-- dump date 20140619_144018 -- class Genbank::misc_feature -- table misc_feature_note -- id note 265072000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 265072000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 265072000003 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 265072000004 Walker A motif; other site 265072000005 ATP binding site [chemical binding]; other site 265072000006 Walker B motif; other site 265072000007 arginine finger; other site 265072000008 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 265072000009 DnaA box-binding interface [nucleotide binding]; other site 265072000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 265072000011 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 265072000012 putative DNA binding surface [nucleotide binding]; other site 265072000013 dimer interface [polypeptide binding]; other site 265072000014 beta-clamp/clamp loader binding surface; other site 265072000015 beta-clamp/translesion DNA polymerase binding surface; other site 265072000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 265072000017 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072000018 Mg2+ binding site [ion binding]; other site 265072000019 G-X-G motif; other site 265072000020 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 265072000021 anchoring element; other site 265072000022 dimer interface [polypeptide binding]; other site 265072000023 ATP binding site [chemical binding]; other site 265072000024 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 265072000025 active site 265072000026 putative metal-binding site [ion binding]; other site 265072000027 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 265072000028 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 265072000029 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 265072000030 Sulfate transporter family; Region: Sulfate_transp; pfam00916 265072000031 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 265072000032 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 265072000033 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 265072000034 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 265072000035 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_8; cd07817 265072000036 putative hydrophobic ligand binding site [chemical binding]; other site 265072000037 DNA polymerase IV; Provisional; Region: PRK14133 265072000038 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 265072000039 active site 265072000040 DNA binding site [nucleotide binding] 265072000041 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 265072000042 TAP-like protein; Region: Abhydrolase_4; pfam08386 265072000043 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 265072000044 BON domain; Region: BON; pfam04972 265072000045 malate:quinone oxidoreductase; Validated; Region: PRK05257 265072000046 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 265072000047 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 265072000048 methionine sulfoxide reductase B; Provisional; Region: PRK00222 265072000049 SelR domain; Region: SelR; pfam01641 265072000050 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 265072000051 Coenzyme A binding pocket [chemical binding]; other site 265072000052 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 265072000053 IHF dimer interface [polypeptide binding]; other site 265072000054 IHF - DNA interface [nucleotide binding]; other site 265072000055 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 265072000056 Mechanosensitive ion channel; Region: MS_channel; pfam00924 265072000057 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 265072000058 HPP family; Region: HPP; pfam04982 265072000059 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 265072000060 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 265072000061 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072000062 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072000063 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 265072000064 dimerization interface [polypeptide binding]; other site 265072000065 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 265072000066 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 265072000067 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 265072000068 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 265072000069 DNA methylase; Region: N6_N4_Mtase; cl17433 265072000070 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 265072000071 S-adenosylmethionine binding site [chemical binding]; other site 265072000072 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 265072000073 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 265072000074 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 265072000075 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 265072000076 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 265072000077 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 265072000078 carboxyltransferase (CT) interaction site; other site 265072000079 biotinylation site [posttranslational modification]; other site 265072000080 Dehydroquinase class II; Region: DHquinase_II; pfam01220 265072000081 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 265072000082 trimer interface [polypeptide binding]; other site 265072000083 active site 265072000084 dimer interface [polypeptide binding]; other site 265072000085 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 265072000086 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072000087 catalytic residues [active] 265072000088 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 265072000089 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 265072000090 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 265072000091 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 265072000092 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 265072000093 DsbD alpha interface [polypeptide binding]; other site 265072000094 catalytic residues [active] 265072000095 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 265072000096 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 265072000097 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 265072000098 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 265072000099 catalytic loop [active] 265072000100 iron binding site [ion binding]; other site 265072000101 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 265072000102 FAD binding pocket [chemical binding]; other site 265072000103 FAD binding motif [chemical binding]; other site 265072000104 phosphate binding motif [ion binding]; other site 265072000105 beta-alpha-beta structure motif; other site 265072000106 NAD binding pocket [chemical binding]; other site 265072000107 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 265072000108 HemY protein N-terminus; Region: HemY_N; pfam07219 265072000109 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 265072000110 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 265072000111 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 265072000112 active site 265072000113 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 265072000114 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 265072000115 domain interfaces; other site 265072000116 active site 265072000117 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 265072000118 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072000119 active site 265072000120 phosphorylation site [posttranslational modification] 265072000121 intermolecular recognition site; other site 265072000122 dimerization interface [polypeptide binding]; other site 265072000123 LytTr DNA-binding domain; Region: LytTR; smart00850 265072000124 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 265072000125 Histidine kinase; Region: His_kinase; pfam06580 265072000126 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 265072000127 ATP binding site [chemical binding]; other site 265072000128 Mg2+ binding site [ion binding]; other site 265072000129 G-X-G motif; other site 265072000130 argininosuccinate lyase; Provisional; Region: PRK00855 265072000131 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 265072000132 active sites [active] 265072000133 tetramer interface [polypeptide binding]; other site 265072000134 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072000135 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072000136 metal binding site [ion binding]; metal-binding site 265072000137 active site 265072000138 I-site; other site 265072000139 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 265072000140 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 265072000141 FeS/SAM binding site; other site 265072000142 HemN C-terminal domain; Region: HemN_C; pfam06969 265072000143 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 265072000144 active site 265072000145 dimerization interface [polypeptide binding]; other site 265072000146 ribonuclease PH; Reviewed; Region: rph; PRK00173 265072000147 Ribonuclease PH; Region: RNase_PH_bact; cd11362 265072000148 hexamer interface [polypeptide binding]; other site 265072000149 active site 265072000150 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 265072000151 active site 265072000152 Protein kinase domain; Region: Pkinase; pfam00069 265072000153 Catalytic domain of Protein Kinases; Region: PKc; cd00180 265072000154 active site 265072000155 ATP binding site [chemical binding]; other site 265072000156 substrate binding site [chemical binding]; other site 265072000157 activation loop (A-loop); other site 265072000158 hypothetical protein; Provisional; Region: PRK11820 265072000159 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 265072000160 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 265072000161 hypothetical protein; Provisional; Region: PRK14013 265072000162 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 265072000163 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 265072000164 catalytic site [active] 265072000165 G-X2-G-X-G-K; other site 265072000166 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 265072000167 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 265072000168 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072000169 Zn2+ binding site [ion binding]; other site 265072000170 Mg2+ binding site [ion binding]; other site 265072000171 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 265072000172 synthetase active site [active] 265072000173 NTP binding site [chemical binding]; other site 265072000174 metal binding site [ion binding]; metal-binding site 265072000175 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 265072000176 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 265072000177 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 265072000178 homotrimer interaction site [polypeptide binding]; other site 265072000179 putative active site [active] 265072000180 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 265072000181 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 265072000182 generic binding surface II; other site 265072000183 ssDNA binding site; other site 265072000184 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 265072000185 ATP binding site [chemical binding]; other site 265072000186 putative Mg++ binding site [ion binding]; other site 265072000187 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 265072000188 nucleotide binding region [chemical binding]; other site 265072000189 ATP-binding site [chemical binding]; other site 265072000190 Chorismate lyase; Region: Chor_lyase; cl01230 265072000191 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 265072000192 UbiA prenyltransferase family; Region: UbiA; pfam01040 265072000193 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 265072000194 23S rRNA interface [nucleotide binding]; other site 265072000195 L3 interface [polypeptide binding]; other site 265072000196 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 265072000197 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 265072000198 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 265072000199 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 265072000200 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 265072000201 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 265072000202 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 265072000203 dimer interface [polypeptide binding]; other site 265072000204 active site 265072000205 citrylCoA binding site [chemical binding]; other site 265072000206 NADH binding [chemical binding]; other site 265072000207 cationic pore residues; other site 265072000208 oxalacetate/citrate binding site [chemical binding]; other site 265072000209 coenzyme A binding site [chemical binding]; other site 265072000210 catalytic triad [active] 265072000211 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 265072000212 putative peptidase; Provisional; Region: PRK11649 265072000213 Peptidase family M23; Region: Peptidase_M23; pfam01551 265072000214 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 265072000215 