General function prediction only]; Region: COG0517 159087009050 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087009051 FOG: CBS domain [General function prediction only]; Region: COG0517 159087009052 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087009053 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 159087009054 PAS fold; Region: PAS_3; pfam08447 159087009055 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087009056 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087009057 GAF domain; Region: GAF; cl00853 159087009058 PAS fold; Region: PAS_3; pfam08447 159087009059 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087009060 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 159087009061 PAS fold; Region: PAS_3; pfam08447 159087009062 putative active site [active] 159087009063 heme pocket [chemical binding]; other site 159087009064 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087009065 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 159087009066 putative active site [active] 159087009067 heme pocket [chemical binding]; other site 159087009068 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 159087009069 dimer interface [polypeptide binding]; other site 159087009070 phosphorylation site [posttranslational modification] 159087009071 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 159087009072 ATP binding site [chemical binding]; other site 159087009073 Mg2+ binding site [ion binding]; other site 159087009074 G-X-G motif; other site 159087009075 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009076 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009077 active site 159087009078 phosphorylation site [posttranslational modification] 159087009079 intermolecular recognition site; other site 159087009080 dimerization interface [polypeptide binding]; other site 159087009081 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 159087009082 putative binding surface; other site 159087009083 active site 159087009084 Predicted flavoproteins [General function prediction only]; Region: COG2081 159087009085 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009086 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 159087009087 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087009088 Uncharacterized conserved protein [Function unknown]; Region: COG2308 159087009089 Domain of unknown function (DUF404); Region: DUF404; pfam04169 159087009090 Domain of unknown function (DUF407); Region: DUF407; pfam04174 159087009091 Bacterial domain of unknown function (DUF403); Region: DUF403; cl00980 159087009092 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087009093 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 159087009094 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087009095 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 159087009096 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 159087009097 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087009098 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 159087009099 Uncharacterised protein family (UPF0150); Region: UPF0150; cl00691 159087009100 Flagellin N-methylase; Region: FliB; cl00497 159087009101 ParB-like nuclease domain; Region: ParBc; cl02129 159087009102 Cytochrome C'; Region: Cytochrom_C_2; cl01610 159087009103 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 159087009104 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009105 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087009106 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 159087009107 dimer interface [polypeptide binding]; other site 159087009108 phosphorylation site [posttranslational modification] 159087009109 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 159087009110 ATP binding site [chemical binding]; other site 159087009111 Mg2+ binding site [ion binding]; other site 159087009112 G-X-G motif; other site 159087009113 Predicted flavoproteins [General function prediction only]; Region: COG2081 159087009114 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009115 Phasin protein; Region: Phasin_2; cl11491 159087009116 Bacterial domain of unknown function (DUF403); Region: DUF403; cl00980 159087009117 Uncharacterized conserved protein [Function unknown]; Region: COG2308 159087009118 Domain of unknown function (DUF404); Region: DUF404; pfam04169 159087009119 Domain of unknown function (DUF407); Region: DUF407; pfam04174 159087009120 beta-ketothiolase; Provisional; Region: PRK09051 159087009121 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 159087009122 dimer interface [polypeptide binding]; other site 159087009123 active site 159087009124 CobD/Cbib protein; Region: CobD_Cbib; cl00561 159087009125 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 159087009126 putative active site [active] 159087009127 putative CoA binding site [chemical binding]; other site 159087009128 nudix motif; other site 159087009129 metal binding site [ion binding]; metal-binding site 159087009130 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 159087009131 catalytic motif [active] 159087009132 Catalytic residue [active] 159087009133 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 159087009134 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 159087009135 catalytic triad [active] 159087009136 Protein of unknown function (DUF520); Region: DUF520; cl00723 159087009137 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 159087009138 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 159087009139 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 159087009140 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 159087009141 ANP binding site [chemical binding]; other site 159087009142 Substrate Binding Site II [chemical binding]; other site 159087009143 Substrate Binding Site I [chemical binding]; other site 159087009144 ornithine carbamoyltransferase; Provisional; Region: PRK00779 159087009145 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 159087009146 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009147 acetylornithine aminotransferase; Provisional; Region: PRK02627 159087009148 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 159087009149 inhibitor-cofactor binding pocket; inhibition site 159087009150 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087009151 catalytic residue [active] 159087009152 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 159087009153 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 159087009154 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 159087009155 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 159087009156 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 159087009157 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 159087009158 Type II transport protein GspH; Region: GspH; pfam12019 159087009159 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 159087009160 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087009161 LytB protein; Region: LYTB; cl00507 159087009162 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 159087009163 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 159087009164 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 159087009165 lipoprotein signal peptidase; Provisional; Region: PRK14787 159087009166 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 159087009167 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087009168 active site 159087009169 HIGH motif; other site 159087009170 nucleotide binding site [chemical binding]; other site 159087009171 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 159087009172 active site 159087009173 KMSKS motif; other site 159087009174 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 159087009175 tRNA binding surface [nucleotide binding]; other site 159087009176 anticodon binding site; other site 159087009177 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 159087009178 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 159087009179 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 159087009180 active site 159087009181 Riboflavin kinase; Region: Flavokinase; cl03312 159087009182 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009183 metal binding site [ion binding]; metal-binding site 159087009184 active site 159087009185 I-site; other site 159087009186 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 159087009187 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 159087009188 active site 159087009189 metal binding site [ion binding]; metal-binding site 159087009190 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 159087009191 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 159087009192 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 159087009193 CHASE domain; Region: CHASE; cl01369 159087009194 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009195 metal binding site [ion binding]; metal-binding site 159087009196 active site 159087009197 I-site; other site 159087009198 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 159087009199 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 159087009200 active site residue [active] 159087009201 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 159087009202 active site residue [active] 159087009203 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 159087009204 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 159087009205 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 159087009206 [2Fe-2S] cluster binding site [ion binding]; other site 159087009207 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 159087009208 alpha subunit interface [polypeptide binding]; other site 159087009209 active site 159087009210 substrate binding site [chemical binding]; other site 159087009211 Fe binding site [ion binding]; other site 159087009212 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 159087009213 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 159087009214 substrate binding pocket [chemical binding]; other site 159087009215 chain length determination region; other site 159087009216 substrate-Mg2+ binding site; other site 159087009217 catalytic residues [active] 159087009218 aspartate-rich region 1; other site 159087009219 active site lid residues [active] 159087009220 aspartate-rich region 2; other site 159087009221 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 159087009222 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 159087009223 TPP-binding site; other site 159087009224 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 159087009225 PYR/PP interface [polypeptide binding]; other site 159087009226 dimer interface [polypeptide binding]; other site 159087009227 TPP binding site [chemical binding]; other site 159087009228 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087009229 Uncharacterized ACR, COG1469; Region: DUF198; cl00642 159087009230 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 159087009231 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 159087009232 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 159087009233 RimM N-terminal domain; Region: RimM; pfam01782 159087009234 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 159087009235 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 159087009236 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 159087009237 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 159087009238 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 159087009239 2-isopropylmalate synthase; Validated; Region: PRK00915 159087009240 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 159087009241 active site 159087009242 catalytic residues [active] 159087009243 metal binding site [ion binding]; metal-binding site 159087009244 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 159087009245 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 159087009246 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 159087009247 ketol-acid reductoisomerase; Provisional; Region: PRK05479 159087009248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009249 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 159087009250 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 159087009251 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 159087009252 putative valine binding site [chemical binding]; other site 159087009253 dimer interface [polypeptide binding]; other site 159087009254 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 159087009255 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 159087009256 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 159087009257 PYR/PP interface [polypeptide binding]; other site 159087009258 dimer interface [polypeptide binding]; other site 159087009259 TPP binding site [chemical binding]; other site 159087009260 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 159087009261 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 159087009262 TPP-binding site [chemical binding]; other site 159087009263 dimer interface [polypeptide binding]; other site 159087009264 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087009265 RNA polymerase factor sigma-70; Validated; Region: PRK09047 159087009266 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 159087009267 DNA binding residues [nucleotide binding] 159087009268 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 159087009269 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 159087009270 RDD family; Region: RDD; cl00746 159087009271 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 159087009272 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 159087009273 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 159087009274 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 159087009275 multifunctional aminopeptidase A; Provisional; Region: PRK00913 159087009276 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 159087009277 interface (dimer of trimers) [polypeptide binding]; other site 159087009278 Substrate-binding/catalytic site; other site 159087009279 Zn-binding sites [ion binding]; other site 159087009280 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 159087009281 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 159087009282 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 159087009283 HIGH motif; other site 159087009284 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 159087009285 active site 159087009286 KMSKS motif; other site 159087009287 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 159087009288 tRNA binding surface [nucleotide binding]; other site 159087009289 anticodon binding site; other site 159087009290 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 159087009291 aminodeoxychorismate synthase; Provisional; Region: PRK07508 159087009292 chorismate binding enzyme; Region: Chorismate_bind; cl10555 159087009293 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 159087009294 substrate-cofactor binding pocket; other site 159087009295 homodimer interface [polypeptide binding]; other site 159087009296 Aminotransferase class IV; Region: Aminotran_4; pfam01063 159087009297 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087009298 catalytic residue [active] 159087009299 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 159087009300 CPxP motif; other site 159087009301 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 159087009302 Peptidase family M48; Region: Peptidase_M48; cl12018 159087009303 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 159087009304 trimer interface [polypeptide binding]; other site 159087009305 dimer interface [polypeptide binding]; other site 159087009306 putative active site [active] 159087009307 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 159087009308 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 159087009309 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 protein; Region: CSP_CDS; cd04458 159087009310 DNA-binding site [nucleotide binding]; DNA binding site 159087009311 RNA-binding motif; other site 159087009312 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 159087009313 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 159087009314 Clp amino terminal domain; Region: Clp_N; pfam02861 159087009315 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 159087009316 Walker A motif; other site 159087009317 ATP binding site [chemical binding]; other site 159087009318 Walker B motif; other site 159087009319 arginine finger; other site 159087009320 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 159087009321 Walker A motif; other site 159087009322 ATP binding site [chemical binding]; other site 159087009323 Walker B motif; other site 159087009324 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 159087009325 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 159087009326 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087009327 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 159087009328 dimerization interface [polypeptide binding]; other site 159087009329 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087009330 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 159087009331 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 159087009332 tetramer interface [polypeptide binding]; other site 159087009333 active site 159087009334 Mg2+/Mn2+ binding site [ion binding]; other site 159087009335 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087009336 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087009337 PAS domain S-box; Region: sensory_box; TIGR00229 159087009338 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 159087009339 putative active site [active] 159087009340 heme pocket [chemical binding]; other site 159087009341 PAS domain S-box; Region: sensory_box; TIGR00229 159087009342 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 159087009343 putative active site [active] 159087009344 heme pocket [chemical binding]; other site 159087009345 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009346 metal binding site [ion binding]; metal-binding site 159087009347 active site 159087009348 I-site; other site 159087009349 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 159087009350 transcriptional regulator; Provisional; Region: PRK10632 159087009351 Helix-turn-helix domains; Region: HTH; cl00088 159087009352 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 159087009353 putative effector binding pocket; other site 159087009354 dimerization interface [polypeptide binding]; other site 159087009355 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 159087009356 malate synthase A; Region: malate_syn_A; TIGR01344 159087009357 active site 159087009358 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 159087009359 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 159087009360 Nucleoside recognition; Region: Gate; cl00486 159087009361 LrgA family; Region: LrgA; cl00608 159087009362 LrgB-like family; Region: LrgB; cl00596 159087009363 PAS domain S-box; Region: sensory_box; TIGR00229 159087009364 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 159087009365 putative active site [active] 159087009366 heme pocket [chemical binding]; other site 159087009367 sensory histidine kinase AtoS; Provisional; Region: PRK11360 159087009368 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 159087009369 dimer interface [polypeptide binding]; other site 159087009370 phosphorylation site [posttranslational modification] 159087009371 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 159087009372 ATP binding site [chemical binding]; other site 159087009373 Mg2+ binding site [ion binding]; other site 159087009374 G-X-G motif; other site 159087009375 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087009376 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009377 active site 159087009378 phosphorylation site [posttranslational modification] 159087009379 intermolecular recognition site; other site 159087009380 dimerization interface [polypeptide binding]; other site 159087009381 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 159087009382 DNA binding residues [nucleotide binding] 159087009383 dimerization interface [polypeptide binding]; other site 159087009384 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087009385 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 159087009386 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087009387 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087009388 Cache domain; Region: Cache_2; cl07034 159087009389 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087009390 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087009391 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 159087009392 CoA-transferase family III; Region: CoA_transf_3; pfam02515 159087009393 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 159087009394 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 159087009395 isocitrate dehydrogenase; Validated; Region: PRK07362 159087009396 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 159087009397 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 159087009398 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 159087009399 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 159087009400 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 159087009401 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 159087009402 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009403 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 159087009404 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 159087009405 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 159087009406 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087009407 YeeE/YedE family (DUF395); Region: DUF395; cl01018 159087009408 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 159087009409 active site residue [active] 159087009410 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 159087009411 active site 159087009412 metal binding site [ion binding]; metal-binding site 159087009413 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 159087009414 Cytochrome c; Region: Cytochrom_C; cl11414 159087009415 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 159087009416 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 159087009417 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 159087009418 Cytochrome c; Region: Cytochrom_C; cl11414 159087009419 Cytochrome c; Region: Cytochrom_C; cl11414 159087009420 bacterial SoxC is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. SoxC is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SoxD, a small c-type heme containing subunit, it forms a...; Region: bact_SoxC_Moco; cd02113 159087009421 Moco binding site; other site 159087009422 metal coordination site [ion binding]; other site 159087009423 dimerization interface [polypeptide binding]; other site 159087009424 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 159087009425 dimerization interface [polypeptide binding]; other site 159087009426 putative DNA binding site [nucleotide binding]; other site 159087009427 putative Zn2+ binding site [ion binding]; other site 159087009428 Cytochrome c; Region: Cytochrom_C; cl11414 159087009429 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 159087009430 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 159087009431 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 159087009432 Cytochrome c; Region: Cytochrom_C; cl11414 159087009433 Cytochrome c; Region: Cytochrom_C; cl11414 159087009434 Cytochrome c; Region: Cytochrom_C; cl11414 159087009435 Cytochrome c; Region: Cytochrom_C; cl11414 159087009436 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 159087009437 trimer interface [polypeptide binding]; other site 159087009438 active site 159087009439 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 159087009440 Flavoprotein; Region: Flavoprotein; cl08021 159087009441 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 159087009442 hypothetical protein; Reviewed; Region: PRK00024 159087009443 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 159087009444 MPN+ (JAMM) motif; other site 159087009445 Zinc-binding site [ion binding]; other site 159087009446 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 159087009447 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 159087009448 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 159087009449 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 159087009450 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009451 active site 159087009452 phosphorylation site [posttranslational modification] 159087009453 intermolecular recognition site; other site 159087009454 dimerization interface [polypeptide binding]; other site 159087009455 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 159087009456 DNA binding site [nucleotide binding] 159087009457 sensor protein RstB; Provisional; Region: PRK10604 159087009458 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 159087009459 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 159087009460 dimer interface [polypeptide binding]; other site 159087009461 phosphorylation site [posttranslational modification] 159087009462 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 159087009463 ATP binding site [chemical binding]; other site 159087009464 Mg2+ binding site [ion binding]; other site 159087009465 G-X-G motif; other site 159087009466 RNA polymerase sigma-70 factor, TIGR02943 family; Region: Sig70_famx1 159087009467 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087009468 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; cl15358 159087009469 Putative zinc-finger; Region: zf-HC2; cl15806 159087009470 Protein of unknown function (DUF692); Region: DUF692; cl01263 159087009471 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 159087009472 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 159087009473 catalytic residues [active] 159087009474 LysE type translocator; Region: LysE; cl00565 159087009475 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 159087009476 N-terminal plug; other site 159087009477 ligand-binding site [chemical binding]; other site 159087009478 Mechanosensitive ion channel; Region: MS_channel; pfam00924 159087009479 16S rRNA methyltransferase B; Provisional; Region: PRK10901 159087009480 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; cl12011 159087009481 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 159087009482 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 159087009483 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 159087009484 active site 159087009485 substrate binding site [chemical binding]; other site 159087009486 cosubstrate binding site; other site 159087009487 catalytic site [active] 159087009488 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 159087009489 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 159087009490 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 159087009491 Mg2+ binding site [ion binding]; other site 159087009492 G-X-G motif; other site 159087009493 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 159087009494 ATP binding site [chemical binding]; other site 159087009495 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 159087009496 DinB superfamily; Region: DinB_2; cl00986 159087009497 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087009498 putative cation:proton antiport protein; Provisional; Region: PRK10669 159087009499 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009500 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 159087009501 Ligand Binding Site [chemical binding]; other site 159087009502 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 159087009503 Ligand Binding Site [chemical binding]; other site 159087009504 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 159087009505 IPP transferase; Region: IPPT; cl00403 159087009506 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009507 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009508 