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 265072000216 active site 265072000217 HIGH motif; other site 265072000218 dimer interface [polypeptide binding]; other site 265072000219 KMSKS motif; other site 265072000220 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 265072000221 RNA binding surface [nucleotide binding]; other site 265072000222 ribosome maturation protein RimP; Reviewed; Region: PRK00092 265072000223 Sm and related proteins; Region: Sm_like; cl00259 265072000224 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 265072000225 putative oligomer interface [polypeptide binding]; other site 265072000226 putative RNA binding site [nucleotide binding]; other site 265072000227 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 265072000228 NusA N-terminal domain; Region: NusA_N; pfam08529 265072000229 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 265072000230 RNA binding site [nucleotide binding]; other site 265072000231 homodimer interface [polypeptide binding]; other site 265072000232 NusA-like KH domain; Region: KH_5; pfam13184 265072000233 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 265072000234 G-X-X-G motif; other site 265072000235 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 265072000236 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 265072000237 translation initiation factor IF-2; Region: IF-2; TIGR00487 265072000238 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 265072000239 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 265072000240 G1 box; other site 265072000241 putative GEF interaction site [polypeptide binding]; other site 265072000242 GTP/Mg2+ binding site [chemical binding]; other site 265072000243 Switch I region; other site 265072000244 G2 box; other site 265072000245 G3 box; other site 265072000246 Switch II region; other site 265072000247 G4 box; other site 265072000248 G5 box; other site 265072000249 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 265072000250 Translation-initiation factor 2; Region: IF-2; pfam11987 265072000251 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 265072000252 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 265072000253 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 265072000254 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 265072000255 RNA binding site [nucleotide binding]; other site 265072000256 active site 265072000257 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 265072000258 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 265072000259 16S/18S rRNA binding site [nucleotide binding]; other site 265072000260 S13e-L30e interaction site [polypeptide binding]; other site 265072000261 25S rRNA binding site [nucleotide binding]; other site 265072000262 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 265072000263 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 265072000264 RNase E interface [polypeptide binding]; other site 265072000265 trimer interface [polypeptide binding]; other site 265072000266 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 265072000267 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 265072000268 RNase E interface [polypeptide binding]; other site 265072000269 trimer interface [polypeptide binding]; other site 265072000270 active site 265072000271 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 265072000272 putative nucleic acid binding region [nucleotide binding]; other site 265072000273 G-X-X-G motif; other site 265072000274 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 265072000275 RNA binding site [nucleotide binding]; other site 265072000276 domain interface; other site 265072000277 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 265072000278 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 265072000279 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 265072000280 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 265072000281 homodimer interface [polypeptide binding]; other site 265072000282 NADP binding site [chemical binding]; other site 265072000283 substrate binding site [chemical binding]; other site 265072000284 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072000285 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 265072000286 active site 265072000287 phosphorylation site [posttranslational modification] 265072000288 intermolecular recognition site; other site 265072000289 dimerization interface [polypeptide binding]; other site 265072000290 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 265072000291 Walker A motif; other site 265072000292 ATP binding site [chemical binding]; other site 265072000293 Walker B motif; other site 265072000294 arginine finger; other site 265072000295 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072000296 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 265072000297 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 265072000298 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072000299 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 265072000300 binding surface 265072000301 TPR motif; other site 265072000302 TPR repeat; Region: TPR_11; pfam13414 265072000303 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 265072000304 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 265072000305 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 265072000306 Walker A motif; other site 265072000307 ATP binding site [chemical binding]; other site 265072000308 Walker B motif; other site 265072000309 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 265072000310 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072000311 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072000312 ABC1 family; Region: ABC1; cl17513 265072000313 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 265072000314 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 265072000315 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 265072000316 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 265072000317 ATP binding site [chemical binding]; other site 265072000318 substrate interface [chemical binding]; other site 265072000319 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 265072000320 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 265072000321 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 265072000322 LemA family; Region: LemA; cl00742 265072000323 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 265072000324 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 265072000325 HIGH motif; other site 265072000326 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 265072000327 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 265072000328 active site 265072000329 KMSKS motif; other site 265072000330 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 265072000331 tRNA binding surface [nucleotide binding]; other site 265072000332 anticodon binding site; other site 265072000333 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 265072000334 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 265072000335 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 265072000336 CPxP motif; other site 265072000337 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 265072000338 active site residue [active] 265072000339 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 265072000340 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 265072000341 N-terminal plug; other site 265072000342 ligand-binding site [chemical binding]; other site 265072000343 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 265072000344 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 265072000345 Sel1-like repeats; Region: SEL1; smart00671 265072000346 Sel1-like repeats; Region: SEL1; smart00671 265072000347 Sel1-like repeats; Region: SEL1; smart00671 265072000348 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 265072000349 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 265072000350 putative dimer interface [polypeptide binding]; other site 265072000351 active site pocket [active] 265072000352 putative cataytic base [active] 265072000353 cobalamin synthase; Reviewed; Region: cobS; PRK00235 265072000354 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 265072000355 catalytic core [active] 265072000356 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 265072000357 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 265072000358 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072000359 homodimer interface [polypeptide binding]; other site 265072000360 catalytic residue [active] 265072000361 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 265072000362 cobyric acid synthase; Provisional; Region: PRK00784 265072000363 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 265072000364 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 265072000365 catalytic triad [active] 265072000366 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 265072000367 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 265072000368 active site 265072000369 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 265072000370 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 265072000371 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 265072000372 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 265072000373 N-terminal plug; other site 265072000374 ligand-binding site [chemical binding]; other site 265072000375 S4 domain; Region: S4_2; pfam13275 265072000376 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 265072000377 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 265072000378 homotrimer interface [polypeptide binding]; other site 265072000379 Walker A motif; other site 265072000380 GTP binding site [chemical binding]; other site 265072000381 Walker B motif; other site 265072000382 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 265072000383 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 265072000384 cobalamin binding residues [chemical binding]; other site 265072000385 putative BtuC binding residues; other site 265072000386 dimer interface [polypeptide binding]; other site 265072000387 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 265072000388 putative FMN binding site [chemical binding]; other site 265072000389 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 265072000390 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 265072000391 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 265072000392 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 265072000393 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 265072000394 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 265072000395 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 265072000396 catalytic triad [active] 265072000397 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 265072000398 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 265072000399 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 265072000400 homodimer interface [polypeptide binding]; other site 265072000401 Walker A motif; other site 265072000402 ATP binding site [chemical binding]; other site 265072000403 hydroxycobalamin binding site [chemical binding]; other site 265072000404 Walker B motif; other site 265072000405 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 265072000406 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 265072000407 N-terminal plug; other site 265072000408 ligand-binding site [chemical binding]; other site 265072000409 Cell division protein ZapA; Region: ZapA; pfam05164 265072000410 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 265072000411 EVE domain; Region: EVE; cl00728 265072000412 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 265072000413 metal binding site 2 [ion binding]; metal-binding site 265072000414 putative DNA binding helix; other site 265072000415 metal binding site 1 [ion binding]; metal-binding site 265072000416 dimer interface [polypeptide binding]; other site 265072000417 structural Zn2+ binding site [ion binding]; other site 265072000418 threonine dehydratase; Reviewed; Region: PRK09224 265072000419 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 265072000420 tetramer interface [polypeptide binding]; other site 265072000421 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072000422 catalytic residue [active] 265072000423 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 265072000424 putative Ile/Val binding site [chemical binding]; other site 265072000425 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 265072000426 putative Ile/Val binding site [chemical binding]; other site 265072000427 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 265072000428 tetramer (dimer of dimers) interface [polypeptide binding]; other site 265072000429 active site 265072000430 dimer interface [polypeptide binding]; other site 265072000431 transcriptional regulator PhoU; Provisional; Region: PRK11115 265072000432 PhoU domain; Region: PhoU; pfam01895 265072000433 PhoU domain; Region: PhoU; pfam01895 265072000434 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 265072000435 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 265072000436 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 265072000437 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 265072000438 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 265072000439 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 265072000440 putative domain interface [polypeptide binding]; other site 265072000441 putative active site [active] 265072000442 catalytic site [active] 265072000443 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 265072000444 putative domain interface [polypeptide binding]; other site 265072000445 putative active site [active] 265072000446 catalytic site [active] 265072000447 oxidative damage protection protein; Provisional; Region: PRK05408 265072000448 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 265072000449 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 265072000450 N-terminal plug; other site 265072000451 ligand-binding site [chemical binding]; other site 265072000452 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072000453 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 265072000454 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 265072000455 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 265072000456 putative active site [active] 265072000457 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 265072000458 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 265072000459 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 265072000460 active site 265072000461 motif I; other site 265072000462 motif II; other site 265072000463 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 265072000464 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 265072000465 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 265072000466 OstA-like protein; Region: OstA; pfam03968 265072000467 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 265072000468 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 265072000469 Walker A/P-loop; other site 265072000470 ATP binding site [chemical binding]; other site 265072000471 Q-loop/lid; other site 265072000472 ABC transporter signature motif; other site 265072000473 Walker B; other site 265072000474 D-loop; other site 265072000475 H-loop/switch region; other site 265072000476 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 265072000477 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 265072000478 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 265072000479 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 265072000480 30S subunit binding site; other site 265072000481 HPr kinase/phosphorylase; Provisional; Region: PRK05428 265072000482 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 265072000483 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 265072000484 Hpr binding site; other site 265072000485 active site 265072000486 homohexamer subunit interaction site [polypeptide binding]; other site 265072000487 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 265072000488 AAA domain; Region: AAA_18; pfam13238 265072000489 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 265072000490 active pocket/dimerization site; other site 265072000491 active site 265072000492 phosphorylation site [posttranslational modification] 265072000493 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 265072000494 dimerization domain swap beta strand [polypeptide binding]; other site 265072000495 regulatory protein interface [polypeptide binding]; other site 265072000496 active site 265072000497 regulatory phosphorylation site [posttranslational modification]; other site 265072000498 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 265072000499 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 265072000500 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 265072000501 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 265072000502 Tic20-like protein; Region: Tic20; pfam09685 265072000503 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 265072000504 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 265072000505 active site 265072000506 Zn binding site [ion binding]; other site 265072000507 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 265072000508 Receptor family ligand binding region; Region: ANF_receptor; pfam01094 265072000509 ligand binding site [chemical binding]; other site 265072000510 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 265072000511 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072000512 Walker A/P-loop; other site 265072000513 ATP binding site [chemical binding]; other site 265072000514 Q-loop/lid; other site 265072000515 ABC transporter signature motif; other site 265072000516 Walker B; other site 265072000517 D-loop; other site 265072000518 H-loop/switch region; other site 265072000519 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 265072000520 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072000521 Walker A/P-loop; other site 265072000522 ATP binding site [chemical binding]; other site 265072000523 Q-loop/lid; other site 265072000524 ABC transporter signature motif; other site 265072000525 Walker B; other site 265072000526 D-loop; other site 265072000527 H-loop/switch region; other site 265072000528 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 265072000529 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 265072000530 TM-ABC transporter signature motif; other site 265072000531 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 265072000532 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 265072000533 TM-ABC transporter signature motif; other site 265072000534 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 265072000535 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072000536 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 265072000537 DNA binding residues [nucleotide binding] 265072000538 dimerization interface [polypeptide binding]; other site 265072000539 YaeQ protein; Region: YaeQ; pfam07152 265072000540 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 265072000541 putative deacylase active site [active] 265072000542 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 265072000543 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 265072000544 S-adenosylmethionine binding site [chemical binding]; other site 265072000545 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 265072000546 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 265072000547 S-adenosylmethionine binding site [chemical binding]; other site 265072000548 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 265072000549 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 265072000550 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 265072000551 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 265072000552 Walker A/P-loop; other site 265072000553 ATP binding site [chemical binding]; other site 265072000554 Q-loop/lid; other site 265072000555 ABC transporter signature motif; other site 265072000556 Walker B; other site 265072000557 D-loop; other site 265072000558 H-loop/switch region; other site 265072000559 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 265072000560 Walker A/P-loop; other site 265072000561 ATP binding site [chemical binding]; other site 265072000562 Q-loop/lid; other site 265072000563 ABC transporter signature motif; other site 265072000564 Walker B; other site 265072000565 D-loop; other site 265072000566 H-loop/switch region; other site 265072000567 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 265072000568 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 265072000569 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072000570 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072000571 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 265072000572 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072000573 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072000574 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 265072000575 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 265072000576 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 265072000577 putative catalytic site [active] 265072000578 putative phosphate binding site [ion binding]; other site 265072000579 active site 265072000580 metal binding site A [ion binding]; metal-binding site 265072000581 DNA binding site [nucleotide binding] 265072000582 putative AP binding site [nucleotide binding]; other site 265072000583 putative metal binding site B [ion binding]; other site 265072000584 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 265072000585 putative FMN binding site [chemical binding]; other site 265072000586 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 265072000587 MgtC family; Region: MgtC; pfam02308 265072000588 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 265072000589 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072000590 Zn2+ binding site [ion binding]; other site 265072000591 Mg2+ binding site [ion binding]; other site 265072000592 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 265072000593 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 265072000594 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 265072000595 amphipathic channel; other site 265072000596 Asn-Pro-Ala signature motifs; other site 265072000597 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 265072000598 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 265072000599 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072000600 active site 265072000601 phosphorylation site [posttranslational modification] 265072000602 intermolecular recognition site; other site 265072000603 dimerization interface [polypeptide binding]; other site 265072000604 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 265072000605 Walker A motif; other site 265072000606 ATP binding site [chemical binding]; other site 265072000607 Walker B motif; other site 265072000608 arginine finger; other site 265072000609 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 265072000610 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 265072000611 dimerization interface [polypeptide binding]; other site 265072000612 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 265072000613 dimer interface [polypeptide binding]; other site 265072000614 phosphorylation site [posttranslational modification] 265072000615 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072000616 ATP binding site [chemical binding]; other site 265072000617 Mg2+ binding site [ion binding]; other site 265072000618 G-X-G motif; other site 265072000619 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 265072000620 16S rRNA methyltransferase B; Provisional; Region: PRK10901 265072000621 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 265072000622 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 265072000623 S-adenosylmethionine binding site [chemical binding]; other site 265072000624 M48 family peptidase; Provisional; Region: PRK03001 265072000625 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 265072000626 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 265072000627 putative active site [active] 265072000628 substrate binding site [chemical binding]; other site 265072000629 putative cosubstrate binding site; other site 265072000630 catalytic site [active] 265072000631 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 265072000632 substrate binding site [chemical binding]; other site 265072000633 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 265072000634 active site 265072000635 catalytic residues [active] 265072000636 metal binding site [ion binding]; metal-binding site 265072000637 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 265072000638 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072000639 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 265072000640 DNA protecting protein DprA; Region: dprA; TIGR00732 265072000641 Protein of unknown function (DUF494); Region: DUF494; pfam04361 265072000642 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 265072000643 FAD binding site [chemical binding]; other site 265072000644 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 265072000645 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 265072000646 homotetramer interface [polypeptide binding]; other site 265072000647 ligand binding site [chemical binding]; other site 265072000648 catalytic site [active] 265072000649 NAD binding site [chemical binding]; other site 265072000650 S-adenosylmethionine synthetase; Validated; Region: PRK05250 265072000651 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 265072000652 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 265072000653 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 265072000654 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 265072000655 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 265072000656 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 265072000657 putative acyl-acceptor binding pocket; other site 265072000658 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 