active site 159087009509 phosphorylation site [posttranslational modification] 159087009510 intermolecular recognition site; other site 159087009511 dimerization interface [polypeptide binding]; other site 159087009512 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 159087009513 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 159087009514 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 159087009515 dimerization interface [polypeptide binding]; other site 159087009516 putative ATP binding site [chemical binding]; other site 159087009517 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 159087009518 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 159087009519 active site 159087009520 HIGH motif; other site 159087009521 dimer interface [polypeptide binding]; other site 159087009522 KMSKS motif; other site 159087009523 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 159087009524 DNA-binding response regulator CreB; Provisional; Region: PRK11083 159087009525 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009526 active site 159087009527 phosphorylation site [posttranslational modification] 159087009528 intermolecular recognition site; other site 159087009529 dimerization interface [polypeptide binding]; other site 159087009530 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 159087009531 DNA binding site [nucleotide binding] 159087009532 sensory histidine kinase CreC; Provisional; Region: PRK11100 159087009533 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 159087009534 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 159087009535 dimer interface [polypeptide binding]; other site 159087009536 phosphorylation site [posttranslational modification] 159087009537 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 159087009538 ATP binding site [chemical binding]; other site 159087009539 Mg2+ binding site [ion binding]; other site 159087009540 G-X-G motif; other site 159087009541 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 159087009542 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; cl12011 159087009543 Inner membrane protein CreD; Region: CreD; cl01844 159087009544 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087009545 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 159087009546 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 159087009547 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087009548 poly(A) polymerase; Region: pcnB; TIGR01942 159087009549 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 159087009550 active site 159087009551 NTP binding site [chemical binding]; other site 159087009552 metal binding triad [ion binding]; metal-binding site 159087009553 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 159087009554 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 159087009555 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 159087009556 catalytic center binding site [active] 159087009557 ATP binding site [chemical binding]; other site 159087009558 Protein of unknown function, DUF486; Region: DUF486; cl01236 159087009559 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 159087009560 oligomerization interface [polypeptide binding]; other site 159087009561 active site 159087009562 metal binding site [ion binding]; metal-binding site 159087009563 pantoate--beta-alanine ligase; Reviewed; Region: panC; PRK00380 159087009564 Pantoate-beta-alanine ligase; Region: PanC; cd00560 159087009565 active site 159087009566 ATP-binding site [chemical binding]; other site 159087009567 pantoate-binding site; other site 159087009568 HXXH motif; other site 159087009569 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 159087009570 tetramerization interface [polypeptide binding]; other site 159087009571 active site 159087009572 LabA_like proteins; Region: LabA_like; cd06167 159087009573 putative metal binding site [ion binding]; other site 159087009574 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cl14879 159087009575 Cytochrome c; Region: Cytochrom_C; cl11414 159087009576 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 159087009577 D-pathway; other site 159087009578 Low-spin heme binding site [chemical binding]; other site 159087009579 Putative water exit pathway; other site 159087009580 Binuclear center (active site) [active] 159087009581 K-pathway; other site 159087009582 Putative proton exit pathway; other site 159087009583 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 159087009584 Subunit I/III interface [polypeptide binding]; other site 159087009585 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 159087009586 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 159087009587 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 159087009588 Walker A motif; other site 159087009589 ATP binding site [chemical binding]; other site 159087009590 Walker B motif; other site 159087009591 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 159087009592 Tic20-like protein; Region: Tic20; pfam09685 159087009593 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087009594 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087009595 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 159087009596 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 159087009597 metal ion-dependent adhesion site (MIDAS); other site 159087009598 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087009599 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 159087009600 ligand binding site [chemical binding]; other site 159087009601 flexible hinge region; other site 159087009602 Helix-turn-helix domains; Region: HTH; cl00088 159087009603 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009604 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009605 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009606 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009607 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009608 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009609 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009610 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009611 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009612 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009613 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009614 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009615 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009616 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009617 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009618 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009619 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009620 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009621 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009622 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009623 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009624 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009625 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087009626 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 159087009627 metal ion-dependent adhesion site (MIDAS); other site 159087009628 type 1 secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 159087009629 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087009630 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 159087009631 DNA binding residues [nucleotide binding] 159087009632 dimerization interface [polypeptide binding]; other site 159087009633 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 159087009634 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 bacteriocins; Region: Peptidase_C39_likeD; cd02421 159087009635 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 159087009636 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 159087009637 ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two...; Region: ABCC_bacteriocin_exporters; cd03245 159087009638 Walker A/P-loop; other site 159087009639 ATP binding site [chemical binding]; other site 159087009640 Q-loop/lid; other site 159087009641 ABC transporter signature motif; other site 159087009642 Walker B; other site 159087009643 D-loop; other site 159087009644 H-loop/switch region; other site 159087009645 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 159087009646 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 159087009647 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 159087009648 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 159087009649 active site 159087009650 ADP/pyrophosphate binding site [chemical binding]; other site 159087009651 dimerization interface [polypeptide binding]; other site 159087009652 allosteric effector site; other site 159087009653 fructose-1,6-bisphosphate binding site; other site 159087009654 adenylate kinase; Reviewed; Region: adk; PRK00279 159087009655 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 159087009656 AMP-binding site [chemical binding]; other site 159087009657 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 159087009658 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 159087009659 Ligand binding site; other site 159087009660 oligomer interface; other site 159087009661 Trm112p-like protein; Region: Trm112p; cl01066 159087009662 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 159087009663 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 159087009664 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 159087009665 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 159087009666 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 159087009667 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 159087009668 generic binding surface II; other site 159087009669 generic binding surface I; other site 159087009670 superoxide dismutase; Provisional; Region: PRK10543 159087009671 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 159087009672 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 159087009673 Predicted membrane protein [Function unknown]; Region: COG2860 159087009674 UPF0126 domain; Region: UPF0126; pfam03458 159087009675 UPF0126 domain; Region: UPF0126; pfam03458 159087009676 TIGR03549 family protein; Region: TIGR03549 159087009677 OsmC-like protein; Region: OsmC; cl00767 159087009678 YcaO-like family; Region: YcaO; cl09146 159087009679 Domain of unknown function DUF21; Region: DUF21; pfam01595 159087009680 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 159087009681 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 159087009682 Transporter associated domain; Region: CorC_HlyC; cl08393 159087009683 Type II secretory pathway, component HofQ [Intracellular trafficking and secretion]; Region: HofQ; COG4796 159087009684 Secretin and TonB N terminus short domain; Region: STN; cl06624 159087009685 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 159087009686 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087009687 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 159087009688 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 159087009689 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 159087009690 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 159087009691 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 159087009692 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 159087009693 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 159087009694 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 catalyze...; Region: LT_GEWL; cd00254 159087009695 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087009696 catalytic residue [active] 159087009697 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 159087009698 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 159087009699 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 159087009700 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087009701 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087009702 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087009703 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 159087009704 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 159087009705 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 159087009706 Walker A motif; other site 159087009707 ATP binding site [chemical binding]; other site 159087009708 Walker B motif; other site 159087009709 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 159087009710 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 159087009711 dimer interface [polypeptide binding]; other site 159087009712 Alkaline phosphatase homologues; Region: alkPPc; smart00098 159087009713 active site 159087009714 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; cl12031 159087009715 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087009716 Dienelactone hydrolase family; Region: DLH; pfam01738 159087009717 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; cl12031 159087009718 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 159087009719 CoenzymeA binding site [chemical binding]; other site 159087009720 subunit interaction site [polypeptide binding]; other site 159087009721 PHB binding site; other site 159087009722 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 159087009723 CoenzymeA binding site [chemical binding]; other site 159087009724 subunit interaction site [polypeptide binding]; other site 159087009725 PHB binding site; other site 159087009726 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087009727 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087009728 Walker A/P-loop; other site 159087009729 ATP binding site [chemical binding]; other site 159087009730 Q-loop/lid; other site 159087009731 ABC transporter signature motif; other site 159087009732 Walker B; other site 159087009733 D-loop; other site 159087009734 H-loop/switch region; other site 159087009735 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087009736 TM-ABC transporter signature motif; other site 159087009737 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087009738 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087009739 Walker A/P-loop; other site 159087009740 ATP binding site [chemical binding]; other site 159087009741 Q-loop/lid; other site 159087009742 ABC transporter signature motif; other site 159087009743 Walker B; other site 159087009744 D-loop; other site 159087009745 H-loop/switch region; other site 159087009746 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087009747 TM-ABC transporter signature motif; other site 159087009748 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087009749 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 159087009750 catalytic loop [active] 159087009751 iron binding site [ion binding]; other site 159087009752 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 159087009753 FAD binding pocket [chemical binding]; other site 159087009754 FAD binding motif [chemical binding]; other site 159087009755 phosphate binding motif [ion binding]; other site 159087009756 beta-alpha-beta structure motif; other site 159087009757 NAD binding pocket [chemical binding]; other site 159087009758 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087009759 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087009760 active site 159087009761 catalytic residues [active] 159087009762 metal binding site [ion binding]; metal-binding site 159087009763 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087009764 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087009765 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009766 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087009767 feruloyl-CoA synthase; Reviewed; Region: PRK08180 159087009768 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087009769 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087009770 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087009771 putative ligand binding site [chemical binding]; other site 159087009772 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087009773 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 159087009774 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 159087009775 FMN binding site [chemical binding]; other site 159087009776 substrate binding site [chemical binding]; other site 159087009777 putative catalytic residue [active] 159087009778 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087009779 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 159087009780 NAD(P) binding site [chemical binding]; other site 159087009781 active site 159087009782 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 159087009783 inter-subunit interface; other site 159087009784 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 159087009785 iron-sulfur cluster [ion binding]; other site 159087009786 [2Fe-2S] cluster binding site [ion binding]; other site 159087009787 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 159087009788 beta subunit interface [polypeptide binding]; other site 159087009789 alpha subunit interface [polypeptide binding]; other site 159087009790 active site 159087009791 substrate binding site [chemical binding]; other site 159087009792 Fe binding site [ion binding]; other site 159087009793 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 159087009794 [2Fe-2S] cluster binding site [ion binding]; other site 159087009795 PhnC is a Class III Extradiol ring-cleavage dioxygenase involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway; Region: PhnC_Bs_like; cd07368 159087009796 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087009797 putative active site [active] 159087009798 Fe(II) binding site [ion binding]; other site 159087009799 putative dimer interface [polypeptide binding]; other site 159087009800 putative tetramer interface [polypeptide binding]; other site 159087009801 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cd07321 159087009802 dimer interface [polypeptide binding]; other site 159087009803 tetramer interface [polypeptide binding]; other site 159087009804 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087009805 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087009806 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087009807 Helix-turn-helix domains; Region: HTH; cl00088 159087009808 UTRA domain; Region: UTRA; cl01230 159087009809 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 159087009810 PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines; Region: PseudoU_synth_RluE; cd02566 159087009811 pseudouridine synthase; Region: TIGR00093 159087009812 probable active site [active] 159087009813 Nucleoside recognition; Region: Gate; cl00486 159087009814 Nucleoside recognition; Region: Gate; cl00486 159087009815 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 159087009816 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 159087009817 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; cl12031 159087009818 Cytochrome c; Region: Cytochrom_C; cl11414 159087009819 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087009820 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 159087009821 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 159087009822 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 159087009823 FeS/SAM binding site; other site 159087009824 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; cl14869 159087009825 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 159087009826 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 159087009827 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the...; Region: ABC_MTABC3_MDL1_MDL2; cd03249 159087009828 Walker A/P-loop; other site 159087009829 ATP binding site [chemical binding]; other site 159087009830 Q-loop/lid; other site 159087009831 ABC transporter signature motif; other site 159087009832 Walker B; other site 159087009833 D-loop; other site 159087009834 H-loop/switch region; other site 159087009835 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 159087009836 cyanophycin synthetase; Provisional; Region: PRK14016 159087009837 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087009838 cyanophycin synthetase; Provisional; Region: PRK14016 159087009839 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087009840 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087009841 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087009842 ferredoxin-NADP reductase; Provisional; Region: PRK10926 159087009843 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 159087009844 FAD binding pocket [chemical binding]; other site 159087009845 FAD binding motif [chemical binding]; other site 159087009846 phosphate binding motif [ion binding]; other site 159087009847 beta-alpha-beta structure motif; other site 159087009848 NAD binding pocket [chemical binding]; other site 159087009849 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087009850 Helix-turn-helix domains; Region: HTH; cl00088 159087009851 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087009852 Helix-turn-helix domains; Region: HTH; cl00088 159087009853 Helix-turn-helix domains; Region: HTH; cl00088 159087009854 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087009855 Cytochrome c; Region: Cytochrom_C; cl11414 159087009856 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 159087009857 Domon-like ligand-binding domains; Region: DOMON_like; cd00241 159087009858 putative ligand binding site [chemical binding]; other site 159087009859 Cytochrome c; Region: Cytochrom_C; cl11414 159087009860 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087009861 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 159087009862 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 159087009863 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 159087009864 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 159087009865 Preprotein translocase subunit; Region: YajC; cl00806 159087009866 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 159087009867 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 159087009868 Protein export membrane protein; Region: SecD_SecF; cl14618 159087009869 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 159087009870 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 159087009871 Protein export membrane protein; Region: SecD_SecF; cl14618 159087009872 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 159087009873 Cytochrome C'; Region: Cytochrom_C_2; cl01610 159087009874 sensory histidine kinase AtoS; Provisional; Region: PRK11360 159087009875 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087009876 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087009877 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 159087009878 dimer interface [polypeptide binding]; other site 159087009879 phosphorylation site [posttranslational modification] 159087009880 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 159087009881 ATP binding site [chemical binding]; other site 159087009882 Mg2+ binding site [ion binding]; other site 159087009883 G-X-G motif; other site 159087009884 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087009885 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009886 active site 159087009887 phosphorylation site [posttranslational modification] 159087009888 intermolecular recognition site; other site 159087009889 dimerization interface [polypeptide binding]; other site 159087009890 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009891 Zn2+ binding site [ion binding]; other site 159087009892 Mg2+ binding site [ion binding]; other site 159087009893 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 159087009894 Uncharacterised protein family UPF0547; Region: UPF0547; pfam10571 159087009895 adenylosuccinate lyase; Provisional; Region: PRK09285 159087009896 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 159087009897 tetramer interface [polypeptide binding]; other site 159087009898 active site 159087009899 putative glutathione S-transferase; Provisional; Region: PRK10357 159087009900 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 159087009901 putative C-terminal domain interface [polypeptide binding]; other site 159087009902 putative GSH binding site (G-site) [chemical binding]; other site 159087009903 putative dimer interface [polypeptide binding]; other site 159087009904 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 159087009905 dimer interface [polypeptide binding]; other site 159087009906 N-terminal domain interface [polypeptide binding]; other site 159087009907 putative substrate binding pocket (H-site) [chemical binding]; other site 159087009908 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009909 Zn2+ binding site [ion binding]; other site 159087009910 Mg2+ binding site [ion binding]; other site 159087009911 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 159087009912 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 159087009913 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 159087009914 nudix motif; other site 159087009915 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 159087009916 homodimer interface [polypeptide binding]; other site 159087009917 substrate-cofactor binding pocket; other site 159087009918 Aminotransferase class IV; Region: Aminotran_4; pfam01063 159087009919 catalytic residue [active] 159087009920 Zinc-finger domain; Region: zf-CHCC; cl01821 159087009921 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087009922 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 159087009923 putative active site [active] 159087009924 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 159087009925 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 159087009926 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 159087009927 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 159087009928 active site 159087009929 substrate binding site [chemical binding]; other site 159087009930 metal binding site [ion binding]; metal-binding site 159087009931 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; cl00290 159087009932 HDOD domain; Region: HDOD; pfam08668 159087009933 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 159087009934 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 formation of...; Region: AlaRS_core; cd00673 159087009935 motif 1; other site 159087009936 active site 159087009937 motif 2; other site 159087009938 motif 3; other site 159087009939 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 159087009940 DHHA1 domain; Region: DHHA1; pfam02272 159087009941 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 159087009942 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 159087009943 putative active site [active] 159087009944 catalytic site [active] 159087009945 putative metal binding site [ion binding]; other site 159087009946 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 159087009947 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 159087009948 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087009949 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 159087009950 dimerization interface [polypeptide binding]; other site 159087009951 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 159087009952 dimer interface [polypeptide binding]; other site 159087009953 phosphorylation site [posttranslational modification] 159087009954 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 159087009955 ATP binding site [chemical binding]; other site 159087009956 Mg2+ binding site [ion binding]; other site 159087009957 G-X-G motif; other site 159087009958 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087009959 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009960 active site 159087009961 phosphorylation site [posttranslational modification] 159087009962 intermolecular recognition site; other site 159087009963 dimerization interface [polypeptide binding]; other site 159087009964 helicase 45; Provisional; Region: PTZ00424 159087009965 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 159087009966 ATP binding site [chemical binding]; other site 159087009967 