265072000659 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 265072000660 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 265072000661 Protein of unknown function, DUF484; Region: DUF484; cl17449 265072000662 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 265072000663 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 265072000664 active site 265072000665 Int/Topo IB signature motif; other site 265072000666 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 265072000667 trimer interface [polypeptide binding]; other site 265072000668 dimer interface [polypeptide binding]; other site 265072000669 putative active site [active] 265072000670 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 265072000671 Peptidase family M48; Region: Peptidase_M48; pfam01435 265072000672 Predicted secreted protein [Function unknown]; Region: COG5501 265072000673 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 265072000674 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 265072000675 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 265072000676 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 265072000677 tetramer interface [polypeptide binding]; other site 265072000678 catalytic Zn binding site [ion binding]; other site 265072000679 NADP binding site [chemical binding]; other site 265072000680 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 265072000681 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 265072000682 Walker A motif; other site 265072000683 ATP binding site [chemical binding]; other site 265072000684 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 265072000685 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 265072000686 dimerization interface [polypeptide binding]; other site 265072000687 putative ATP binding site [chemical binding]; other site 265072000688 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 265072000689 16S rRNA methyltransferase B; Provisional; Region: PRK14901 265072000690 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 265072000691 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 265072000692 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 265072000693 azurin; Region: azurin; TIGR02695 265072000694 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 265072000695 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072000696 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072000697 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072000698 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 265072000699 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 265072000700 amidase catalytic site [active] 265072000701 Zn binding residues [ion binding]; other site 265072000702 substrate binding site [chemical binding]; other site 265072000703 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 265072000704 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072000705 active site 265072000706 phosphorylation site [posttranslational modification] 265072000707 intermolecular recognition site; other site 265072000708 dimerization interface [polypeptide binding]; other site 265072000709 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 265072000710 Walker A motif; other site 265072000711 ATP binding site [chemical binding]; other site 265072000712 Walker B motif; other site 265072000713 arginine finger; other site 265072000714 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072000715 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 265072000716 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 265072000717 dimer interface [polypeptide binding]; other site 265072000718 phosphorylation site [posttranslational modification] 265072000719 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072000720 ATP binding site [chemical binding]; other site 265072000721 Mg2+ binding site [ion binding]; other site 265072000722 G-X-G motif; other site 265072000723 RNA polymerase factor sigma-70; Validated; Region: PRK09047 265072000724 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072000725 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 265072000726 DNA binding residues [nucleotide binding] 265072000727 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 265072000728 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 265072000729 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 265072000730 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 265072000731 Predicted permeases [General function prediction only]; Region: COG0795 265072000732 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 265072000733 multifunctional aminopeptidase A; Provisional; Region: PRK00913 265072000734 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 265072000735 interface (dimer of trimers) [polypeptide binding]; other site 265072000736 Substrate-binding/catalytic site; other site 265072000737 Zn-binding sites [ion binding]; other site 265072000738 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 265072000739 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 265072000740 lipoyl attachment site [posttranslational modification]; other site 265072000741 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 265072000742 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 265072000743 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 265072000744 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 265072000745 active site 265072000746 interdomain interaction site; other site 265072000747 putative metal-binding site [ion binding]; other site 265072000748 nucleotide binding site [chemical binding]; other site 265072000749 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 265072000750 domain I; other site 265072000751 DNA binding groove [nucleotide binding] 265072000752 phosphate binding site [ion binding]; other site 265072000753 domain II; other site 265072000754 domain III; other site 265072000755 nucleotide binding site [chemical binding]; other site 265072000756 catalytic site [active] 265072000757 domain IV; other site 265072000758 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 265072000759 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 265072000760 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 265072000761 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 265072000762 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 265072000763 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 265072000764 Ligand Binding Site [chemical binding]; other site 265072000765 pteridine reductase; Provisional; Region: PRK09135 265072000766 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 265072000767 NADP binding site [chemical binding]; other site 265072000768 substrate binding pocket [chemical binding]; other site 265072000769 active site 265072000770 Uncharacterized conserved protein [Function unknown]; Region: COG1565 265072000771 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 265072000772 S-adenosylmethionine binding site [chemical binding]; other site 265072000773 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 265072000774 G1 box; other site 265072000775 GTP/Mg2+ binding site [chemical binding]; other site 265072000776 Switch I region; other site 265072000777 G2 box; other site 265072000778 G3 box; other site 265072000779 Switch II region; other site 265072000780 G4 box; other site 265072000781 G5 box; other site 265072000782 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 265072000783 ResB-like family; Region: ResB; pfam05140 265072000784 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 265072000785 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 265072000786 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072000787 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072000788 ATP binding site [chemical binding]; other site 265072000789 Mg2+ binding site [ion binding]; other site 265072000790 G-X-G motif; other site 265072000791 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 265072000792 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 265072000793 Walker A/P-loop; other site 265072000794 ATP binding site [chemical binding]; other site 265072000795 Q-loop/lid; other site 265072000796 ABC transporter signature motif; other site 265072000797 Walker B; other site 265072000798 D-loop; other site 265072000799 H-loop/switch region; other site 265072000800 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 265072000801 Permease; Region: Permease; pfam02405 265072000802 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 265072000803 mce related protein; Region: MCE; pfam02470 265072000804 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 265072000805 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 265072000806 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 265072000807 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 265072000808 Walker A/P-loop; other site 265072000809 ATP binding site [chemical binding]; other site 265072000810 Q-loop/lid; other site 265072000811 ABC transporter signature motif; other site 265072000812 Walker B; other site 265072000813 D-loop; other site 265072000814 H-loop/switch region; other site 265072000815 ABC-2 type transporter; Region: ABC2_membrane; cl17235 265072000816 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 265072000817 BolA-like protein; Region: BolA; pfam01722 265072000818 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 265072000819 putative GSH binding site [chemical binding]; other site 265072000820 catalytic residues [active] 265072000821 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 265072000822 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 265072000823 hinge; other site 265072000824 active site 265072000825 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 265072000826 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 265072000827 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 265072000828 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 265072000829 NAD binding site [chemical binding]; other site 265072000830 dimerization interface [polypeptide binding]; other site 265072000831 product binding site; other site 265072000832 substrate binding site [chemical binding]; other site 265072000833 zinc binding site [ion binding]; other site 265072000834 catalytic residues [active] 265072000835 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 265072000836 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 265072000837 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072000838 homodimer interface [polypeptide binding]; other site 265072000839 catalytic residue [active] 265072000840 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 265072000841 active site 265072000842 dimer interface [polypeptide binding]; other site 265072000843 magnesium binding site [ion binding]; other site 265072000844 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 265072000845 putative active site pocket [active] 265072000846 4-fold oligomerization interface [polypeptide binding]; other site 265072000847 metal binding residues [ion binding]; metal-binding site 265072000848 3-fold/trimer interface [polypeptide binding]; other site 265072000849 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 265072000850 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 265072000851 putative active site [active] 265072000852 oxyanion strand; other site 265072000853 catalytic triad [active] 265072000854 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 265072000855 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 265072000856 catalytic residues [active] 265072000857 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 265072000858 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 265072000859 substrate binding site [chemical binding]; other site 265072000860 glutamase interaction surface [polypeptide binding]; other site 265072000861 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 265072000862 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 265072000863 metal binding site [ion binding]; metal-binding site 265072000864 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 265072000865 nucleotide binding site/active site [active] 265072000866 HIT family signature motif; other site 265072000867 catalytic residue [active] 265072000868 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 265072000869 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 265072000870 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 265072000871 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 265072000872 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 265072000873 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 265072000874 protein binding site [polypeptide binding]; other site 265072000875 Uncharacterized conserved protein [Function unknown]; Region: COG0327 265072000876 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 265072000877 stringent starvation protein A; Provisional; Region: sspA; PRK09481 265072000878 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 265072000879 C-terminal domain interface [polypeptide binding]; other site 265072000880 putative GSH binding site (G-site) [chemical binding]; other site 265072000881 dimer interface [polypeptide binding]; other site 265072000882 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 265072000883 dimer interface [polypeptide binding]; other site 265072000884 N-terminal domain interface [polypeptide binding]; other site 265072000885 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 265072000886 elongation factor Tu; Reviewed; Region: PRK00049 265072000887 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 265072000888 G1 box; other site 265072000889 GEF interaction site [polypeptide binding]; other site 265072000890 GTP/Mg2+ binding site [chemical binding]; other site 265072000891 Switch I region; other site 265072000892 G2 box; other site 265072000893 G3 box; other site 265072000894 Switch II region; other site 265072000895 G4 box; other site 265072000896 G5 box; other site 265072000897 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 265072000898 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 265072000899 Antibiotic Binding Site [chemical binding]; other site 265072000900 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 265072000901 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 265072000902 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 265072000903 putative homodimer interface [polypeptide binding]; other site 265072000904 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 265072000905 heterodimer interface [polypeptide binding]; other site 265072000906 homodimer interface [polypeptide binding]; other site 265072000907 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 265072000908 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 265072000909 23S rRNA interface [nucleotide binding]; other site 265072000910 L7/L12 interface [polypeptide binding]; other site 265072000911 putative thiostrepton binding site; other site 265072000912 L25 interface [polypeptide binding]; other site 265072000913 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 265072000914 mRNA/rRNA interface [nucleotide binding]; other site 265072000915 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 265072000916 23S rRNA interface [nucleotide binding]; other site 265072000917 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 265072000918 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 265072000919 core dimer interface [polypeptide binding]; other site 265072000920 peripheral dimer interface [polypeptide binding]; other site 265072000921 L10 interface [polypeptide binding]; other site 265072000922 L11 interface [polypeptide binding]; other site 265072000923 putative EF-Tu interaction site [polypeptide binding]; other site 265072000924 putative EF-G interaction site [polypeptide binding]; other site 265072000925 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 265072000926 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 265072000927 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 265072000928 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 265072000929 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 265072000930 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 265072000931 RPB3 interaction site [polypeptide binding]; other site 265072000932 RPB1 interaction site [polypeptide binding]; other site 265072000933 RPB11 interaction site [polypeptide binding]; other site 265072000934 RPB10 interaction site [polypeptide binding]; other site 265072000935 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 265072000936 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 265072000937 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 265072000938 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 265072000939 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 265072000940 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 265072000941 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 265072000942 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 265072000943 DNA binding site [nucleotide binding] 265072000944 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 265072000945 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 265072000946 S17 interaction site [polypeptide binding]; other site 265072000947 S8 interaction site; other site 265072000948 16S rRNA interaction site [nucleotide binding]; other site 265072000949 streptomycin interaction site [chemical binding]; other site 265072000950 23S rRNA interaction site [nucleotide binding]; other site 265072000951 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 265072000952 30S ribosomal protein S7; Validated; Region: PRK05302 265072000953 elongation factor G; Reviewed; Region: PRK00007 265072000954 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 265072000955 G1 box; other site 265072000956 putative GEF interaction site [polypeptide binding]; other site 265072000957 GTP/Mg2+ binding site [chemical binding]; other site 265072000958 Switch I region; other site 265072000959 G2 box; other site 265072000960 G3 box; other site 265072000961 Switch II region; other site 265072000962 G4 box; other site 265072000963 G5 box; other site 265072000964 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 265072000965 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 265072000966 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 265072000967 elongation factor Tu; Reviewed; Region: PRK00049 265072000968 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 265072000969 G1 box; other site 265072000970 GEF interaction site [polypeptide binding]; other site 265072000971 GTP/Mg2+ binding site [chemical binding]; other site 265072000972 Switch I region; other site 265072000973 G2 box; other site 265072000974 G3 box; other site 265072000975 Switch II region; other site 265072000976 G4 box; other site 265072000977 G5 box; other site 265072000978 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 265072000979 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 265072000980 Antibiotic Binding Site [chemical binding]; other site 265072000981 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 265072000982 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 265072000983 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 265072000984 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 265072000985 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 265072000986 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 265072000987 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 265072000988 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 265072000989 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 265072000990 putative translocon binding site; other site 265072000991 protein-rRNA interface [nucleotide binding]; other site 265072000992 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 265072000993 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 265072000994 G-X-X-G motif; other site 265072000995 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 265072000996 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 265072000997 23S rRNA interface [nucleotide binding]; other site 265072000998 5S rRNA interface [nucleotide binding]; other site 265072000999 putative antibiotic binding site [chemical binding]; other site 265072001000 L25 interface [polypeptide binding]; other site 265072001001 L27 interface [polypeptide binding]; other site 265072001002 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 265072001003 putative translocon interaction site; other site 265072001004 23S rRNA interface [nucleotide binding]; other site 265072001005 signal recognition particle (SRP54) interaction site; other site 265072001006 L23 interface [polypeptide binding]; other site 265072001007 trigger factor interaction site; other site 265072001008 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 265072001009 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 265072001010 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 265072001011 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 265072001012 RNA binding site [nucleotide binding]; other site 265072001013 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 265072001014 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 265072001015 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 265072001016 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 265072001017 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 265072001018 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 265072001019 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 265072001020 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 265072001021 5S rRNA interface [nucleotide binding]; other site 265072001022 23S rRNA interface [nucleotide binding]; other site 265072001023 L5 interface [polypeptide binding]; other site 265072001024 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 265072001025 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 265072001026 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 265072001027 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 265072001028 23S rRNA binding site [nucleotide binding]; other site 265072001029 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 265072001030 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 265072001031 SecY translocase; Region: SecY; pfam00344 265072001032 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 265072001033 rRNA binding site [nucleotide binding]; other site 265072001034 predicted 30S ribosome binding site; other site 265072001035 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 265072001036 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 265072001037 30S ribosomal protein S13; Region: bact_S13; TIGR03631 265072001038 30S ribosomal protein S11; Validated; Region: PRK05309 265072001039 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 265072001040 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 265072001041 alphaNTD homodimer interface [polypeptide binding]; other site 265072001042 alphaNTD - beta interaction site [polypeptide binding]; other site 265072001043 alphaNTD - beta' interaction site [polypeptide binding]; other site 265072001044 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 265072001045 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 265072001046 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 265072001047 MgtE intracellular N domain; Region: MgtE_N; smart00924 265072001048 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 265072001049 Divalent cation transporter; Region: MgtE; cl00786 265072001050 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 265072001051 Mechanosensitive ion channel; Region: MS_channel; pfam00924 265072001052 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072001053 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072001054 Cupin domain; Region: Cupin_2; pfam07883 265072001055 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 265072001056 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 265072001057 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 265072001058 trimer interface [polypeptide binding]; other site 265072001059 active site 265072001060 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 265072001061 Flavoprotein; Region: Flavoprotein; pfam02441 265072001062 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 265072001063 hypothetical protein; Reviewed; Region: PRK00024 265072001064 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 265072001065 MPN+ (JAMM) motif; other site 265072001066 Zinc-binding site [ion binding]; other site 265072001067 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 265072001068 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 265072001069 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 265072001070 [4Fe-4S] binding site [ion binding]; other site 265072001071 molybdopterin cofactor binding site; other site 265072001072 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 265072001073 molybdopterin cofactor binding site; other site 265072001074 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 265072001075 Flavodoxin; Region: Flavodoxin_1; pfam00258 265072001076 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 265072001077 FAD binding pocket [chemical binding]; other site 265072001078 FAD binding motif [chemical binding]; other site 265072001079 catalytic residues [active] 265072001080 NAD binding pocket [chemical binding]; other site 265072001081 phosphate binding motif [ion binding]; other site 265072001082 beta-alpha-beta structure motif; other site 265072001083 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 265072001084 nitrite reductase subunit NirD; Provisional; Region: PRK14989 265072001085 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 265072001086 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072001087 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 265072001088 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 265072001089 