Mg++ binding site [ion binding]; other site 159087009968 motif III; other site 159087009969 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 159087009970 nucleotide binding region [chemical binding]; other site 159087009971 ATP-binding site [chemical binding]; other site 159087009972 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087009973 active site 159087009974 HDOD domain; Region: HDOD; pfam08668 159087009975 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 159087009976 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 159087009977 Cysteine-rich domain; Region: CCG; pfam02754 159087009978 Cysteine-rich domain; Region: CCG; pfam02754 159087009979 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 159087009980 FAD binding domain; Region: FAD_binding_4; pfam01565 159087009981 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 159087009982 FAD binding domain; Region: FAD_binding_4; pfam01565 159087009983 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 159087009984 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 159087009985 enoyl-CoA hydratase; Provisional; Region: PRK06142 159087009986 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 159087009987 substrate binding site [chemical binding]; other site 159087009988 oxyanion hole (OAH) forming residues; other site 159087009989 trimer interface [polypeptide binding]; other site 159087009990 Cytochrome c; Region: Cytochrom_C; cl11414 159087009991 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087009992 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 159087009993 ligand binding site [chemical binding]; other site 159087009994 flexible hinge region; other site 159087009995 Helix-turn-helix domains; Region: HTH; cl00088 159087009996 Cytochrome c; Region: Cytochrom_C; cl11414 159087009997 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087009998 NeuB family; Region: NeuB; cl00496 159087009999 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 159087010000 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 159087010001 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 159087010002 FeS/SAM binding site; other site 159087010003 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 159087010004 Cytochrome c; Region: Cytochrom_C; cl11414 159087010005 Cytochrome c; Region: Cytochrom_C; cl11414 159087010006 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 159087010007 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 159087010008 Predicted amidohydrolase [General function prediction only]; Region: COG0388 159087010009 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 159087010010 putative active site [active] 159087010011 catalytic triad [active] 159087010012 dimer interface [polypeptide binding]; other site 159087010013 TIGR02099 family protein; Region: TIGR02099 159087010014 hypothetical protein; Provisional; Region: PRK10899 159087010015 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 159087010016 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087010017 metal binding triad; other site 159087010018 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 159087010019 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087010020 metal binding triad; other site 159087010021 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 159087010022 methionine aminotransferase; Validated; Region: PRK09082 159087010023 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 159087010024 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087010025 homodimer interface [polypeptide binding]; other site 159087010026 catalytic residue [active] 159087010027 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 159087010028 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 159087010029 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 159087010030 intersubunit interface [polypeptide binding]; other site 159087010031 active site 159087010032 Zn2+ binding site [ion binding]; other site 159087010033 Cation efflux family; Region: Cation_efflux; cl00316 159087010034 Flagellar regulator YcgR; Region: YcgR; pfam07317 159087010035 PilZ domain; Region: PilZ; cl01260 159087010036 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 159087010037 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010038 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010039 2-hydroxy-3-oxopropionate reductase; Region: tartro_sem_red; TIGR01505 159087010040 PAS domain S-box; Region: sensory_box; TIGR00229 159087010041 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 159087010042 putative active site [active] 159087010043 heme pocket [chemical binding]; other site 159087010044 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010045 metal binding site [ion binding]; metal-binding site 159087010046 active site 159087010047 I-site; other site 159087010048 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 159087010049 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 159087010050 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087010051 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087010052 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 159087010053 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087010054 putative substrate translocation pore; other site 159087010055 Cytochrome c; Region: Cytochrom_C; cl11414 159087010056 Ion channel; Region: Ion_trans_2; cl11596 159087010057 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 159087010058 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010059 Protein of unknown function (DUF3124); Region: DUF3124; pfam11322 159087010060 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010061 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010062 active site 159087010063 phosphorylation site [posttranslational modification] 159087010064 intermolecular recognition site; other site 159087010065 dimerization interface [polypeptide binding]; other site 159087010066 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087010067 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 159087010068 dimerization interface [polypeptide binding]; other site 159087010069 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 159087010070 dimer interface [polypeptide binding]; other site 159087010071 phosphorylation site [posttranslational modification] 159087010072 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 159087010073 ATP binding site [chemical binding]; other site 159087010074 Mg2+ binding site [ion binding]; other site 159087010075 G-X-G motif; other site 159087010076 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087010077 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010078 active site 159087010079 phosphorylation site [posttranslational modification] 159087010080 intermolecular recognition site; other site 159087010081 dimerization interface [polypeptide binding]; other site 159087010082 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010083 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010084 active site 159087010085 phosphorylation site [posttranslational modification] 159087010086 intermolecular recognition site; other site 159087010087 dimerization interface [polypeptide binding]; other site 159087010088 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 159087010089 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087010090 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010091 active site 159087010092 phosphorylation site [posttranslational modification] 159087010093 intermolecular recognition site; other site 159087010094 dimerization interface [polypeptide binding]; other site 159087010095 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 159087010096 DNA binding site [nucleotide binding] 159087010097 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 159087010098 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 159087010099 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 159087010100 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010101 metal binding site [ion binding]; metal-binding site 159087010102 active site 159087010103 I-site; other site 159087010104 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 159087010105 Uncharacterized conserved protein [Function unknown]; Region: COG3025 159087010106 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 159087010107 putative active site [active] 159087010108 putative metal binding residues [ion binding]; other site 159087010109 signature motif; other site 159087010110 putative triphosphate binding site [ion binding]; other site 159087010111 CHAD domain; Region: CHAD; cl10506 159087010112 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 159087010113 Pilin (bacterial filament); Region: Pilin; pfam00114 159087010114 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087010115 GAF domain; Region: GAF; cl00853 159087010116 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087010117 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087010118 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087010119 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087010120 phosphopeptide binding site; other site 159087010121 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087010122 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 159087010123 active site 159087010124 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 159087010125 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010126 Integral membrane protein TerC family; Region: TerC; cl10468 159087010127 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 159087010128 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010129 CoA-ligase; Region: Ligase_CoA; pfam00549 159087010130 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 159087010131 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087010132 CoA-ligase; Region: Ligase_CoA; pfam00549 159087010133 multidrug efflux protein; Reviewed; Region: PRK01766 159087010134 MatE; Region: MatE; cl10513 159087010135 MatE; Region: MatE; cl10513 159087010136 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087010137 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087010138 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 159087010139 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 159087010140 Uncharacterized conserved protein [Function unknown]; Region: COG0327 159087010141 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 159087010142 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 159087010143 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 159087010144 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 159087010145 protein binding site [polypeptide binding]; other site 159087010146 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 159087010147 putative active site [active] 159087010148 putative dimer interface [polypeptide binding]; other site 159087010149 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 159087010150 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 159087010151 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 159087010152 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 159087010153 nucleotide binding site/active site [active] 159087010154 HIT family signature motif; other site 159087010155 catalytic residue [active] 159087010156 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 159087010157 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 159087010158 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 159087010159 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 159087010160 substrate binding site [chemical binding]; other site 159087010161 glutamase interaction surface [polypeptide binding]; other site 159087010162 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 159087010163 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 159087010164 catalytic residues [active] 159087010165 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 159087010166 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 159087010167 putative active site [active] 159087010168 oxyanion strand; other site 159087010169 catalytic triad [active] 159087010170 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 159087010171 putative active site pocket [active] 159087010172 4-fold oligomerization interface [polypeptide binding]; other site 159087010173 metal binding residues [ion binding]; metal-binding site 159087010174 3-fold/trimer interface [polypeptide binding]; other site 159087010175 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 159087010176 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 159087010177 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087010178 homodimer interface [polypeptide binding]; other site 159087010179 catalytic residue [active] 159087010180 Chromate transporter; Region: Chromate_transp; pfam02417 159087010181 Chromate transporter; Region: Chromate_transp; pfam02417 159087010182 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 159087010183 histidinol dehydrogenase; Region: hisD; TIGR00069 159087010184 NAD binding site [chemical binding]; other site 159087010185 dimerization interface [polypeptide binding]; other site 159087010186 product binding site; other site 159087010187 substrate binding site [chemical binding]; other site 159087010188 zinc binding site [ion binding]; other site 159087010189 catalytic residues [active] 159087010190 ATP phosphoribosyltransferase; Region: HisG; cl15266 159087010191 DctM-like transporters; Region: DctM; pfam06808 159087010192 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 159087010193 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 159087010194 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087010195 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087010196 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 protein; Region: CSP_CDS; cd04458 159087010197 DNA-binding site [nucleotide binding]; DNA binding site 159087010198 RNA-binding motif; other site 159087010199 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 159087010200 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 159087010201 hinge; other site 159087010202 active site 159087010203 BolA-like protein; Region: BolA; cl00386 159087010204 ABC-2 type transporter; Region: ABC2_membrane; cl11417 159087010205 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 159087010206 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087010207 Walker A/P-loop; other site 159087010208 ATP binding site [chemical binding]; other site 159087010209 Q-loop/lid; other site 159087010210 ABC transporter signature motif; other site 159087010211 Walker B; other site 159087010212 D-loop; other site 159087010213 H-loop/switch region; other site 159087010214 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 159087010215 anti sigma factor interaction site; other site 159087010216 regulatory phosphorylation site [posttranslational modification]; other site 159087010217 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 159087010218 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 159087010219 VacJ like lipoprotein; Region: VacJ; cl01073 159087010220 mce related protein; Region: MCE; cl15431 159087010221 Domain of unknown function DUF140; Region: DUF140; cl00510 159087010222 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 159087010223 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 159087010224 Walker A/P-loop; other site 159087010225 ATP binding site [chemical binding]; other site 159087010226 Q-loop/lid; other site 159087010227 ABC transporter signature motif; other site 159087010228 Walker B; other site 159087010229 D-loop; other site 159087010230 H-loop/switch region; other site 159087010231 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010232 active site 159087010233 phosphorylation site [posttranslational modification] 159087010234 intermolecular recognition site; other site 159087010235 dimerization interface [polypeptide binding]; other site 159087010236 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 159087010237 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 159087010238 Walker A motif; other site 159087010239 ATP binding site [chemical binding]; other site 159087010240 Walker B motif; other site 159087010241 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087010242 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 159087010243 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 159087010244 Walker A motif; other site 159087010245 ATP binding site [chemical binding]; other site 159087010246 Walker B motif; other site 159087010247 arginine finger; other site 159087010248 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 159087010249 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 159087010250 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 159087010251 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087010252 probable pectinesterase/pectinesterase inhibitor; Region: PLN02217 159087010253 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 159087010254 binding surface 159087010255 TPR motif; other site 159087010256 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 159087010257 binding surface 159087010258 TPR motif; other site 159087010259 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 159087010260 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 159087010261 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 159087010262 Walker A motif; other site 159087010263 ATP binding site [chemical binding]; other site 159087010264 Walker B motif; other site 159087010265 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087010266 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087010267 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 159087010268 Heme NO binding associated; Region: HNOBA; pfam07701 159087010269 cyclase homology domain; Region: CHD; cd07302 159087010270 nucleotidyl binding site; other site 159087010271 metal binding site [ion binding]; metal-binding site 159087010272 dimer interface [polypeptide binding]; other site 159087010273 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087010274 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 159087010275 ATP binding site [chemical binding]; other site 159087010276 Mg2+ binding site [ion binding]; other site 159087010277 G-X-G motif; other site 159087010278 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 159087010279 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087010280 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010281 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 159087010282 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 159087010283 putative active site [active] 159087010284 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 159087010285 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 159087010286 active site 159087010287 motif I; other site 159087010288 motif II; other site 159087010289 phosphoglycolate phosphatase; Provisional; Region: PRK01158 159087010290 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 159087010291 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 159087010292 OstA-like protein; Region: OstA; cl00844 159087010293 Phasin protein; Region: Phasin_2; cl11491 159087010294 Phasin protein; Region: Phasin_2; cl11491 159087010295 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 159087010296 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 159087010297 putative MPT binding site; other site 159087010298 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 159087010299 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 159087010300 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 159087010301 ATP binding site [chemical binding]; other site 159087010302 putative Mg++ binding site [ion binding]; other site 159087010303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087010304 Helicase associated domain (HA2); Region: HA2; cl04503 159087010305 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 159087010306 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 159087010307 integron integrase; Region: integrase_gron; TIGR02249 159087010308 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 159087010309 Int/Topo IB signature motif; other site 159087010310 DnaK-type molecular chaperone; Provisional; Region: PTZ00400 159087010311 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 159087010312 SseB protein; Region: SseB; cl06279 159087010313 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 159087010314 Transposase; Region: DEDD_Tnp_IS110; pfam01548 159087010315 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 159087010316 Domain of unknown function (DUF3601); Region: DUF3601; pfam12208 159087010317 Protein of unknown function (DUF1211); Region: DUF1211; cl01421 159087010318 putative acetyltransferase; Provisional; Region: PRK03624 159087010319 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087010320 Coenzyme A binding pocket [chemical binding]; other site 159087010321 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 159087010322 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087010323 amino-acid N-acetyltransferase; Region: PLN02825 159087010324 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087010325 Coenzyme A binding pocket [chemical binding]; other site 159087010326 Haemolysin-III related; Region: HlyIII; cl03831 159087010327 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 protein; Region: CSP_CDS; cd04458 159087010328 DNA-binding site [nucleotide binding]; DNA binding site 159087010329 RNA-binding motif; other site 159087010330 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 159087010331 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; cl12031 159087010332 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 159087010333 PAS fold; Region: PAS_4; pfam08448 159087010334 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 159087010335 putative active site [active] 159087010336 heme pocket [chemical binding]; other site 159087010337 PAS domain S-box; Region: sensory_box; TIGR00229 159087010338 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087010339 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087010340 GAF domain; Region: GAF; cl00853 159087010341 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010342 metal binding site [ion binding]; metal-binding site 159087010343 active site 159087010344 I-site; other site 159087010345 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 159087010346 CrcB-like protein; Region: CRCB; cl09114 159087010347 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 159087010348 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087010349 active site 159087010350 HIGH motif; other site 159087010351 nucleotide binding site [chemical binding]; other site 159087010352 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087010353 active site 159087010354 KMSKS motif; other site 159087010355 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 159087010356 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 159087010357 S-adenosylmethionine binding site [chemical binding]; other site 159087010358 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 contains two...; Region: OMP_decarboxylase_like; cd04725 159087010359 active site 159087010360 dimer interface [polypeptide binding]; other site 159087010361 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 159087010362 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 159087010363 catalytic residues [active] 159087010364 Peptidase family M23; Region: Peptidase_M23; pfam01551 159087010365 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 159087010366 homotrimer interaction site [polypeptide binding]; other site 159087010367 putative active site [active] 159087010368 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 159087010369 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087010370 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010371 active site 159087010372 phosphorylation site [posttranslational modification] 159087010373 intermolecular recognition site; other site 159087010374 dimerization interface [polypeptide binding]; other site 159087010375 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087010376 Zn2+ binding site [ion binding]; other site 159087010377 Mg2+ binding site [ion binding]; other site 159087010378 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 159087010379 dimer interface [polypeptide binding]; other site 159087010380 phosphorylation site [posttranslational modification] 159087010381 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 159087010382 ATP binding site [chemical binding]; other site 159087010383 Mg2+ binding site [ion binding]; other site 159087010384 G-X-G motif; other site 159087010385 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010386 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010387 active site 159087010388 phosphorylation site [posttranslational modification] 159087010389 intermolecular recognition site; other site 159087010390 dimerization interface [polypeptide binding]; other site 159087010391 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010392 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010393 active site 159087010394 phosphorylation site [posttranslational modification] 159087010395 intermolecular recognition site; other site 159087010396 dimerization interface [polypeptide binding]; other site 159087010397 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 159087010398 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087010399 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087010400 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087010401 Walker A/P-loop; other site 159087010402 ATP binding site [chemical binding]; other site 159087010403 Q-loop/lid; other site 159087010404 ABC transporter signature motif; other site 159087010405 Walker B; other site 159087010406 D-loop; other site 159087010407 H-loop/switch region; other site 159087010408 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087010409 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087010410 FtsX-like permease family; Region: FtsX; pfam02687 159087010411 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087010412 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087010413 FtsX-like permease family; Region: FtsX; pfam02687 159087010414 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 159087010415 dimer interaction site [polypeptide binding]; other site 159087010416 substrate-binding tunnel; other site 159087010417 active site 159087010418 catalytic site [active] 159087010419 substrate binding site [chemical binding]; other site 159087010420 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 159087010421 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 159087010422 RNA binding surface [nucleotide binding]; other site 159087010423 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 159087010424 active site 159087010425 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 159087010426 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 159087010427 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 159087010428 GTPase CgtA; Reviewed; Region: obgE; PRK12299 159087010429 GTP1/OBG; Region: GTP1_OBG; pfam01018 159087010430 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 159087010431 G1 box; other site 159087010432 GTP/Mg2+ binding site [chemical binding]; other site 159087010433 Switch I region; other site 159087010434 G2 box; other site 159087010435 G3 box; other site 159087010436 Switch II region; other site 159087010437 G4 box; other site 159087010438 G5 box; other site 159087010439 gamma-glutamyl kinase; Provisional; Region: PRK05429 159087010440 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 159087010441 nucleotide binding site [chemical binding]; other site 159087010442 homotetrameric interface [polypeptide binding]; other site 159087010443 putative phosphate binding