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 265072001090 Protein phosphatase 2C; Region: PP2C; pfam00481 265072001091 active site 265072001092 Protein kinase domain; Region: Pkinase; pfam00069 265072001093 Catalytic domain of Protein Kinases; Region: PKc; cd00180 265072001094 active site 265072001095 ATP binding site [chemical binding]; other site 265072001096 substrate binding site [chemical binding]; other site 265072001097 activation loop (A-loop); other site 265072001098 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 265072001099 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 265072001100 putative substrate translocation pore; other site 265072001101 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 265072001102 active site 265072001103 SAM binding site [chemical binding]; other site 265072001104 homodimer interface [polypeptide binding]; other site 265072001105 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 265072001106 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072001107 putative CheW interface [polypeptide binding]; other site 265072001108 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 265072001109 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 265072001110 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 265072001111 Walker A/P-loop; other site 265072001112 ATP binding site [chemical binding]; other site 265072001113 Q-loop/lid; other site 265072001114 ABC transporter signature motif; other site 265072001115 Walker B; other site 265072001116 D-loop; other site 265072001117 H-loop/switch region; other site 265072001118 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 265072001119 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 265072001120 dimer interface [polypeptide binding]; other site 265072001121 conserved gate region; other site 265072001122 putative PBP binding loops; other site 265072001123 ABC-ATPase subunit interface; other site 265072001124 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 265072001125 NMT1-like family; Region: NMT1_2; pfam13379 265072001126 Nitrate and nitrite sensing; Region: NIT; pfam08376 265072001127 ANTAR domain; Region: ANTAR; pfam03861 265072001128 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 265072001129 active site 265072001130 Protein kinase domain; Region: Pkinase; pfam00069 265072001131 Catalytic domain of Protein Kinases; Region: PKc; cd00180 265072001132 active site 265072001133 ATP binding site [chemical binding]; other site 265072001134 substrate binding site [chemical binding]; other site 265072001135 activation loop (A-loop); other site 265072001136 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 265072001137 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 265072001138 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072001139 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 265072001140 Walker A/P-loop; other site 265072001141 ATP binding site [chemical binding]; other site 265072001142 Q-loop/lid; other site 265072001143 ABC transporter signature motif; other site 265072001144 Walker B; other site 265072001145 D-loop; other site 265072001146 H-loop/switch region; other site 265072001147 carbon starvation protein A; Provisional; Region: PRK15015 265072001148 Carbon starvation protein CstA; Region: CstA; pfam02554 265072001149 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 265072001150 Protein of unknown function (DUF466); Region: DUF466; cl01082 265072001151 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 265072001152 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 265072001153 DNA-binding site [nucleotide binding]; DNA binding site 265072001154 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 265072001155 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072001156 homodimer interface [polypeptide binding]; other site 265072001157 catalytic residue [active] 265072001158 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 265072001159 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 265072001160 putative molybdopterin cofactor binding site [chemical binding]; other site 265072001161 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 265072001162 putative molybdopterin cofactor binding site; other site 265072001163 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 265072001164 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 265072001165 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 265072001166 active site 265072001167 phosphate binding residues; other site 265072001168 catalytic residues [active] 265072001169 Cytochrome c; Region: Cytochrom_C; cl11414 265072001170 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 265072001171 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 265072001172 Walker A motif; other site 265072001173 ATP binding site [chemical binding]; other site 265072001174 Walker B motif; other site 265072001175 arginine finger; other site 265072001176 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072001177 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 265072001178 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 265072001179 Trp docking motif [polypeptide binding]; other site 265072001180 dimer interface [polypeptide binding]; other site 265072001181 active site 265072001182 small subunit binding site [polypeptide binding]; other site 265072001183 amino acid transporter; Region: 2A0306; TIGR00909 265072001184 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 265072001185 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 265072001186 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 265072001187 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 265072001188 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 265072001189 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 265072001190 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 265072001191 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 265072001192 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 265072001193 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 265072001194 purine monophosphate binding site [chemical binding]; other site 265072001195 dimer interface [polypeptide binding]; other site 265072001196 putative catalytic residues [active] 265072001197 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 265072001198 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 265072001199 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 265072001200 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 265072001201 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 265072001202 FMN binding site [chemical binding]; other site 265072001203 active site 265072001204 catalytic residues [active] 265072001205 substrate binding site [chemical binding]; other site 265072001206 Cache domain; Region: Cache_1; pfam02743 265072001207 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 265072001208 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072001209 dimer interface [polypeptide binding]; other site 265072001210 putative CheW interface [polypeptide binding]; other site 265072001211 Protein of unknown function DUF72; Region: DUF72; pfam01904 265072001212 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 265072001213 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 265072001214 conserved cys residue [active] 265072001215 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072001216 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072001217 Flagellin N-methylase; Region: FliB; cl00497 265072001218 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 265072001219 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 265072001220 putative MPT binding site; other site 265072001221 DNA polymerase I; Provisional; Region: PRK05755 265072001222 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 265072001223 active site 265072001224 metal binding site 1 [ion binding]; metal-binding site 265072001225 putative 5' ssDNA interaction site; other site 265072001226 metal binding site 3; metal-binding site 265072001227 metal binding site 2 [ion binding]; metal-binding site 265072001228 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 265072001229 putative DNA binding site [nucleotide binding]; other site 265072001230 putative metal binding site [ion binding]; other site 265072001231 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 265072001232 active site 265072001233 catalytic site [active] 265072001234 substrate binding site [chemical binding]; other site 265072001235 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 265072001236 active site 265072001237 DNA binding site [nucleotide binding] 265072001238 catalytic site [active] 265072001239 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 265072001240 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 265072001241 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 265072001242 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 265072001243 putative active site [active] 265072001244 putative substrate binding site [chemical binding]; other site 265072001245 ATP binding site [chemical binding]; other site 265072001246 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 265072001247 Part of AAA domain; Region: AAA_19; pfam13245 265072001248 Family description; Region: UvrD_C_2; pfam13538 265072001249 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 265072001250 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 265072001251 ring oligomerisation interface [polypeptide binding]; other site 265072001252 ATP/Mg binding site [chemical binding]; other site 265072001253 stacking interactions; other site 265072001254 hinge regions; other site 265072001255 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 265072001256 oligomerisation interface [polypeptide binding]; other site 265072001257 mobile loop; other site 265072001258 roof hairpin; other site 265072001259 Protein of unknown function (DUF2380); Region: DUF3280; pfam11684 265072001260 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072001261 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072001262 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 265072001263 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 265072001264 active site 265072001265 FMN binding site [chemical binding]; other site 265072001266 substrate binding site [chemical binding]; other site 265072001267 homotetramer interface [polypeptide binding]; other site 265072001268 catalytic residue [active] 265072001269 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 265072001270 putative DNA binding site [nucleotide binding]; other site 265072001271 putative Zn2+ binding site [ion binding]; other site 265072001272 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072001273 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 265072001274 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072001275 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072001276 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072001277 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 265072001278 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 265072001279 inhibitor-cofactor binding pocket; inhibition site 265072001280 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072001281 catalytic residue [active] 265072001282 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 265072001283 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 265072001284 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 265072001285 OsmC-like protein; Region: OsmC; cl00767 265072001286 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 265072001287 active site 265072001288 metal binding site [ion binding]; metal-binding site 265072001289 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 265072001290 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 265072001291 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 265072001292 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 265072001293 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 265072001294 protein binding site [polypeptide binding]; other site 265072001295 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 265072001296 Catalytic dyad [active] 265072001297 Rdx family; Region: Rdx; cl01407 265072001298 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 265072001299 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 265072001300 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 265072001301 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 265072001302 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 265072001303 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 265072001304 NlpC/P60 family; Region: NLPC_P60; pfam00877 265072001305 ABC1 family; Region: ABC1; cl17513 265072001306 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 265072001307 Uncharacterized conserved protein [Function unknown]; Region: COG2308 265072001308 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 265072001309 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 265072001310 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 265072001311 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 265072001312 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 265072001313 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 265072001314 Peptidase family U32; Region: Peptidase_U32; pfam01136 265072001315 Collagenase; Region: DUF3656; pfam12392 265072001316 Cupin domain; Region: Cupin_2; cl17218 265072001317 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 265072001318 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 265072001319 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 265072001320 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 265072001321 putative ligand binding site [chemical binding]; other site 265072001322 putative NAD binding site [chemical binding]; other site 265072001323 catalytic site [active] 265072001324 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 265072001325 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 265072001326 active site 265072001327 catalytic tetrad [active] 265072001328 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 265072001329 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 265072001330 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072001331 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072001332 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 265072001333 dimerization interface [polypeptide binding]; other site 265072001334 Predicted membrane protein [Function unknown]; Region: COG4125 265072001335 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 265072001336 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 265072001337 DEAD/DEAH box helicase; Region: DEAD; pfam00270 265072001338 ATP binding site [chemical binding]; other site 265072001339 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 265072001340 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 265072001341 active site 265072001342 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 265072001343 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 265072001344 integron integrase; Region: integrase_gron; TIGR02249 265072001345 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 265072001346 Int/Topo IB signature motif; other site 265072001347 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 265072001348 DEAD/DEAH box helicase; Region: DEAD; pfam00270 265072001349 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 265072001350 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 265072001351 Glycoprotease family; Region: Peptidase_M22; pfam00814 265072001352 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 265072001353 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 265072001354 Coenzyme A binding pocket [chemical binding]; other site 265072001355 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 265072001356 Fe-S cluster binding site [ion binding]; other site 265072001357 active site 265072001358 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 265072001359 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 265072001360 Repair protein; Region: Repair_PSII; pfam04536 265072001361 Repair protein; Region: Repair_PSII; pfam04536 265072001362 prolyl-tRNA synthetase; Provisional; Region: PRK09194 265072001363 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 265072001364 dimer interface [polypeptide binding]; other site 265072001365 motif 1; other site 265072001366 active site 265072001367 motif 2; other site 265072001368 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 265072001369 putative deacylase active site [active] 265072001370 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 265072001371 active site 265072001372 motif 3; other site 265072001373 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 265072001374 anticodon binding site; other site 265072001375 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 265072001376 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 265072001377 N-acetyl-D-glucosamine binding site [chemical binding]; other site 265072001378 catalytic residue [active] 265072001379 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 265072001380 Glycosyltransferase family 28 C-terminal domain; Region: Glyco_tran_28_C; cl17369 265072001381 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 265072001382 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 265072001383 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 265072001384 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 265072001385 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 265072001386 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 265072001387 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 265072001388 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 265072001389 ApbE family; Region: ApbE; pfam02424 265072001390 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 265072001391 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 265072001392 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like1; cd06200 265072001393 FAD binding pocket [chemical binding]; other site 265072001394 FAD binding motif [chemical binding]; other site 265072001395 catalytic residues [active] 265072001396 NAD binding pocket [chemical binding]; other site 265072001397 phosphate binding motif [ion binding]; other site 265072001398 beta-alpha-beta structure motif; other site 265072001399 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072001400 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072001401 metal binding site [ion binding]; metal-binding site 265072001402 active site 265072001403 I-site; other site 265072001404 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 265072001405 CHASE2 domain; Region: CHASE2; pfam05226 265072001406 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 265072001407 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 265072001408 dimer interface [polypeptide binding]; other site 265072001409 phosphorylation site [posttranslational modification] 265072001410 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072001411 ATP binding site [chemical binding]; other site 265072001412 Mg2+ binding site [ion binding]; other site 265072001413 G-X-G motif; other site 265072001414 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 265072001415 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072001416 FecR protein; Region: FecR; pfam04773 265072001417 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 265072001418 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072001419 active site 265072001420 phosphorylation site [posttranslational modification] 265072001421 intermolecular recognition site; other site 265072001422 dimerization interface [polypeptide binding]; other site 265072001423 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 265072001424 DNA binding site [nucleotide binding] 265072001425 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 265072001426 Nitrogen regulatory protein P-II; Region: P-II; smart00938 265072001427 ammonium transporter; Provisional; Region: PRK10666 265072001428 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 265072001429 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 265072001430 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 265072001431 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 265072001432 non-specific DNA binding site [nucleotide binding]; other site 265072001433 salt bridge; other site 265072001434 sequence-specific DNA binding site [nucleotide binding]; other site 265072001435 Cupin domain; Region: Cupin_2; pfam07883 265072001436 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 265072001437 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 265072001438 catalytic triad [active] 265072001439 Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]; Region: GcvT; COG0404 265072001440 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 265072001441 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 265072001442 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 265072001443 FMN-binding pocket [chemical binding]; other site 265072001444 flavin binding motif; other site 265072001445 phosphate binding motif [ion binding]; other site 265072001446 beta-alpha-beta structure motif; other site 265072001447 NAD binding pocket [chemical binding]; other site 265072001448 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 265072001449 catalytic loop [active] 265072001450 iron binding site [ion binding]; other site 265072001451 Protein of unknown function (DUF3445); Region: DUF3445; pfam11927 265072001452 PAS domain; Region: PAS_9; pfam13426 265072001453 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072001454 putative active site [active] 265072001455 heme pocket [chemical binding]; other site 265072001456 PAS domain; Region: PAS_9; pfam13426 265072001457 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072001458 putative active site [active] 265072001459 heme pocket [chemical binding]; other site 265072001460 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072001461 PAS fold; Region: PAS_3; pfam08447 265072001462 putative active site [active] 265072001463 heme pocket [chemical binding]; other site 265072001464 Histidine kinase; Region: HisKA_3; pfam07730 265072001465 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 265072001466 ATP binding site [chemical binding]; other site 265072001467 Mg2+ binding site [ion binding]; other site 265072001468 transcriptional regulator NarL; Provisional; Region: PRK10651 265072001469 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072001470 active site 265072001471 phosphorylation site [posttranslational modification] 265072001472 intermolecular recognition site; other site 265072001473 dimerization interface [polypeptide binding]; other site 265072001474 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 265072001475 DNA binding residues [nucleotide binding] 265072001476 dimerization interface [polypeptide binding]; other site 265072001477 Amino acid permease; Region: AA_permease_2; pfam13520 265072001478 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072001479 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072001480 active site 265072001481 phosphorylation site [posttranslational modification] 265072001482 intermolecular recognition site; other site 265072001483 dimerization interface [polypeptide binding]; other site 265072001484 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 265072001485 DNA binding residues [nucleotide binding] 265072001486 dimerization interface [polypeptide binding]; other site 265072001487 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 265072001488 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072001489 ATP binding site [chemical binding]; other site 265072001490 Mg2+ binding site [ion binding]; other site 265072001491 G-X-G motif; other site 265072001492 Autotransporter beta-domain; Region: Autotransporter; pfam03797 265072001493 inner membrane protein; Provisional; Region: PRK10995 265072001494 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 265072001495 active site 265072001496 dimer interface [polypeptide binding]; other site 265072001497 PEP-CTERM motif; Region: VPEP; pfam07589 265072001498 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 265072001499 hydroxyglutarate oxidase; Provisional; Region: PRK11728 265072001500 Sarcosine oxidase, delta subunit family; Region: SoxD; pfam04267 265072001501 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 265072001502 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 265072001503 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 265072001504 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 265072001505 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 265072001506 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 265072001507 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 265072001508 Glutamate synthase domain 1 [Amino acid transport and metabolism]; Region: GltB; COG0067 265072001509 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 265072001510 Glutamine amidotransferases class-II (Gn-AT)_GlxB-type. GlxB is a glutamine amidotransferase-like protein of unknown function found in bacteria and archaea. GlxB has a structural fold similar to that of other class II glutamine amidotransferases...; Region: GlxB; cd01907 265072001511 putative active site [active] 265072001512 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 265072001513 domain_subunit interface; other site 265072001514 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 265072001515 Conserved region in glutamate synthase; Region: Glu_synthase; pfam01645 265072001516 active site 265072001517 FMN binding site [chemical binding]; other site 265072001518 substrate binding site [chemical binding]; other site 265072001519 3Fe-4S cluster binding site [ion binding]; other site 265072001520 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 265072001521 ANTAR domain; Region: ANTAR; pfam03861 265072001522 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 