site [ion binding]; other site 159087010444 putative allosteric binding site; other site 159087010445 PUA domain; Region: PUA; cl00607 159087010446 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 159087010447 trimer interface [polypeptide binding]; other site 159087010448 eyelet of channel; other site 159087010449 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 159087010450 active site 159087010451 ribulose/triose binding site [chemical binding]; other site 159087010452 phosphate binding site [ion binding]; other site 159087010453 substrate (anthranilate) binding pocket [chemical binding]; other site 159087010454 product (indole) binding pocket [chemical binding]; other site 159087010455 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 159087010456 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 159087010457 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 159087010458 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 159087010459 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 159087010460 glutamine binding [chemical binding]; other site 159087010461 catalytic triad [active] 159087010462 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087010463 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 159087010464 active site 159087010465 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 159087010466 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 159087010467 Ligand binding site; other site 159087010468 Putative Catalytic site; other site 159087010469 DXD motif; other site 159087010470 anthranilate synthase component I; Provisional; Region: PRK13565 159087010471 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 159087010472 chorismate binding enzyme; Region: Chorismate_bind; cl10555 159087010473 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 159087010474 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 159087010475 motif II; other site 159087010476 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 159087010477 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 159087010478 substrate binding site [chemical binding]; other site 159087010479 hexamer interface [polypeptide binding]; other site 159087010480 metal binding site [ion binding]; metal-binding site 159087010481 Protein of unknown function (DUF525); Region: DUF525; cl01119 159087010482 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 159087010483 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 159087010484 S-adenosylmethionine binding site [chemical binding]; other site 159087010485 Domain of unknown function DUF20; Region: UPF0118; cl00465 159087010486 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 159087010487 heterotetramer interface [polypeptide binding]; other site 159087010488 active site pocket [active] 159087010489 cleavage site 159087010490 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 159087010491 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087010492 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 159087010493 SEC-C motif; Region: SEC-C; pfam02810 159087010494 Peptidase family M23; Region: Peptidase_M23; pfam01551 159087010495 Protein of unknown function (DUF721); Region: DUF721; cl02324 159087010496 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 159087010497 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 159087010498 cell division protein FtsZ; Validated; Region: PRK09330 159087010499 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 159087010500 nucleotide binding site [chemical binding]; other site 159087010501 SulA interaction site; other site 159087010502 cell division protein FtsA; Region: ftsA; TIGR01174 159087010503 Cell division protein FtsA; Region: FtsA; cl11496 159087010504 Cell division protein FtsA; Region: FtsA; cl11496 159087010505 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 159087010506 Cell division protein FtsQ; Region: FtsQ; pfam03799 159087010507 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 159087010508 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 159087010509 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087010510 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 159087010511 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087010512 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087010513 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087010514 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 159087010515 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 159087010516 active site 159087010517 homodimer interface [polypeptide binding]; other site 159087010518 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 159087010519 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 159087010520 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010521 NAD(P) binding pocket [chemical binding]; other site 159087010522 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087010523 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087010524 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 159087010525 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 159087010526 Mg++ binding site [ion binding]; other site 159087010527 putative catalytic motif [active] 159087010528 putative substrate binding site [chemical binding]; other site 159087010529 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087010530 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 159087010531 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087010532 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087010533 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 159087010534 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087010535 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087010536 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087010537 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 159087010538 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 159087010539 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 159087010540 Septum formation initiator; Region: DivIC; cl11433 159087010541 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 159087010542 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; cl12011 159087010543 cell division protein MraZ; Reviewed; Region: PRK00326 159087010544 MraZ protein; Region: MraZ; pfam02381 159087010545 MraZ protein; Region: MraZ; pfam02381 159087010546 Cache domain; Region: Cache_1; pfam02743 159087010547 PAS domain S-box; Region: sensory_box; TIGR00229 159087010548 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087010549 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010550 metal binding site [ion binding]; metal-binding site 159087010551 active site 159087010552 I-site; other site 159087010553 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 159087010554 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 159087010555 dimerization domain [polypeptide binding]; other site 159087010556 dimer interface [polypeptide binding]; other site 159087010557 catalytic residues [active] 159087010558 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010559 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 159087010560 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 159087010561 IHF dimer interface [polypeptide binding]; other site 159087010562 IHF - DNA interface [nucleotide binding]; other site 159087010563 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 159087010564 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 159087010565 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 159087010566 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 159087010567 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 159087010568 [4Fe-4S] binding site [ion binding]; other site 159087010569 molybdopterin cofactor binding site; other site 159087010570 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 159087010571 molybdopterin cofactor binding site; other site 159087010572 NapD protein; Region: NapD; cl01163 159087010573 peroxiredoxin; Region: AhpC; TIGR03137 159087010574 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 159087010575 dimer interface [polypeptide binding]; other site 159087010576 decamer (pentamer of dimers) interface [polypeptide binding]; other site 159087010577 catalytic triad [active] 159087010578 peroxidatic and resolving cysteines [active] 159087010579 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 159087010580 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 159087010581 catalytic residue [active] 159087010582 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 159087010583 catalytic residues [active] 159087010584 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010585 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 159087010586 BRO family, N-terminal domain; Region: Bro-N; cl10591 159087010587 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 159087010588 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 159087010589 catalytic residues [active] 159087010590 catalytic nucleophile [active] 159087010591 Presynaptic Site I dimer interface [polypeptide binding]; other site 159087010592 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 159087010593 Synaptic Flat tetramer interface [polypeptide binding]; other site 159087010594 Synaptic Site I dimer interface [polypeptide binding]; other site 159087010595 DNA binding site [nucleotide binding] 159087010596 Restriction endonuclease BglII; Region: Endonuc-BglII; pfam09195 159087010597 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; cl12011 159087010598 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 159087010599 cofactor binding site; other site 159087010600 DNA binding site [nucleotide binding] 159087010601 substrate interaction site [chemical binding]; other site 159087010602 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 159087010603 Int/Topo IB signature motif; other site 159087010604 active site 159087010605 DNA binding site [nucleotide binding] 159087010606 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 159087010607 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 159087010608 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 159087010609 FeS/SAM binding site; other site 159087010610 TRAM domain; Region: TRAM; cl01282 159087010611 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 159087010612 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087010613 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 159087010614 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 159087010615 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 159087010616 Transporter associated domain; Region: CorC_HlyC; cl08393 159087010617 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 159087010618 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 159087010619 putative active site [active] 159087010620 catalytic triad [active] 159087010621 putative dimer interface [polypeptide binding]; other site 159087010622 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 159087010623 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 catalyze...; Region: LT_GEWL; cd00254 159087010624 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087010625 catalytic residue [active] 159087010626 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 159087010627 dimer interface [polypeptide binding]; other site 159087010628 motif 1; other site 159087010629 active site 159087010630 motif 2; other site 159087010631 motif 3; other site 159087010632 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 159087010633 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 159087010634 active site 159087010635 motif I; other site 159087010636 motif II; other site 159087010637 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 159087010638 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087010639 putative acyl-acceptor binding pocket; other site 159087010640 Protein of unknown function DUF45; Region: DUF45; cl00636 159087010641 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087010642 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 159087010643 dimer interface [polypeptide binding]; other site 159087010644 active site 159087010645 metal binding site [ion binding]; metal-binding site 159087010646 glutathione binding site [chemical binding]; other site 159087010647 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087010648 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087010649 putative ligand binding site [chemical binding]; other site 159087010650 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010651 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010652 active site 159087010653 phosphorylation site [posttranslational modification] 159087010654 intermolecular recognition site; other site 159087010655 dimerization interface [polypeptide binding]; other site 159087010656 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 159087010657 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 159087010658 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 159087010659 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 159087010660 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 159087010661 ligand binding site [chemical binding]; other site 159087010662 flexible hinge region; other site 159087010663 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087010664 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 159087010665 putative ADP-binding pocket [chemical binding]; other site 159087010666 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 159087010667 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087010668 putative active site [active] 159087010669 putative metal binding site [ion binding]; other site 159087010670 PAS domain S-box; Region: sensory_box; TIGR00229 159087010671 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 159087010672 putative active site [active] 159087010673 heme pocket [chemical binding]; other site 159087010674 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087010675 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 159087010676 putative active site [active] 159087010677 heme pocket [chemical binding]; other site 159087010678 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 159087010679 dimer interface [polypeptide binding]; other site 159087010680 phosphorylation site [posttranslational modification] 159087010681 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 159087010682 ATP binding site [chemical binding]; other site 159087010683 Mg2+ binding site [ion binding]; other site 159087010684 G-X-G motif; other site 159087010685 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010686 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010687 active site 159087010688 phosphorylation site [posttranslational modification] 159087010689 intermolecular recognition site; other site 159087010690 dimerization interface [polypeptide binding]; other site 159087010691 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 159087010692 active site 159087010693 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087010694 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 159087010695 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010696 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087010697 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087010698 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010699 active site 159087010700 phosphorylation site [posttranslational modification] 159087010701 intermolecular recognition site; other site 159087010702 dimerization interface [polypeptide binding]; other site 159087010703 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087010704 Zn2+ binding site [ion binding]; other site 159087010705 Mg2+ binding site [ion binding]; other site 159087010706 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 159087010707 Chromate transporter; Region: Chromate_transp; pfam02417 159087010708 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 159087010709 Chromate transporter; Region: Chromate_transp; pfam02417 159087010710 Amino acid permease; Region: AA_permease; cl00524 159087010711 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 159087010712 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010713 active site 159087010714 phosphorylation site [posttranslational modification] 159087010715 intermolecular recognition site; other site 159087010716 dimerization interface [polypeptide binding]; other site 159087010717 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 159087010718 DNA binding site [nucleotide binding] 159087010719 sensor protein KdpD; Provisional; Region: PRK10490 159087010720 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 159087010721 dimer interface [polypeptide binding]; other site 159087010722 phosphorylation site [posttranslational modification] 159087010723 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 159087010724 ATP binding site [chemical binding]; other site 159087010725 Mg2+ binding site [ion binding]; other site 159087010726 G-X-G motif; other site 159087010727 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 159087010728 tetramer (dimer of dimers) interface [polypeptide binding]; other site 159087010729 active site 159087010730 dimer interface [polypeptide binding]; other site 159087010731 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 159087010732 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 159087010733 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 159087010734 dimer interface [polypeptide binding]; other site 159087010735 conserved gate region; other site 159087010736 putative PBP binding loops; other site 159087010737 ABC-ATPase subunit interface; other site 159087010738 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 159087010739 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 159087010740 dimer interface [polypeptide binding]; other site 159087010741 conserved gate region; other site 159087010742 putative PBP binding loops; other site 159087010743 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 159087010744 ABC-ATPase subunit interface; other site 159087010745 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14252 159087010746 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 159087010747 Walker A/P-loop; other site 159087010748 ATP binding site [chemical binding]; other site 159087010749 Q-loop/lid; other site 159087010750 ABC transporter signature motif; other site 159087010751 Walker B; other site 159087010752 D-loop; other site 159087010753 H-loop/switch region; other site 159087010754 transcriptional regulator PhoU; Provisional; Region: PRK11115 159087010755 PhoU domain; Region: PhoU; pfam01895 159087010756 PhoU domain; Region: PhoU; pfam01895 159087010757 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 159087010758 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087010759 active site 159087010760 phosphorylation site [posttranslational modification] 159087010761 intermolecular recognition site; other site 159087010762 dimerization interface [polypeptide binding]; other site 159087010763 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 159087010764 DNA binding site [nucleotide binding] 159087010765 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 159087010766 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087010767 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087010768 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 159087010769 dimer interface [polypeptide binding]; other site 159087010770 phosphorylation site [posttranslational modification] 159087010771 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 159087010772 ATP binding site [chemical binding]; other site 159087010773 Mg2+ binding site [ion binding]; other site 159087010774 G-X-G motif; other site 159087010775 Cupin domain; Region: Cupin_2; cl09118 159087010776 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 159087010777 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087010778 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087010779 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 159087010780 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 159087010781 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087010782 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 159087010783 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 159087010784 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010785 metal binding site [ion binding]; metal-binding site 159087010786 active site 159087010787 I-site; other site 159087010788 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087010789 Coenzyme A binding pocket [chemical binding]; other site 159087010790 sensory histidine kinase CreC; Provisional; Region: PRK11100 159087010791 BON domain; Region: BON; cl02771 159087010792 BON domain; Region: BON; cl02771 159087010793 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 159087010794 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087010795 methyl-accepting chemotaxis protein I; Provisional; Region: PRK15041 159087010796 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane...; Region: TarH; cl00144 159087010797 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 159087010798 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087010799 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 159087010800 dimerization interface [polypeptide binding]; other site 159087010801 substrate binding pocket [chemical binding]; other site 159087010802 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 159087010803 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 159087010804 putative substrate translocation pore; other site 159087010805 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 159087010806 CoenzymeA binding site [chemical binding]; other site 159087010807 subunit interaction site [polypeptide binding]; other site 159087010808 PHB binding site; other site 159087010809 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 159087010810 N-acetylglutamate synthase; Validated; Region: PRK05279 159087010811 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 159087010812 putative feedback inhibition sensing region; other site 159087010813 putative nucleotide binding site [chemical binding]; other site 159087010814 putative substrate binding site [chemical binding]; other site 159087010815 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 159087010816 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087010817 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087010818 Coenzyme A binding pocket [chemical binding]; other site 159087010819 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 159087010820 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 159087010821 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 159087010822 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 159087010823 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 159087010824 putative catalytic residue [active] 159087010825 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087010826 PAS fold; Region: PAS_7; pfam12860 159087010827 PAS fold; Region: PAS_7; pfam12860 159087010828 PAS fold; Region: PAS; pfam00989 159087010829 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 159087010830 putative active site [active] 159087010831 heme pocket [chemical binding]; other site 159087010832 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010833 metal binding site [ion binding]; metal-binding site 159087010834 active site 159087010835 I-site; other site 159087010836 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 159087010837 fructose-1,6-bisphosphatase family protein; Region: PLN02628 159087010838 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 159087010839 AMP binding site [chemical binding]; other site 159087010840 metal binding site [ion binding]; metal-binding site 159087010841 active site 159087010842 transketolase; Reviewed; Region: PRK12753 159087010843 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 159087010844 TPP-binding site [chemical binding]; other site 159087010845 dimer interface [polypeptide binding]; other site 159087010846 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 159087010847 PYR/PP interface [polypeptide binding]; other site 159087010848 dimer interface [polypeptide binding]; other site 159087010849 TPP binding site [chemical binding]; other site 159087010850 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087010851 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 159087010852 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 159087010853 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 159087010854 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 159087010855 erythrose-4-phosphate dehydrogenase; Region: E4PD_g-proteo; TIGR01532 159087010856 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 159087010857 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 159087010858 Phosphoglycerate kinase; Region: PGK; pfam00162 159087010859 substrate binding site [chemical binding]; other site 159087010860 hinge regions; other site 159087010861 ADP binding site [chemical binding]; other site 159087010862 catalytic site [active] 159087010863 pyruvate kinase; Provisional; Region: PRK05826 159087010864 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; cl09155 159087010865 domain interfaces; other site 159087010866 active site 159087010867 hypothetical protein; Provisional; Region: PRK08185 159087010868 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 159087010869 intersubunit interface [polypeptide binding]; other site 159087010870 active site 159087010871 zinc binding site [ion binding]; other site 159087010872 Na+ binding site [ion binding]; other site 159087010873 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087010874 ligand binding site [chemical binding]; other site 159087010875 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 159087010876 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; cd00200 159087010877 structural tetrad; other site 159087010878 FOG: WD40 repeat [General function prediction only]; Region: COG2319 159087010879 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; cd00200 159087010880 structural tetrad; other site 159087010881 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 159087010882 TIR domain; Region: TIR_2; cl15770 159087010883 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK12323 159087010884 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 159087010885 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 159087010886 Walker A motif; other site 159087010887 ATP binding site [chemical binding]; other site 159087010888 Walker B motif; other site 159087010889 arginine finger; other site 159087010890 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 159087010891 metal ion-dependent adhesion site (MIDAS); other site 159087010892 Baseplate J-like protein; Region: Baseplate_J; cl01294 159087010893 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 159087010894 Uncharacterized conserved protein [Function unknown]; Region: COG4104 159087010895 PAAR motif; Region: PAAR_motif; pfam05488 159087010896 Phage protein D [General function prediction only]; Region: COG3500; cl12180 159087010897 Rhs element Vgr protein; Region: vgr_GE; TIGR01646 159087010898 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087010899 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 159087010900 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; cl12125 159087010901 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; cl12125 159087010902 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 159087010903 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 159087010904 Protein of unknown function (DUF4255); Region: DUF4255; pfam14065 159087010905 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 159087010906 Lecithin:cholesterol acyltransferase; Region: LACT; pfam02450 159087010907 CHAT domain; Region: CHAT; cl02083 159087010908 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 159087010909 Peptidase M15; Region: Peptidase_M15_3; cl01194 159087010910 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010911 metal binding site [ion binding]; metal-binding site 159087010912 active site 159087010913 I-site; other site 159087010914 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 159087010915 PAS fold; Region: PAS_4; pfam08448 159087010916 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 159087010917 putative active site [active] 159087010918 heme pocket [chemical binding]; other site 159087010919 hypothetical protein; Provisional; Region: PRK13560 159087010920 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087010921 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087010922 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010923 metal binding site [ion binding]; metal-binding site 159087010924 active site 159087010925 I-site; other site 159087010926 hypothetical protein; Provisional; Region: PRK08185 159087010927 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 159087010928 intersubunit interface [polypeptide binding]; other site 159087010929 active site 159087010930 zinc binding site [ion binding]; other site 159087010931 Na+ binding site [ion binding]; other site 159087010932 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 159087010933 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 159087010934 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 159087010935 transketolase; Reviewed; Region: PRK12753 159087010936 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 159087010937 TPP-binding site [chemical binding]; other site 159087010938 dimer interface [polypeptide binding]; other site 159087010939 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 159087010940 PYR/PP interface [polypeptide binding]; other site 159087010941 dimer interface [polypeptide binding]; other site 159087010942 TPP binding site [chemical binding]; other site 159087010943 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087010944 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087010945 active site 159087010946 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 159087010947 AMP binding site [chemical binding]; other site 159087010948 metal binding site [ion binding]; metal-binding site 159087010949 active site 159087010950 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087010951 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 159087010952 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 159087010953 motif II; other site 159087010954 UPF0126 domain; Region: UPF0126; pfam03458 159087010955 UPF0126 domain; Region: UPF0126; pfam03458 159087010956 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 159087010957 HSP70 interaction site [polypeptide binding]; other site 159087010958 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 159087010959 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 159087010960 dimer interface [polypeptide binding]; other site 159087010961 active site 159087010962 catalytic residue [active] 159087010963 metal binding site [ion binding]; metal-binding site 159087010964 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087010965 Helix-turn-helix domains; Region: HTH; cl00088 159087010966 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 159087010967 putative dimerization interface [polypeptide binding]; other site 159087010968 Protein of unknown function (DUF3422); Region: DUF3422; cl02073 159087010969 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 159087010970 ATP binding site [chemical binding]; other site 159087010971 active site 159087010972 substrate binding site [chemical binding]; other site 159087010973 Protein of unknown function (DUF2743); Region: DUF2743; pfam10899 159087010974 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 159087010975 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 159087010976 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 159087010977 active site 159087010978 Zn binding site [ion binding]; other site 159087010979 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 159087010980 catalytic residues [active] 159087010981 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 159087010982 putative phosphate binding site [ion binding]; other site 159087010983 putative catalytic site [active] 159087010984 active site 159087010985 metal binding site A [ion binding]; metal-binding site 159087010986 DNA binding site [nucleotide binding] 159087010987 putative AP binding site [nucleotide binding]; other site 159087010988 putative metal binding site B [ion binding]; other site 159087010989 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087010990 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 159087010991 ligand binding site [chemical binding]; other site 159087010992 flexible hinge region; other site 159087010993 Helix-turn-helix domains; Region: HTH; cl00088 159087010994 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 159087010995 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 159087010996 multiple promoter invertase; Provisional; Region: mpi; PRK13413 159087010997 catalytic residues [active] 159087010998 catalytic nucleophile [active] 159087010999 Presynaptic Site I dimer interface [polypeptide binding]; other site 159087011000 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 159087011001 Synaptic Flat tetramer interface [polypeptide binding]; other site 159087011002 Synaptic Site I dimer interface [polypeptide binding]; other site 159087011003 DNA binding site [nucleotide binding] 159087011004 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 159087011005 DNA-binding interface [nucleotide binding]; DNA binding site 159087011006 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 159087011007 Walker A motif; other site 159087011008 ATP binding site [chemical binding]; other site 159087011009 Walker B motif; other site 159087011010 arginine finger; other site 159087011011 TIR domain; Region: TIR; cl02060 159087011012 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 159087011013 Phage integrase family; Region: Phage_integrase; pfam00589 159087011014 DNA binding site [nucleotide binding] 159087011015 Int/Topo IB signature motif; other site 159087011016 active site 159087011017 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 159087011018 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; cl12011 159087011019 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 159087011020 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 159087011021 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 159087011022 SurA N-terminal domain; Region: SurA_N; pfam09312 159087011023 PPIC-type PPIASE domain; Region: Rotamase; cl08278 159087011024 PPIC-type PPIASE domain; Region: Rotamase; cl08278 159087011025 OstA-like protein; Region: OstA; cl00844 159087011026 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 159087011027 Organic solvent tolerance protein; Region: OstA_C; pfam04453 159087011028 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; cl15691 159087011029 Phosphotransferase enzyme family; Region: APH; pfam01636 159087011030 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 159087011031 Substrate binding site; other site 159087011032 metal-binding site 159087011033 proline aminopeptidase P II; Provisional; Region: PRK10879 159087011034 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 159087011035 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 159087011036 active site 159087011037 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011038 hypothetical protein; Provisional; Region: PRK06996 159087011039 UbiA prenyltransferase family; Region: UbiA; cl00337 159087011040 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 159087011041 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 159087011042 FMN binding site [chemical binding]; other site 159087011043 active site 159087011044 catalytic residues [active] 159087011045 substrate binding site [chemical binding]; other site 159087011046 Helix-turn-helix domains; Region: HTH; cl00088 159087011047 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 159087011048 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 159087011049 purine monophosphate binding site [chemical binding]; other site 159087011050 dimer interface [polypeptide binding]; other site 159087011051 putative catalytic residues [active] 159087011052 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 159087011053 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 159087011054 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 159087011055 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 159087011056 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087011057 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 159087011058 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 159087011059 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 159087011060 HemY protein N-terminus; Region: HemY_N; pfam07219 159087011061 HemX; Region: HemX; cl14667 159087011062 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 159087011063 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 159087011064 active site 159087011065 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 159087011066 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 159087011067 domain interfaces; other site 159087011068 active site 159087011069 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 159087011070 S-adenosylmethionine binding site [chemical binding]; other site 159087011071 aminopeptidase N; Provisional; Region: pepN; PRK14015 159087011072 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 159087011073 active site 159087011074 Zn binding site [ion binding]; other site 159087011075 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 159087011076 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087011077 active site 159087011078 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 159087011079 catalytic residues [active] 159087011080 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 159087011081 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011082 active site 159087011083 phosphorylation site [posttranslational modification] 159087011084 intermolecular recognition site; other site 159087011085 dimerization interface [polypeptide binding]; other site 159087011086 LytTr DNA-binding domain; Region: LytTR; cl04498 159087011087 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 159087011088 Histidine kinase; Region: His_kinase; pfam06580 159087011089 argininosuccinate lyase; Provisional; Region: PRK00855 159087011090 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 159087011091 active sites [active] 159087011092 tetramer interface [polypeptide binding]; other site 159087011093 OsmC-like protein; Region: OsmC; cl00767 159087011094 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 159087011095 putative GSH binding site [chemical binding]; other site 159087011096 catalytic residues [active] 159087011097 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 159087011098 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 159087011099 S-adenosylmethionine binding site [chemical binding]; other site 159087011100 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087011101 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087011102 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087011103 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 159087011104 dimerization interface [polypeptide binding]; other site 159087011105 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 159087011106 dimer interface [polypeptide binding]; other site 159087011107 phosphorylation site [posttranslational modification] 159087011108 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 159087011109 ATP binding site [chemical binding]; other site 159087011110 Mg2+ binding site [ion binding]; other site 159087011111 G-X-G motif; other site 159087011112 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011113 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011114 active site 159087011115 phosphorylation site [posttranslational modification] 159087011116 intermolecular recognition site; other site 159087011117 dimerization interface [polypeptide binding]; other site 159087011118 peptide chain release factor 1; Validated; Region: prfA; PRK00591 159087011119 RF-1 domain; Region: RF-1; cl02875 159087011120 RF-1 domain; Region: RF-1; cl02875 159087011121 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011122 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011123 active site 159087011124 phosphorylation site [posttranslational modification] 159087011125 intermolecular recognition site; other site 159087011126 dimerization interface [polypeptide binding]; other site 159087011127 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011128 metal binding site [ion binding]; metal-binding site 159087011129 active site 159087011130 I-site; other site 159087011131 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 159087011132 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 159087011133 tRNA; other site 159087011134 putative tRNA binding site [nucleotide binding]; other site 159087011135 putative NADP binding site [chemical binding]; other site 159087011136 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 159087011137 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 159087011138 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a...; Region: ABC_CysA_sulfate_importer; cd03296 159087011139 Walker A/P-loop; other site 159087011140 ATP binding site [chemical binding]; other site 159087011141 Q-loop/lid; other site 159087011142 ABC transporter signature motif; other site 159087011143 Walker B; other site 159087011144 D-loop; other site 159087011145 H-loop/switch region; other site 159087011146 TOBE domain; Region: TOBE_2; cl01440 159087011147 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 159087011148 dimer interface [polypeptide binding]; other site 159087011149 conserved gate region; other site 159087011150 putative PBP binding loops; other site 159087011151 ABC-ATPase subunit interface; other site 159087011152 sulfate ABC transporter, permease protein CysT; Region: permease_CysT; TIGR02139 159087011153 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 159087011154 dimer interface [polypeptide binding]; other site 159087011155 conserved gate region; other site 159087011156 putative PBP binding loops; other site 159087011157 ABC-ATPase subunit interface; other site 159087011158 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 159087011159 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087011160 ligand binding site [chemical binding]; other site 159087011161 Nitrate and nitrite sensing; Region: NIT; pfam08376 159087011162 PAS domain S-box; Region: sensory_box; TIGR00229 159087011163 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 159087011164 putative active site [active] 159087011165 heme pocket [chemical binding]; other site 159087011166 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011167 metal binding site [ion binding]; metal-binding site 159087011168 active site 159087011169 I-site; other site 159087011170 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 159087011171 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 159087011172 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087011173 octamerization interface [polypeptide binding]; other site 159087011174 diferric-oxygen binding site [ion binding]; other site 159087011175 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087011176 GAF domain; Region: GAF; cl00853 159087011177 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 159087011178 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 159087011179 tetramer interface [polypeptide binding]; other site 159087011180 TPP-binding site [chemical binding]; other site 159087011181 heterodimer interface [polypeptide binding]; other site 159087011182 phosphorylation loop region [posttranslational modification] 159087011183 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 159087011184 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 159087011185 PYR/PP interface [polypeptide binding]; other site 159087011186 dimer interface [polypeptide binding]; other site 159087011187 TPP binding site [chemical binding]; other site 159087011188 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087011189 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 159087011190 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 159087011191 MltA specific insert domain; Region: MltA; cl08398 159087011192 3D domain; Region: 3D; cl01439 159087011193 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 159087011194 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 159087011195 Walker A motif; other site 159087011196 ATP binding site [chemical binding]; other site 159087011197 Walker B motif; other site 159087011198 hypothetical protein; Provisional; Region: PRK08999 159087011199 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 159087011200 active site 159087011201 8-oxo-dGMP binding site [chemical binding]; other site 159087011202 nudix motif; other site 159087011203 metal binding site [ion binding]; metal-binding site 159087011204 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 159087011205 active site 159087011206 thiamine phosphate binding site [chemical binding]; other site 159087011207 pyrophosphate binding site [ion binding]; other site 159087011208 Domain of unknown function (DUF329); Region: DUF329; cl01144 159087011209 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 159087011210 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 159087011211 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 159087011212 CoA-binding site [chemical binding]; other site 159087011213 ATP-binding [chemical binding]; other site 159087011214 Sporulation related domain; Region: SPOR; cl10051 159087011215 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 159087011216 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 159087011217 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087011218 catalytic residue [active] 159087011219 Domon-like domain of UDP-N-acetylenolpyruvoylglucosamine reductase; Region: DOMON_murB_like; cd09627 159087011220 putative heme binding site [chemical binding]; other site 159087011221 Protein of unknown function (DUF1343); Region: DUF1343; cl01598 159087011222 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087011223 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087011224 PAS domain S-box; Region: sensory_box; TIGR00229 159087011225 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 159087011226 putative active site [active] 159087011227 heme pocket [chemical binding]; other site 159087011228 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087011229 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 159087011230 putative active site [active] 159087011231 heme pocket [chemical binding]; other site 159087011232 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 159087011233 dimer interface [polypeptide binding]; other site 159087011234 phosphorylation site [posttranslational modification] 159087011235 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 159087011236 ATP binding site [chemical binding]; other site 159087011237 Mg2+ binding site [ion binding]; other site 159087011238 G-X-G motif; other site 159087011239 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011240 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011241 active site 159087011242 phosphorylation site [posttranslational modification] 159087011243 intermolecular recognition site; other site 159087011244 dimerization interface [polypeptide binding]; other site 159087011245 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011246 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 159087011247 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 159087011248 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087011249 Walker A/P-loop; other site 159087011250 ATP binding site [chemical binding]; other site 159087011251 Q-loop/lid; other site 159087011252 ABC transporter signature motif; other site 159087011253 Walker B; other site 159087011254 D-loop; other site 159087011255 H-loop/switch region; other site 159087011256 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 159087011257 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 159087011258 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 159087011259 P loop; other site 159087011260 GTP binding site [chemical binding]; other site 159087011261 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 159087011262 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 159087011263 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 159087011264 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 159087011265 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 159087011266 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 159087011267 Predicted methyltransferase [General function prediction only]; Region: COG2520 159087011268 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 159087011269 S-adenosylmethionine binding site [chemical binding]; other site 159087011270 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 159087011271 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 159087011272 active site 159087011273 (T/H)XGH motif; other site 159087011274 ferredoxin; Validated; Region: PRK07118 159087011275 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087011276 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs); Region: Era_like; cd00880 159087011277 Switch II region; other site 159087011278 G3 box; other site 159087011279 G4 box; other site 159087011280 G5 box; other site 159087011281 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 159087011282 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 159087011283 DNA binding site [nucleotide binding] 159087011284 catalytic residue [active] 159087011285 H2TH interface [polypeptide binding]; other site 159087011286 putative catalytic residues [active] 159087011287 turnover-facilitating residue; other site 159087011288 intercalation triad [nucleotide binding]; other site 159087011289 8OG recognition residue [nucleotide binding]; other site 159087011290 putative reading head residues; other site 159087011291 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 159087011292 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 159087011293 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 159087011294 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 159087011295 TPR motif; other site 159087011296 binding surface 159087011297 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 159087011298 binding surface 159087011299 TPR motif; other site 159087011300 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 159087011301 binding surface 159087011302 TPR motif; other site 159087011303 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 159087011304 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 159087011305 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 159087011306 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 159087011307 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 159087011308 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 159087011309 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087011310 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 159087011311 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 159087011312 5S rRNA interface [nucleotide binding]; other site 159087011313 CTC domain interface [polypeptide binding]; other site 159087011314 L16 interface [polypeptide binding]; other site 159087011315 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 159087011316 putative active site [active] 159087011317 catalytic residue [active] 159087011318 GTP-binding protein YchF; Reviewed; Region: PRK09601 159087011319 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 159087011320 G1 box; other site 159087011321 GTP/Mg2+ binding site [chemical binding]; other site 159087011322 Switch I region; other site 159087011323 G2 box; other site 159087011324 Switch II region; other site 159087011325 G3 box; other site 159087011326 G4 box; other site 159087011327 G5 box; other site 159087011328 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 159087011329 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 159087011330 putative active site [active] 159087011331 heme pocket [chemical binding]; other site 159087011332 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011333 metal binding site [ion binding]; metal-binding site 159087011334 active site 159087011335 I-site; other site 159087011336 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 159087011337 spermidine synthase; Provisional; Region: PRK03612 159087011338 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 159087011339 YceI-like domain; Region: YceI; cl01001 159087011340 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 159087011341 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 159087011342 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; cl00522 159087011343 dimerization interface [polypeptide binding]; other site 159087011344 active site 159087011345 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 159087011346 homopentamer interface [polypeptide binding]; other site 159087011347 active site 159087011348 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 159087011349 thiamine monophosphate kinase; Provisional; Region: PRK05731 159087011350 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 159087011351 ATP binding site [chemical binding]; other site 159087011352 dimerization interface [polypeptide binding]; other site 159087011353 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 159087011354 tetramer interfaces [polypeptide binding]; other site 159087011355 binuclear metal-binding site [ion binding]; other site 159087011356 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011357 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011358 active site 159087011359 phosphorylation site [posttranslational modification] 159087011360 intermolecular recognition site; other site 159087011361 dimerization interface [polypeptide binding]; other site 159087011362 PAS domain S-box; Region: sensory_box; TIGR00229 159087011363 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 159087011364 putative active site [active] 159087011365 heme pocket [chemical binding]; other site 159087011366 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011367 metal binding site [ion binding]; metal-binding site 159087011368 active site 159087011369 I-site; other site 159087011370 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 159087011371 HDOD domain; Region: HDOD; pfam08668 159087011372 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087011373 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 159087011374 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 159087011375 ATP binding site [chemical binding]; other site 159087011376 Mg2+ binding site [ion binding]; other site 159087011377 G-X-G motif; other site 159087011378 HDOD domain; Region: HDOD; pfam08668 159087011379 NlpC/P60 family; Region: NLPC_P60; cl11438 159087011380 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 159087011381 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 159087011382 tetramerization interface [polypeptide binding]; other site 159087011383 NAD(P) binding site [chemical binding]; other site 159087011384 catalytic residues [active] 159087011385 Uncharacterized conserved protein [Function unknown]; Region: COG4278 159087011386 NMT1/THI5 like; Region: NMT1; pfam09084 159087011387 PAS domain S-box; Region: sensory_box; TIGR00229 159087011388 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 159087011389 putative active site [active] 159087011390 heme pocket [chemical binding]; other site 159087011391 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011392 metal binding site [ion binding]; metal-binding site 159087011393 active site 159087011394 I-site; other site 159087011395 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 159087011396 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. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 159087011397 Predicted membrane protein [Function unknown]; Region: COG3766 159087011398 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 159087011399 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 159087011400 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 159087011401 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 159087011402 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087011403 Zn2+ binding site [ion binding]; other site 159087011404 Mg2+ binding site [ion binding]; other site 159087011405 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 159087011406 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 159087011407 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 159087011408 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 159087011409 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 159087011410 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011411 active site 159087011412 phosphorylation site [posttranslational modification] 159087011413 intermolecular recognition site; other site 159087011414 dimerization interface [polypeptide binding]; other site 159087011415 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 159087011416 Walker A motif; other site 159087011417 ATP binding site [chemical binding]; other site 159087011418 Walker B motif; other site 159087011419 arginine finger; other site 159087011420 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087011421 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 159087011422 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 159087011423 putative active site [active] 159087011424 heme pocket [chemical binding]; other site 159087011425 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 159087011426 dimer interface [polypeptide binding]; other site 159087011427 phosphorylation site [posttranslational modification] 159087011428 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 159087011429 ATP binding site [chemical binding]; other site 159087011430 Mg2+ binding site [ion binding]; other site 159087011431 G-X-G motif; other site 159087011432 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087011433 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087011434 glutamine synthetase; Provisional; Region: glnA; PRK09469 159087011435 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 159087011436 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 159087011437 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 159087011438 Cation efflux family; Region: Cation_efflux; cl00316 159087011439 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 159087011440 active site residue [active] 159087011441 Quinolinate synthetase A protein; Region: NadA; cl00420 159087011442 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 159087011443 putative catalytic site [active] 159087011444 putative metal binding site [ion binding]; other site 159087011445 putative phosphate binding site [ion binding]; other site 159087011446 cardiolipin synthase 2; Provisional; Region: PRK11263 159087011447 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 159087011448 putative active site [active] 159087011449 catalytic site [active] 159087011450 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 159087011451 putative active site [active] 159087011452 catalytic site [active] 159087011453 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087011454 active site 159087011455 HIGH motif; other site 159087011456 nucleotide binding site [chemical binding]; other site 159087011457 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087011458 active site 159087011459 KMSKS motif; other site 159087011460 PAS domain S-box; Region: sensory_box; TIGR00229 159087011461 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 159087011462 putative active site [active] 159087011463 heme pocket [chemical binding]; other site 159087011464 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011465 metal binding site [ion binding]; metal-binding site 159087011466 active site 159087011467 I-site; other site 159087011468 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 159087011469 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 159087011470 catalytic residues [active] 159087011471 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 159087011472 tartrate dehydrogenase; Provisional; Region: PRK08194 159087011473 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 159087011474 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 159087011475 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 159087011476 VPS10 domain; Region: VPS10; smart00602 159087011477 Ycf48-like protein; Provisional; Region: PRK13684 159087011478 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 159087011479 active site 1 [active] 159087011480 dimer interface [polypeptide binding]; other site 159087011481 hexamer interface [polypeptide binding]; other site 159087011482 active site 2 [active] 159087011483 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087011484 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087011485 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087011486 active site 159087011487 catalytic residues [active] 159087011488 metal binding site [ion binding]; metal-binding site 159087011489 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087011490 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087011491 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011492 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087011493 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087011494 classical (c) SDRs; Region: SDR_c; cd05233 159087011495 NAD(P) binding site [chemical binding]; other site 159087011496 active site 159087011497 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087011498 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087011499 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 159087011500 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 159087011501 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 159087011502 NAD binding site [chemical binding]; other site 159087011503 catalytic residues [active] 159087011504 Domain of unknown function (DUF336); Region: DUF336; cl01249 159087011505 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 159087011506 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 159087011507 tetramer interface [polypeptide binding]; other site 159087011508 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 159087011509 tetramer interface [polypeptide binding]; other site 159087011510 active site 159087011511 Fe binding site [ion binding]; other site 159087011512 DNA-binding transcriptional regulator CsiR; Provisional; Region: PRK11534 159087011513 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087011514 DNA-binding site [nucleotide binding]; DNA binding site 159087011515 FCD domain; Region: FCD; cl11656 159087011516 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 159087011517 catalytic loop [active] 159087011518 iron binding site [ion binding]; other site 159087011519 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087011520 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 159087011521 catalytic loop [active] 159087011522 iron binding site [ion binding]; other site 159087011523 Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H...; Region: phenol_2-monooxygenase_like; cd06211 159087011524 FAD binding pocket [chemical binding]; other site 159087011525 FAD binding motif [chemical binding]; other site 159087011526 phosphate binding motif [ion binding]; other site 159087011527 beta-alpha-beta structure motif; other site 159087011528 NAD binding pocket [chemical binding]; other site 159087011529 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 159087011530 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 159087011531 dimerization interface [polypeptide binding]; other site 159087011532 putative path to active site cavity [active] 159087011533 diiron center [ion binding]; other site 159087011534 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 159087011535 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 159087011536 dimerization interface [polypeptide binding]; other site 159087011537 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 159087011538 Activator of aromatic catabolism; Region: XylR_N; pfam06505 159087011539 Heme NO binding; Region: HNOB; cl15268 159087011540 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 159087011541 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 159087011542 Walker A motif; other site 159087011543 ATP binding site [chemical binding]; other site 159087011544 Walker B motif; other site 159087011545 arginine finger; other site 159087011546 Helix-turn-helix domains; Region: HTH; cl00088 159087011547 Helix-turn-helix domains; Region: HTH; cl00088 159087011548 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 159087011549 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_Chlorocatechol; cd08446 159087011550 dimerization interface [polypeptide binding]; other site 159087011551 putative substrate binding pocket [chemical binding]; other site 159087011552 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 159087011553 PAS domain S-box; Region: sensory_box; TIGR00229 159087011554 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 159087011555 putative active site [active] 159087011556 heme pocket [chemical binding]; other site 159087011557 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 159087011558 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; cl09155 159087011559 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 159087011560 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 159087011561 tetramer interface [polypeptide binding]; other site 159087011562 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 159087011563 tetramer interface [polypeptide binding]; other site 159087011564 active site 159087011565 Fe binding site [ion binding]; other site 159087011566 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 159087011567 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 159087011568 NAD binding site [chemical binding]; other site 159087011569 catalytic residues [active] 159087011570 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087011571 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011572 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087011573 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087011574 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087011575 active site 159087011576 catalytic residues [active] 159087011577 metal binding site [ion binding]; metal-binding site 159087011578 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087011579 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011580 active site 159087011581 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 159087011582 active site 1 [active] 159087011583 dimer interface [polypeptide binding]; other site 159087011584 hexamer interface [polypeptide binding]; other site 159087011585 active site 2 [active] 159087011586 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 159087011587 active site 1 [active] 159087011588 dimer interface [polypeptide binding]; other site 159087011589 hexamer interface [polypeptide binding]; other site 159087011590 active site 2 [active] 159087011591 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 159087011592 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087011593 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087011594 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087011595 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011596 active site 159087011597 phosphorylation site [posttranslational modification] 159087011598 intermolecular recognition site; other site 159087011599 dimerization interface [polypeptide binding]; other site 159087011600 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 159087011601 DNA binding residues [nucleotide binding] 159087011602 dimerization interface [polypeptide binding]; other site 159087011603 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 159087011604 putative active site [active] 159087011605 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087011606 heme pocket [chemical binding]; other site 159087011607 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 159087011608 dimer interface [polypeptide binding]; other site 159087011609 phosphorylation site [posttranslational modification] 159087011610 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 159087011611 ATP binding site [chemical binding]; other site 159087011612 Mg2+ binding site [ion binding]; other site 159087011613 G-X-G motif; other site 159087011614 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011615 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011616 active site 159087011617 phosphorylation site [posttranslational modification] 159087011618 intermolecular recognition site; other site 159087011619 dimerization interface [polypeptide binding]; other site 159087011620 PAS domain S-box; Region: sensory_box; TIGR00229 159087011621 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 159087011622 putative active site [active] 159087011623 heme pocket [chemical binding]; other site 159087011624 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 159087011625 dimer interface [polypeptide binding]; other site 159087011626 phosphorylation site [posttranslational modification] 159087011627 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 159087011628 ATP binding site [chemical binding]; other site 159087011629 G-X-G motif; other site 159087011630 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 159087011631 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 159087011632 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087011633 catalytic loop [active] 159087011634 iron binding site [ion binding]; other site 159087011635 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 159087011636 FAD binding pocket [chemical binding]; other site 159087011637 FAD binding motif [chemical binding]; other site 159087011638 phosphate binding motif [ion binding]; other site 159087011639 beta-alpha-beta structure motif; other site 159087011640 NAD binding pocket [chemical binding]; other site 159087011641 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 159087011642 dimerization interface [polypeptide binding]; other site 159087011643 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 159087011644 Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent...; Region: Rieske_T4moC; cd03474 159087011645 [2Fe-2S] cluster binding site [ion binding]; other site 159087011646 Toluene-4-monooxygenase system protein B (TmoB); Region: TmoB; pfam06234 159087011647 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 159087011648 dinuclear metal binding motif [ion binding]; other site 159087011649 Cache domain; Region: Cache_1; pfam02743 159087011650 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087011651 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 159087011652 dimerization interface [polypeptide binding]; other site 159087011653 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 159087011654 dimer interface [polypeptide binding]; other site 159087011655 phosphorylation site [posttranslational modification] 159087011656 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 159087011657 ATP binding site [chemical binding]; other site 159087011658 Mg2+ binding site [ion binding]; other site 159087011659 G-X-G motif; other site 159087011660 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011661 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011662 active site 159087011663 phosphorylation site [posttranslational modification] 159087011664 intermolecular recognition site; other site 159087011665 dimerization interface [polypeptide binding]; other site 159087011666 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 159087011667 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 159087011668 putative active site [active] 159087011669 putative NTP binding site [chemical binding]; other site 159087011670 putative nucleic acid binding site [nucleotide binding]; other site 159087011671 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 159087011672 Transposase domain (DUF772); Region: DUF772; cl12084 159087011673 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 159087011674 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 159087011675 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087011676 putative active site [active] 159087011677 putative metal binding site [ion binding]; other site 159087011678 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 159087011679 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 159087011680 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087011681 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; cl12031 159087011682 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 159087011683 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087011684 Helix-turn-helix domains; Region: HTH; cl00088 159087011685 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 159087011686 putative effector binding pocket; other site 159087011687 putative dimerization interface [polypeptide binding]; other site 159087011688 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 159087011689 Uncharacterized conserved protein [Function unknown]; Region: COG2128 159087011690 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR6; cd08272 159087011691 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 159087011692 putative NAD(P) binding site [chemical binding]; other site 159087011693 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087011694 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087011695 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 159087011696 dimerization interface [polypeptide binding]; other site 159087011697 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 159087011698 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 159087011699 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 159087011700 dimer interface [polypeptide binding]; other site 159087011701 active site 159087011702 heme binding site [chemical binding]; other site 159087011703 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 159087011704 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 159087011705 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087011706 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 159087011707 DNA binding residues [nucleotide binding] 159087011708 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 159087011709 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 159087011710 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 159087011711 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 159087011712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011713 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 159087011714 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 159087011715 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 159087011716 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 159087011717 catalytic site [active] 159087011718 G-X2-G-X-G-K; other site 159087011719 PAS domain S-box; Region: sensory_box; TIGR00229 159087011720 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 159087011721 putative active site [active] 159087011722 heme pocket [chemical binding]; other site 159087011723 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 159087011724 dimer interface [polypeptide binding]; other site 159087011725 phosphorylation site [posttranslational modification] 159087011726 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 159087011727 ATP binding site [chemical binding]; other site 159087011728 Mg2+ binding site [ion binding]; other site 159087011729 G-X-G motif; other site 159087011730 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011731 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011732 active site 159087011733 phosphorylation site [posttranslational modification] 159087011734 intermolecular recognition site; other site 159087011735 dimerization interface [polypeptide binding]; other site 159087011736 hypothetical protein; Provisional; Region: PRK11820 159087011737 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 159087011738 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 159087011739 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087011740 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087011741 active site 159087011742 ATP binding site [chemical binding]; other site 159087011743 substrate binding site [chemical binding]; other site 159087011744 activation loop (A-loop); other site 159087011745 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087011746 active site 159087011747 ribonuclease PH; Reviewed; Region: rph; PRK00173 159087011748 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 159087011749 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 159087011750 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 159087011751 active site 159087011752 dimerization interface [polypeptide binding]; other site 159087011753 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 159087011754 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 159087011755 FeS/SAM binding site; other site 159087011756 HemN C-terminal region; Region: HemN_C; pfam06969 159087011757 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087011758 ligand binding site [chemical binding]; other site 159087011759 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 159087011760 ATP-binding cassette protein, ChvD family; Region: ABC_ABC_ChvD; TIGR03719 159087011761 SEC-C motif; Region: SEC-C; pfam02810 159087011762 hypothetical protein; Provisional; Region: PRK01842 159087011763 Putative exonuclease, RdgC; Region: RdgC; cl01122 159087011764 Cytochrome c; Region: Cytochrom_C; cl11414 159087011765 Cytochrome c; Region: Cytochrom_C; cl11414 159087011766 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 159087011767 S-adenosylmethionine binding site [chemical binding]; other site 159087011768 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 159087011769 ThiS interaction site; other site 159087011770 putative active site [active] 159087011771 tetramer interface [polypeptide binding]; other site 159087011772 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 159087011773 thiS-thiF/thiG interaction site; other site 159087011774 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 159087011775 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011776 NAD(P) binding site [chemical binding]; other site 159087011777 active site 159087011778 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 159087011779 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 159087011780 catalytic residues [active] 159087011781 hinge region; other site 159087011782 alpha helical domain; other site 159087011783 Sporulation related domain; Region: SPOR; cl10051 159087011784 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 159087011785 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 159087011786 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087011787 active site 159087011788 HIGH motif; other site 159087011789 nucleotide binding site [chemical binding]; other site 159087011790 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 159087011791 KMSK motif region; other site 159087011792 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 159087011793 tRNA binding surface [nucleotide binding]; other site 159087011794 anticodon binding site; other site 159087011795 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 159087011796 putative active site [active] 159087011797 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 159087011798 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011799 metal binding site [ion binding]; metal-binding site 159087011800 active site 159087011801 I-site; other site 159087011802 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 159087011803 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; cl15691 159087011804 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 159087011805 active site 159087011806 ATP binding site [chemical binding]; other site 159087011807 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 159087011808 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 159087011809 ATP binding site [chemical binding]; other site 159087011810 putative Mg++ binding site [ion binding]; other site 159087011811 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 159087011812 nucleotide binding region [chemical binding]; other site 159087011813 ATP-binding site [chemical binding]; other site 159087011814 Domain of unknown function DUF302; Region: DUF302; cl01364 159087011815 PAS fold; Region: PAS_4; pfam08448 159087011816 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 159087011817 putative active site [active] 159087011818 heme pocket [chemical binding]; other site 159087011819 bacterio-opsin activator; Provisional; Region: PRK13558 159087011820 PAS fold; Region: PAS_4; pfam08448 159087011821 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 159087011822 putative active site [active] 159087011823 heme pocket [chemical binding]; other site 159087011824 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 159087011825 dimer interface [polypeptide binding]; other site 159087011826 phosphorylation site [posttranslational modification] 159087011827 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 159087011828 ATP binding site [chemical binding]; other site 159087011829 Mg2+ binding site [ion binding]; other site 159087011830 G-X-G motif; other site 159087011831 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011832 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011833 active site 159087011834 phosphorylation site [posttranslational modification] 159087011835 intermolecular recognition site; other site 159087011836 dimerization interface [polypeptide binding]; other site 159087011837 Uncharacterized conserved protein [Function unknown]; Region: COG3287 159087011838 FIST N domain; Region: FIST; cl10701 159087011839 FIST C domain; Region: FIST_C; pfam10442 159087011840 Competence-damaged protein; Region: CinA; cl00666 159087011841 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 159087011842 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 159087011843 GTP binding site; other site 159087011844 Cytochrome c; Region: Cytochrom_C; cl11414 159087011845 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 159087011846 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087011847 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 159087011848 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 159087011849 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087011850 Walker A motif; other site 159087011851 ATP binding site [chemical binding]; other site 159087011852 Walker B motif; other site 159087011853 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 159087011854 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 159087011855 Walker A motif; other site 159087011856 ATP binding site [chemical binding]; other site 159087011857 Walker B motif; other site 159087011858 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 159087011859 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087011860 catalytic residue [active] 159087011861 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011862 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 159087011863 YGGT family; Region: YGGT; cl00508 159087011864 Uncharacterised ACR, YggU family COG1872; Region: DUF167; cl00811 159087011865 comEA protein; Region: comE; TIGR01259 159087011866 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 159087011867 dihydroorotase; Provisional; Region: PRK07627 159087011868 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 159087011869 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 159087011870 active site 159087011871 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 159087011872 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 159087011873 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011874 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 159087011875 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 includes...; Region: RuvC_resolvase; cl00243 159087011876 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 159087011877 DNA photolyase; Region: DNA_photolyase; pfam00875 159087011878 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 159087011879 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 159087011880 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 159087011881 putative binding surface; other site 159087011882 active site 159087011883 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087011884 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 159087011885 putative binding surface; other site 159087011886 active site 159087011887 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087011888 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 159087011889 ATP binding site [chemical binding]; other site 159087011890 Mg2+ binding site [ion binding]; other site 159087011891 G-X-G motif; other site 159087011892 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 159087011893 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011894 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011895 active site 159087011896 phosphorylation site [posttranslational modification] 159087011897 intermolecular recognition site; other site 159087011898 dimerization interface [polypeptide binding]; other site 159087011899 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087011900 Methyl-accepting chemotaxis protein (MCP) signaling domain; Region: MCPsignal; pfam00015 159087011901 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087011902 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011903 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011904 active site 159087011905 phosphorylation site [posttranslational modification] 159087011906 intermolecular recognition site; other site 159087011907 dimerization interface [polypeptide binding]; other site 159087011908 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011909 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087011910 active site 159087011911 phosphorylation site [posttranslational modification] 159087011912 intermolecular recognition site; other site 159087011913 dimerization interface [polypeptide binding]; other site 159087011914 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 159087011915 substrate binding site [chemical binding]; other site 159087011916 dimer interface [polypeptide binding]; other site 159087011917 ATP binding site [chemical binding]; other site 159087011918 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 159087011919 thiamine phosphate binding site [chemical binding]; other site 159087011920 active site 159087011921 pyrophosphate binding site [ion binding]; other site 159087011922 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 159087011923 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 159087011924 inhibitor-cofactor binding pocket; inhibition site 159087011925 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087011926 catalytic residue [active] 159087011927 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 159087011928 Permease family; Region: Xan_ur_permease; cl00967 159087011929 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 159087011930 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 159087011931 ligand binding site [chemical binding]; other site 159087011932 flexible hinge region; other site 159087011933 magnesium Mg(2+) and cobalt Co(2+) transport protein (corA); Region: corA; TIGR00383 159087011934 Transglycosylase; Region: Transgly; cl07896 159087011935 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 159087011936 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 159087011937 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 159087011938 shikimate binding site; other site 159087011939 NAD(P) binding site [chemical binding]; other site 159087011940 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 159087011941 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087011942 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 159087011943 RNB domain; Region: RNB; pfam00773 159087011944 Exoribonuclease R [Transcription]; Region: VacB; COG0557 159087011945 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 159087011946 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 159087011947 Bacitracin resistance protein BacA; Region: BacA; cl00858 159087011948 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087011949 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 159087011950 Helix-turn-helix domains; Region: HTH; cl00088 159087011951 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 159087011952 dimerization interface [polypeptide binding]; other site 159087011953 substrate binding pocket [chemical binding]; other site 159087011954 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087011955 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087011956 FtsX-like permease family; Region: FtsX; pfam02687 159087011957 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087011958 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 159087011959 Walker A/P-loop; other site 159087011960 ATP binding site [chemical binding]; other site 159087011961 Q-loop/lid; other site 159087011962 ABC transporter signature motif; other site 159087011963 Walker B; other site 159087011964 D-loop; other site 159087011965 H-loop/switch region; other site 159087011966 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087011967 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 159087011968 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 159087011969 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 159087011970 dimer interface [polypeptide binding]; other site 159087011971 ThiC family; Region: ThiC; cl08031 159087011972 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 159087011973 active site 159087011974 zinc binding site [ion binding]; other site 159087011975 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087011976 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087011977 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 159087011978 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 159087011979 S-adenosylmethionine binding site [chemical binding]; other site 159087011980 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains; Region: RHOD_2; cd01528 159087011981 active site residue [active] 159087011982 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 159087011983 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 159087011984 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 159087011985 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087011986 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 159087011987 putative active site [active] 159087011988 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 159087011989 putative metal binding site; other site 159087011990 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 159087011991 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 159087011992 putative NAD(P) binding site [chemical binding]; other site 159087011993 active site 159087011994 putative substrate binding site [chemical binding]; other site 159087011995 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 159087011996 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 159087011997 glutaminase active site [active] 159087011998 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 159087011999 dimer interface [polypeptide binding]; other site 159087012000 active site 159087012001 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 159087012002 dimer interface [polypeptide binding]; other site 159087012003 active site 159087012004 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 159087012005 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 159087012006 active site 159087012007 metal binding site [ion binding]; metal-binding site 159087012008 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087012009 putative acyl-acceptor binding pocket; other site 159087012010 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 159087012011 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 159087012012 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 159087012013 substrate binding site [chemical binding]; other site 159087012014 ATP binding site [chemical binding]; other site 159087012015 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 159087012016 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 159087012017 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 159087012018 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 159087012019 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087012020 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087012021 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 159087012022 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 159087012023 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 159087012024 carboxyltransferase (CT) interaction site; other site 159087012025 biotinylation site [posttranslational modification]; other site 159087012026 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 159087012027 trimer interface [polypeptide binding]; other site 159087012028 active site 159087012029 dimer interface [polypeptide binding]; other site 159087012030 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 159087012031 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087012032 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 159087012033 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 159087012034 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 159087012035 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 159087012036 N-terminal plug; other site 159087012037 ligand-binding site [chemical binding]; other site 159087012038 High-affinity nickel-transport protein; Region: NicO; cl00964 159087012039 PAS fold; Region: PAS_4; pfam08448 159087012040 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 159087012041 putative active site [active] 159087012042 heme pocket [chemical binding]; other site 159087012043 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012044 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 159087012045 dimer interface [polypeptide binding]; other site 159087012046 phosphorylation site [posttranslational modification] 159087012047 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 159087012048 ATP binding site [chemical binding]; other site 159087012049 G-X-G motif; other site 159087012050 nickel responsive regulator; Provisional; Region: PRK02967 159087012051 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15375 159087012052 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 159087012053 Domain of unknown function DUF59; Region: DUF59; cl00941 159087012054 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 159087012055 Walker A motif; other site 159087012056 ATP binding site [chemical binding]; other site 159087012057 Walker B motif; other site 159087012058 arginine finger; other site 159087012059 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 159087012060 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 159087012061 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 159087012062 hemerythrin-like metal-binding domain; Region: hemeryth_dom; TIGR02481 159087012063 Fic family protein [Function unknown]; Region: COG3177 159087012064 Fic/DOC family; Region: Fic; cl00960 159087012065 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 159087012066 Integrase core domain; Region: rve; cl01316 159087012067 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087012068 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087012069 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 159087012070 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087012071 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087012072 active site 159087012073 phosphorylation site [posttranslational modification] 159087012074 intermolecular recognition site; other site 159087012075 dimerization interface [polypeptide binding]; other site 159087012076 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 159087012077 Walker A motif; other site 159087012078 ATP binding site [chemical binding]; other site 159087012079 Walker B motif; other site 159087012080 arginine finger; other site 159087012081 Helix-turn-helix domains; Region: HTH; cl00088 159087012082 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 159087012083 HypX protein, N-terminal hydrolase domain; Region: FMT_core_HypX_N; cd08650 159087012084 putative active site [active] 159087012085 putative substrate binding site [chemical binding]; other site 159087012086 putative cosubstrate binding site; other site 159087012087 catalytic site [active] 159087012088 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 159087012089 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 159087012090 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 159087012091 substrate binding site [chemical binding]; other site 159087012092 oxyanion hole (OAH) forming residues; other site 159087012093 trimer interface [polypeptide binding]; other site 159087012094 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 159087012095 dimerization interface [polypeptide binding]; other site 159087012096 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 159087012097 ATP binding site [chemical binding]; other site 159087012098 Hydrogenase formation hypA family; Region: HypD; cl12072 159087012099 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypD; COG0409 159087012100 HupF/HypC family; Region: HupF_HypC; cl00394 159087012101 Protein of unknown function (DUF3457); Region: DUF3457; cl08122 159087012102 HupF/HypC family; Region: HupF_HypC; cl00394 159087012103 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 159087012104 Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing...; Region: H2MP; cl00477 159087012105 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087012106 Polysulphide reductase, NrfD; Region: NrfD; cl01295 159087012107 hydrogenase 2 protein HybA; Provisional; Region: PRK10882 159087012108 4Fe-4S binding domain; Region: Fer4; cl02805 159087012109 hydrogenase 2 small subunit; Provisional; Region: PRK10468 159087012110 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 159087012111 CHASE domain; Region: CHASE; cl01369 159087012112 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012113 metal binding site [ion binding]; metal-binding site 159087012114 active site 159087012115 I-site; other site 159087012116 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 159087012117 substrate binding pocket [chemical binding]; other site 159087012118 membrane-bound complex binding site; other site 159087012119 hinge residues; other site 159087012120 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 159087012121 Acylphosphatase; Region: Acylphosphatase; cl00551 159087012122 HypF finger; Region: zf-HYPF; pfam07503 159087012123 HypF finger; Region: zf-HYPF; pfam07503 159087012124 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 159087012125 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087012126 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; cl00418 159087012127 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 159087012128 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087012129 Protein of unknown function (DUF3457); Region: DUF3457; cl08122 159087012130 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 159087012131 Rubredoxin; Region: Rubredoxin; pfam00301 159087012132 iron binding site [ion binding]; other site 159087012133 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 159087012134 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the...; Region: HyaE; cd02965 159087012135 HupF/HypC family; Region: HupF_HypC; cl00394 159087012136 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 159087012137 putative substrate-binding site; other site 159087012138 nickel binding site [ion binding]; other site 159087012139 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 159087012140 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 159087012141 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 159087012142 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 159087012143 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 159087012144 FOG: CBS domain [General function prediction only]; Region: COG0517 159087012145 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087012146 FOG: CBS domain [General function prediction only]; Region: COG0517 159087012147 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087012148 PAS fold; Region: PAS_4; pfam08448 159087012149 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087012150 PAS domain S-box; Region: sensory_box; TIGR00229 159087012151 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 159087012152 PAS domain S-box; Region: sensory_box; TIGR00229 159087012153 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 159087012154 putative active site [active] 159087012155 heme pocket [chemical binding]; other site 159087012156 PAS domain S-box; Region: sensory_box; TIGR00229 159087012157 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 159087012158 putative active site [active] 159087012159 heme pocket [chemical binding]; other site 159087012160 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012161 metal binding site [ion binding]; metal-binding site 159087012162 active site 159087012163 I-site; other site 159087012164 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 159087012165 diguanylate cyclase; Provisional; Region: PRK09894 159087012166 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 159087012167 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087012168 Walker A/P-loop; other site 159087012169 ATP binding site [chemical binding]; other site 159087012170 Q-loop/lid; other site 159087012171 ABC transporter signature motif; other site 159087012172 Walker B; other site 159087012173 D-loop; other site 159087012174 H-loop/switch region; other site 159087012175 CcmB protein; Region: CcmB; cl01016 159087012176 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 159087012177 Heme exporter protein D (CcmD); Region: CcmD; cl11475 159087012178 CcmE; Region: CcmE; cl00994 159087012179 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 159087012180 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 159087012181 catalytic residues [active] 159087012182 central insert; other site 159087012183 Cytochrome C biogenesis protein; Region: CcmH; cl01179 159087012184 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 159087012185 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 159087012186 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 159087012187 binding surface 159087012188 TPR motif; other site 159087012189 ferredoxin-type protein; Provisional; Region: PRK10194 159087012190 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 159087012191 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087012192 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 159087012193 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 159087012194 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 159087012195 carboxyltransferase (CT) interaction site; other site 159087012196 biotinylation site [posttranslational modification]; other site 159087012197 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 159087012198 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; cl14780 159087012199 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; cl14780 159087012200 membrane ATPase/protein kinase; Provisional; Region: PRK09435 159087012201 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 159087012202 Walker A; other site 159087012203 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087012204 G4 box; other site 159087012205 G5 box; other site 159087012206 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 159087012207 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 159087012208 active site 159087012209 substrate binding site [chemical binding]; other site 159087012210 coenzyme B12 binding site [chemical binding]; other site 159087012211 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 159087012212 B12 binding site [chemical binding]; other site 159087012213 cobalt ligand [ion binding]; other site 159087012214 Transcriptional regulators [Transcription]; Region: GntR; COG1802 159087012215 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087012216 DNA-binding site [nucleotide binding]; DNA binding site 159087012217 FCD domain; Region: FCD; cl11656 159087012218 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 159087012219 PAS fold; Region: PAS_3; pfam08447 159087012220 putative active site [active] 159087012221 heme pocket [chemical binding]; other site 159087012222 Sodium:solute symporter family; Region: SSF; cl00456 159087012223 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 159087012224 Protein of unknown function, DUF485; Region: DUF485; cl01231 159087012225 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 159087012226 enoyl-CoA hydratase; Provisional; Region: PRK06127 159087012227 substrate binding site [chemical binding]; other site 159087012228 oxyanion hole (OAH) forming residues; other site 159087012229 trimer interface [polypeptide binding]; other site 159087012230 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087012231 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 159087012232 Acyl transferase domain; Region: Acyl_transf_1; cl08282 159087012233 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 159087012234 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; cl07913 159087012235 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; cl14780 159087012236 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; cl14780 159087012237 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 159087012238 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 159087012239 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 159087012240 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 159087012241 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087012242 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087012243 Transcriptional regulators [Transcription]; Region: GntR; COG1802 159087012244 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087012245 DNA-binding site [nucleotide binding]; DNA binding site 159087012246 FCD domain; Region: FCD; cl11656 159087012247 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 159087012248 EVE domain; Region: EVE; cl00728 159087012249 Cell division protein ZapA; Region: ZapA; cl01146 159087012250 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 159087012251 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 159087012252 N-terminal plug; other site 159087012253 ligand-binding site [chemical binding]; other site 159087012254 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 159087012255 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 159087012256 N-terminal plug; other site 159087012257 ligand-binding site [chemical binding]; other site 159087012258 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 159087012259 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 159087012260 ABC-ATPase subunit interface; other site 159087012261 dimer interface [polypeptide binding]; other site 159087012262 putative PBP binding regions; other site 159087012263 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 159087012264 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 159087012265 Walker A/P-loop; other site 159087012266 ATP binding site [chemical binding]; other site 159087012267 Q-loop/lid; other site 159087012268 ABC transporter signature motif; other site 159087012269 Walker B; other site 159087012270 D-loop; other site 159087012271 H-loop/switch region; other site 159087012272 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 159087012273 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087012274 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 159087012275 homodimer interface [polypeptide binding]; other site 159087012276 Walker A motif; other site 159087012277 ATP binding site [chemical binding]; other site 159087012278 hydroxycobalamin binding site [chemical binding]; other site 159087012279 Walker B motif; other site 159087012280 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 159087012281 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; cd01983 159087012282 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 159087012283 catalytic triad [active] 159087012284 Tim44-like domain; Region: Tim44; cl09208 159087012285 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 159087012286 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012287 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 159087012288 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 159087012289 dimer interface [polypeptide binding]; other site 159087012290 phosphorylation site [posttranslational modification] 159087012291 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 159087012292 ATP binding site [chemical binding]; other site 159087012293 Mg2+ binding site [ion binding]; other site 159087012294 G-X-G motif; other site 159087012295 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012296 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087012297 active site 159087012298 phosphorylation site [posttranslational modification] 159087012299 intermolecular recognition site; other site 159087012300 dimerization interface [polypeptide binding]; other site 159087012301 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 159087012302 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 159087012303 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 159087012304 YeeE/YedE family (DUF395); Region: DUF395; cl01018 159087012305 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 159087012306 Ligand Binding Site [chemical binding]; other site 159087012307 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087012308 Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; Region: PBP1_Nba_like; cd06359 159087012309 putative ligand binding site [chemical binding]; other site 159087012310 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087012311 TM-ABC transporter signature motif; other site 159087012312 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087012313 TM-ABC transporter signature motif; other site 159087012314 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087012315 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087012316 Walker A/P-loop; other site 159087012317 ATP binding site [chemical binding]; other site 159087012318 Q-loop/lid; other site 159087012319 ABC transporter signature motif; other site 159087012320 Walker B; other site 159087012321 D-loop; other site 159087012322 H-loop/switch region; other site 159087012323 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087012324 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087012325 Walker A/P-loop; other site 159087012326 ATP binding site [chemical binding]; other site 159087012327 Q-loop/lid; other site 159087012328 ABC transporter signature motif; other site 159087012329 Walker B; other site 159087012330 D-loop; other site 159087012331 H-loop/switch region; other site 159087012332 PAS domain S-box; Region: sensory_box; TIGR00229 159087012333 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 159087012334 putative active site [active] 159087012335 heme pocket [chemical binding]; other site 159087012336 PAS domain S-box; Region: sensory_box; TIGR00229 159087012337 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 159087012338 putative active site [active] 159087012339 heme pocket [chemical binding]; other site 159087012340 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012341 metal binding site [ion binding]; metal-binding site 159087012342 active site 159087012343 I-site; other site 159087012344 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 159087012345 PilZ domain; Region: PilZ; cl01260 159087012346 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Region: rSAM_QueE_Clost; TIGR03963 159087012347 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; cl15367 159087012348 PV-1 protein (PLVAP); Region: PV-1; pfam06637 159087012349 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 159087012350 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087012351 ligand binding site [chemical binding]; other site 159087012352 translocation protein TolB; Provisional; Region: tolB; PRK02889 159087012353 TolB amino-terminal domain; Region: TolB_N; cl00639 159087012354 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087012355 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087012356 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087012357 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087012358 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087012359 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 159087012360 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 159087012361 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 159087012362 active site 159087012363 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 159087012364 Uncharacterized protein conserved in bacteria (DUF2330); Region: DUF2330; cl01827 159087012365 Holliday junction DNA helicase, RuvB subunit; Region: ruvB; TIGR00635 159087012366 Domain of unknown function DUF20; Region: UPF0118; cl00465 159087012367 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 159087012368 RuvA N terminal domain; Region: RuvA_N; pfam01330 159087012369 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 159087012370 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 includes...; Region: RuvC_resolvase; cd00529 159087012371 active site 159087012372 putative DNA-binding cleft [nucleotide binding]; other site 159087012373 dimer interface [polypeptide binding]; other site 159087012374 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 159087012375 EamA-like transporter family; Region: EamA; cl01037 159087012376 Domain of unknown function DUF28; Region: DUF28; cl00361 159087012377 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 159087012378 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 159087012379 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 159087012380 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; cl02712 159087012381 Bacterial SH3 domain; Region: SH3_3; cl02551 159087012382 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 159087012383 putative hydrophobic ligand binding site [chemical binding]; other site 159087012384 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 159087012385 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 159087012386 EamA-like transporter family; Region: EamA; cl01037 159087012387 EamA-like transporter family; Region: EamA; cl01037 159087012388 Chorismate mutase type II; Region: CM_2; cl00693 159087012389 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 159087012390 Helix-turn-helix domains; Region: HTH; cl00088 159087012391 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 159087012392 dimerization interface [polypeptide binding]; other site 159087012393 substrate binding pocket [chemical binding]; other site 159087012394 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 159087012395 homodimer interface [polypeptide binding]; other site 159087012396 substrate-cofactor binding pocket; other site 159087012397 Aminotransferase class IV; Region: Aminotran_4; pfam01063 159087012398 catalytic residue [active] 159087012399 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087012400 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087012401 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087012402 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 159087012403 putative dimerization interface [polypeptide binding]; other site 159087012404 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 159087012405 EamA-like transporter family; Region: EamA; cl01037 159087012406 EamA-like transporter family; Region: EamA; cl01037 159087012407 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 159087012408 active pocket/dimerization site; other site 159087012409 active site 159087012410 phosphorylation site [posttranslational modification] 159087012411 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 159087012412 dimerization domain swap beta strand [polypeptide binding]; other site 159087012413 regulatory protein interface [polypeptide binding]; other site 159087012414 active site 159087012415 regulatory phosphorylation site [posttranslational modification]; other site 159087012416 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 159087012417 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 159087012418 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 159087012419 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; cl09155 159087012420 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 159087012421 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087012422 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012423 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 159087012424 dimerization interface [polypeptide binding]; other site 159087012425 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 159087012426 dimer interface [polypeptide binding]; other site 159087012427 phosphorylation site [posttranslational modification] 159087012428 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 159087012429 ATP binding site [chemical binding]; other site 159087012430 Mg2+ binding site [ion binding]; other site 159087012431 G-X-G motif; other site 159087012432 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012433 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087012434 active site 159087012435 phosphorylation site [posttranslational modification] 159087012436 intermolecular recognition site; other site 159087012437 dimerization interface [polypeptide binding]; other site 159087012438 Sel1 repeat; Region: Sel1; cl02723 159087012439 Sel1 repeat; Region: Sel1; cl02723 159087012440 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 159087012441 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 159087012442 N-terminal plug; other site 159087012443 ligand-binding site [chemical binding]; other site 159087012444 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; cl00047 159087012445 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 159087012446 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 159087012447 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 159087012448 N-terminal plug; other site 159087012449 ligand-binding site [chemical binding]; other site 159087012450 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 159087012451 catalytic residues [active] 159087012452 Gram-negative bacterial tonB protein; Region: TonB; cl10048 159087012453 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 159087012454 Lumazine binding domain; Region: Lum_binding; pfam00677 159087012455 Lumazine binding domain; Region: Lum_binding; pfam00677 159087012456 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087012457 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087012458 putative ligand binding site [chemical binding]; other site 159087012459 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087012460 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087012461 putative ligand binding site [chemical binding]; other site 159087012462 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087012463 TM-ABC transporter signature motif; other site 159087012464 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087012465 TM-ABC transporter signature motif; other site 159087012466 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087012467 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 159087012468 Walker A/P-loop; other site 159087012469 ATP binding site [chemical binding]; other site 159087012470 Q-loop/lid; other site 159087012471 ABC transporter signature motif; other site 159087012472 Walker B; other site 159087012473 D-loop; other site 159087012474 H-loop/switch region; other site 159087012475 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087012476 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 159087012477 Walker A/P-loop; other site 159087012478 ATP binding site [chemical binding]; other site 159087012479 Q-loop/lid; other site 159087012480 ABC transporter signature motif; other site 159087012481 Walker B; other site 159087012482 D-loop; other site 159087012483 H-loop/switch region; other site 159087012484 membrane protein P6; Region: PHA01399 159087012485 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK12323 159087012486 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012487 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087012488 active site 159087012489 phosphorylation site [posttranslational modification] 159087012490 intermolecular recognition site; other site 159087012491 dimerization interface [polypeptide binding]; other site 159087012492 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 159087012493 binding surface 159087012494 TPR motif; other site 159087012495 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087012496 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 159087012497 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 159087012498 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335; cl15440 159087012499 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 159087012500 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; cl12011 159087012501 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 159087012502 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 159087012503 P-loop; other site 159087012504 Magnesium ion binding site [ion binding]; other site 159087012505 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 159087012506 Magnesium ion binding site [ion binding]; other site 159087012507 ParB-like partition proteins; Region: parB_part; TIGR00180 159087012508 ParB-like nuclease domain; Region: ParBc; cl02129 159087012509 ATP synthase A chain; Region: ATP-synt_A; cl00413 159087012510 ATP synthase subunit C; Region: ATP-synt_C; cl00466 159087012511 Mitochondrial ATP synthase B chain precursor (ATP-synt_B); Region: Mt_ATP-synt_B; cl07975 159087012512 ATP synthase B/B' CF(0); Region: ATP-synt_B; pfam00430 159087012513 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl15360 159087012514 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 159087012515 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 159087012516 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 159087012517 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 159087012518 beta subunit interaction interface [polypeptide binding]; other site 159087012519 Walker A motif; other site 159087012520 ATP binding site [chemical binding]; other site 159087012521 Walker B motif; other site 159087012522 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 159087012523 NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]; Region: NuoC; cl00365 159087012524 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 159087012525 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 159087012526 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 159087012527 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 159087012528 alpha subunit interaction interface [polypeptide binding]; other site 159087012529 Walker A motif; other site 159087012530 ATP binding site [chemical binding]; other site 159087012531 Walker B motif; other site 159087012532 inhibitor binding site; inhibition site 159087012533 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 159087012534 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 159087012535 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 159087012536 SCP-2 sterol transfer family; Region: SCP2; cl01225 159087012537 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 159087012538 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 159087012539 S-adenosylmethionine binding site [chemical binding]; other site 159087012540 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; cl12011 159087012541 Protein of unknown function (DUF971); Region: DUF971; cl01414 159087012542 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 159087012543 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 159087012544 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087012545 FAD binding domain; Region: FAD_binding_4; pfam01565 159087012546 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 159087012547 Heterodisulfide reductase, subunit C [Energy production and conversion]; Region: HdrC; COG1150 159087012548 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087012549 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 159087012550 threonine dehydratase; Reviewed; Region: PRK09224 159087012551 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 159087012552 tetramer interface [polypeptide binding]; other site 159087012553 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087012554 catalytic residue [active] 159087012555 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 159087012556 putative Ile/Val binding site [chemical binding]; other site 159087012557 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 159087012558 putative Ile/Val binding site [chemical binding]; other site 159087012559 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 159087012560 AzlC protein; Region: AzlC; cl00570 159087012561 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 159087012562 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 159087012563 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 159087012564 dimer interface [polypeptide binding]; other site 159087012565 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087012566 catalytic residue [active] 159087012567 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 159087012568 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 159087012569 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087012570 homodimer interface [polypeptide binding]; other site 159087012571 catalytic residue [active] 159087012572 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 159087012573 lytic murein transglycosylase; Provisional; Region: PRK11619 159087012574 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 catalyze...; Region: LT_GEWL; cd00254 159087012575 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087012576 catalytic residue [active] 159087012577 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 159087012578 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 159087012579 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 159087012580 putative NAD(P) binding site [chemical binding]; other site 159087012581 active site 159087012582 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 159087012583 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 159087012584 active site 159087012585 NTP binding site [chemical binding]; other site 159087012586 metal binding triad [ion binding]; metal-binding site 159087012587 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 159087012588 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 159087012589 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 159087012590 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; cl12031 159087012591 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087012592 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; cl12031 159087012593 Putative motility protein; Region: YjfB_motility; pfam14070 159087012594 Uncharacterized conserved protein [Function unknown]; Region: COG1565 159087012595 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 159087012596 FIST N domain; Region: FIST; cl10701 159087012597 Uncharacterized conserved protein [Function unknown]; Region: COG3287 159087012598 FIST C domain; Region: FIST_C; pfam10442 159087012599 PAS domain S-box; Region: sensory_box; TIGR00229 159087012600 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 159087012601 putative active site [active] 159087012602 heme pocket [chemical binding]; other site 159087012603 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087012604 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 159087012605 putative active site [active] 159087012606 heme pocket [chemical binding]; other site 159087012607 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 159087012608 dimer interface [polypeptide binding]; other site 159087012609 phosphorylation site [posttranslational modification] 159087012610 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 159087012611 ATP binding site [chemical binding]; other site 159087012612 Mg2+ binding site [ion binding]; other site 159087012613 G-X-G motif; other site 159087012614 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087012615 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012616 active site 159087012617 phosphorylation site [posttranslational modification] 159087012618 intermolecular recognition site; other site 159087012619 dimerization interface [polypeptide binding]; other site 159087012620 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012621 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 159087012622 active site 159087012623 phosphorylation site [posttranslational modification] 159087012624 intermolecular recognition site; other site 159087012625 dimerization interface [polypeptide binding]; other site 159087012626 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 159087012627 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 159087012628 Ligand Binding Site [chemical binding]; other site 159087012629 cyclase homology domain; Region: CHD; cd07302 159087012630 nucleotidyl binding site; other site 159087012631 metal binding site [ion binding]; metal-binding site 159087012632 dimer interface [polypeptide binding]; other site 159087012633 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087012634 phosphopeptide binding site; other site 159087012635 Hpr(Ser) kinase/phosphatase; Region: hpr-ser; TIGR00679 159087012636 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 159087012637 active site 159087012638 phosphorylation site [posttranslational modification] 159087012639 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 A site; Region: RaiA; cd00552 159087012640 30S subunit binding site; other site 159087012641 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 159087012642 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 159087012643 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 159087012644 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 159087012645 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 159087012646 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 159087012647 Walker A/P-loop; other site 159087012648 ATP binding site [chemical binding]; other site 159087012649 Q-loop/lid; other site 159087012650 ABC transporter signature motif; other site 159087012651 Walker B; other site 159087012652 D-loop; other site 159087012653 H-loop/switch region; other site 159087012654 RecX family; Region: RecX; cl00936 159087012655 recombinase A; Provisional; Region: recA; PRK09354 159087012656 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 159087012657 hexamer interface [polypeptide binding]; other site 159087012658 Walker A motif; other site 159087012659 ATP binding site [chemical binding]; other site 159087012660 Walker B motif; other site 159087012661 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 159087012662 active site 159087012663 Sodium:solute symporter family; Region: SSF; cl00456 159087012664 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 159087012665 VanZ like family; Region: VanZ; cl01971 159087012666 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 159087012667 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 159087012668 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087012669 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087012670 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 159087012671 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 159087012672 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 159087012673 dimer interface [polypeptide binding]; other site 159087012674 [2Fe-2S] cluster binding site [ion binding]; other site 159087012675 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 159087012676 nodulation ABC transporter NodI; Provisional; Region: PRK13537 159087012677 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 159087012678 Walker A/P-loop; other site 159087012679 ATP binding site [chemical binding]; other site 159087012680 Q-loop/lid; other site 159087012681 ABC transporter signature motif; other site 159087012682 Walker B; other site 159087012683 D-loop; other site 159087012684 H-loop/switch region; other site 159087012685 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 159087012686 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 159087012687 active site 159087012688 motif I; other site 159087012689 motif II; other site 159087012690 2-phosphosulpholactate phosphatase; Region: 2-ph_phosp; cl00895 159087012691 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 159087012692 B12 binding site [chemical binding]; other site 159087012693 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 159087012694 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 159087012695 FeS/SAM binding site; other site 159087012696 HDOD domain; Region: HDOD; pfam08668 159087012697 ABC-2 type transporter; Region: ABC2_membrane; cl11417 159087012698 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 159087012699 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 159087012700 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 159087012701 LysE type translocator; Region: LysE; cl00565 159087012702 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 159087012703 DsbD alpha interface [polypeptide binding]; other site 159087012704 catalytic residues [active] 159087012705 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 159087012706 active site 159087012707 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087012708 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 159087012709 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 159087012710 dimer interface [polypeptide binding]; other site 159087012711 active site 159087012712 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087012713 Predicted membrane protein [Function unknown]; Region: COG4648 159087012714 acetate--CoA ligase; Provisional; Region: PLN03052 159087012715 Acyl-protein synthetase, LuxE; Region: LuxE; cl15695 159087012716 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 159087012717 active site 2 [active] 159087012718 dimer interface [polypeptide binding]; other site 159087012719 active site 1 [active] 159087012720 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 159087012721 putative acyl-acceptor binding pocket; other site 159087012722 Predicted exporter [General function prediction only]; Region: COG4258 159087012723 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 159087012724 NodB motif; other site 159087012725 active site 159087012726 catalytic site [active] 159087012727 metal binding site [ion binding]; metal-binding site 159087012728 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 159087012729 S-adenosylmethionine binding site [chemical binding]; other site 159087012730 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 159087012731 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 159087012732 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087012733 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087012734 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087012735 putative ligand binding site [chemical binding]; other site 159087012736 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 159087012737 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 159087012738 dimer interface [polypeptide binding]; other site 159087012739 active site 159087012740 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 159087012741 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 159087012742 putative active site 1 [active] 159087012743 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087012744 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087012745 NAD(P) binding site [chemical binding]; other site 159087012746 active site 159087012747 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 159087012748 catalytic residues [active] 159087012749 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087012750 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 159087012751 HPP family; Region: HPP; pfam04982 159087012752 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 159087012753 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 159087012754 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 159087012755 Ligand binding site; other site 159087012756 Putative Catalytic site; other site 159087012757 DXD motif; other site 159087012758 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087012759 putative acyl-acceptor binding pocket; other site 159087012760 MltA-interacting protein MipA; Region: MipA; cl01504 159087012761 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_5; cd06153 159087012762 homotrimer interaction site [polypeptide binding]; other site 159087012763 putative active site [active] 159087012764 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 159087012765 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087012766 magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; Region: BchE; TIGR02026 159087012767 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 159087012768 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 159087012769 FeS/SAM binding site; other site 159087012770 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 159087012771 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 159087012772 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 159087012773 G1 box; other site 159087012774 GTP/Mg2+ binding site [chemical binding]; other site 159087012775 Switch I region; other site 159087012776 G2 box; other site 159087012777 Switch II region; other site 159087012778 G3 box; other site 159087012779 G4 box; other site 159087012780 G5 box; other site 159087012781 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 159087012782 membrane protein insertase; Provisional; Region: PRK01318 159087012783 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 159087012784 Domain of unknown function DUF37; Region: DUF37; cl00506 159087012785 Ribonuclease P; Region: Ribonuclease_P; cl00457 159087012786 Ribosomal protein L34; Region: Ribosomal_L34; cl00370