265072001523 Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family; Region: PBP1_AmiC; cd06357 265072001524 ligand binding site [chemical binding]; other site 265072001525 regulator interaction site; other site 265072001526 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 265072001527 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 265072001528 multimer interface [polypeptide binding]; other site 265072001529 active site 265072001530 catalytic triad [active] 265072001531 dimer interface [polypeptide binding]; other site 265072001532 Protein of unknown function DUF262; Region: DUF262; pfam03235 265072001533 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 265072001534 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 265072001535 active site 265072001536 metal binding site [ion binding]; metal-binding site 265072001537 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 265072001538 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 265072001539 putative acyl-acceptor binding pocket; other site 265072001540 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 265072001541 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 265072001542 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 265072001543 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 265072001544 substrate binding site [chemical binding]; other site 265072001545 ATP binding site [chemical binding]; other site 265072001546 putative transcriptional regulator; Provisional; Region: PRK11640 265072001547 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072001548 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 265072001549 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 265072001550 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072001551 catalytic residues [active] 265072001552 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 265072001553 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 265072001554 FAD binding domain; Region: FAD_binding_4; pfam01565 265072001555 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 265072001556 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 265072001557 Cysteine-rich domain; Region: CCG; pfam02754 265072001558 Cysteine-rich domain; Region: CCG; pfam02754 265072001559 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 265072001560 Transposase IS200 like; Region: Y1_Tnp; pfam01797 265072001561 haemagglutination activity domain; Region: Haemagg_act; pfam05860 265072001562 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 265072001563 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 265072001564 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 265072001565 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 265072001566 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 265072001567 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 265072001568 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 265072001569 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 265072001570 hypothetical protein; Provisional; Region: PRK02237 265072001571 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 265072001572 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 265072001573 This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant...; Region: GT1_AviGT4_like; cd03802 265072001574 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072001575 putative ADP-binding pocket [chemical binding]; other site 265072001576 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 265072001577 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 265072001578 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072001579 putative active site [active] 265072001580 heme pocket [chemical binding]; other site 265072001581 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 265072001582 dimer interface [polypeptide binding]; other site 265072001583 phosphorylation site [posttranslational modification] 265072001584 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072001585 ATP binding site [chemical binding]; other site 265072001586 Mg2+ binding site [ion binding]; other site 265072001587 G-X-G motif; other site 265072001588 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 265072001589 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072001590 active site 265072001591 phosphorylation site [posttranslational modification] 265072001592 intermolecular recognition site; other site 265072001593 dimerization interface [polypeptide binding]; other site 265072001594 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 265072001595 DNA binding site [nucleotide binding] 265072001596 Major Facilitator Superfamily; Region: MFS_1; pfam07690 265072001597 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 265072001598 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 265072001599 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 265072001600 homopentamer interface [polypeptide binding]; other site 265072001601 active site 265072001602 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 265072001603 putative RNA binding site [nucleotide binding]; other site 265072001604 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 265072001605 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 265072001606 phosphopeptide binding site; other site 265072001607 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 265072001608 putative active site [active] 265072001609 putative metal binding site [ion binding]; other site 265072001610 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 265072001611 substrate binding site [chemical binding]; other site 265072001612 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 265072001613 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 265072001614 substrate binding site [chemical binding]; other site 265072001615 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 265072001616 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 265072001617 binding surface 265072001618 TPR motif; other site 265072001619 TPR repeat; Region: TPR_11; pfam13414 265072001620 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 265072001621 binding surface 265072001622 TPR motif; other site 265072001623 SnoaL-like domain; Region: SnoaL_3; pfam13474 265072001624 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 265072001625 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 265072001626 active site 265072001627 HIGH motif; other site 265072001628 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 265072001629 KMSKS motif; other site 265072001630 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 265072001631 tRNA binding surface [nucleotide binding]; other site 265072001632 anticodon binding site; other site 265072001633 Outer membrane efflux protein; Region: OEP; pfam02321 265072001634 Outer membrane efflux protein; Region: OEP; pfam02321 265072001635 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072001636 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072001637 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072001638 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 265072001639 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 265072001640 Nitrogen regulatory protein P-II; Region: P-II; smart00938 265072001641 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 265072001642 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 265072001643 quinone interaction residues [chemical binding]; other site 265072001644 active site 265072001645 catalytic residues [active] 265072001646 FMN binding site [chemical binding]; other site 265072001647 substrate binding site [chemical binding]; other site 265072001648 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 265072001649 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 265072001650 putative GSH binding site (G-site) [chemical binding]; other site 265072001651 active site cysteine [active] 265072001652 putative C-terminal domain interface [polypeptide binding]; other site 265072001653 putative dimer interface [polypeptide binding]; other site 265072001654 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 265072001655 putative N-terminal domain interface [polypeptide binding]; other site 265072001656 putative dimer interface [polypeptide binding]; other site 265072001657 putative substrate binding pocket (H-site) [chemical binding]; other site 265072001658 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 265072001659 Clp amino terminal domain; Region: Clp_N; pfam02861 265072001660 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 265072001661 Walker A motif; other site 265072001662 ATP binding site [chemical binding]; other site 265072001663 Walker B motif; other site 265072001664 arginine finger; other site 265072001665 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 265072001666 Walker A motif; other site 265072001667 ATP binding site [chemical binding]; other site 265072001668 Walker B motif; other site 265072001669 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 265072001670 Uncharacterized conserved protein [Function unknown]; Region: COG2127 265072001671 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 265072001672 Domain of unknown function DUF21; Region: DUF21; pfam01595 265072001673 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 265072001674 Transporter associated domain; Region: CorC_HlyC; smart01091 265072001675 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 265072001676 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 265072001677 Protein export membrane protein; Region: SecD_SecF; pfam02355 265072001678 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 265072001679 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 265072001680 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 265072001681 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 265072001682 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 265072001683 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 265072001684 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 265072001685 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 265072001686 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 265072001687 Peptidase C13 family; Region: Peptidase_C13; cl02159 265072001688 2-isopropylmalate synthase; Validated; Region: PRK00915 265072001689 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 265072001690 active site 265072001691 catalytic residues [active] 265072001692 metal binding site [ion binding]; metal-binding site 265072001693 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 265072001694 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 265072001695 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 265072001696 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 265072001697 Predicted membrane protein [Function unknown]; Region: COG3235 265072001698 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 265072001699 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 265072001700 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 265072001701 signal recognition particle protein; Provisional; Region: PRK10867 265072001702 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 265072001703 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 265072001704 P loop; other site 265072001705 GTP binding site [chemical binding]; other site 265072001706 Signal peptide binding domain; Region: SRP_SPB; pfam02978 265072001707 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 265072001708 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 265072001709 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 265072001710 Protein of unknown function, DUF481; Region: DUF481; pfam04338 265072001711 CHASE domain; Region: CHASE; cl01369 265072001712 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072001713 PAS domain; Region: PAS_9; pfam13426 265072001714 putative active site [active] 265072001715 heme pocket [chemical binding]; other site 265072001716 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072001717 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072001718 metal binding site [ion binding]; metal-binding site 265072001719 active site 265072001720 I-site; other site 265072001721 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 265072001722 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 265072001723 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 265072001724 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072001725 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072001726 metal binding site [ion binding]; metal-binding site 265072001727 active site 265072001728 I-site; other site 265072001729 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 265072001730 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 265072001731 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072001732 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072001733 active site 265072001734 phosphorylation site [posttranslational modification] 265072001735 intermolecular recognition site; other site 265072001736 dimerization interface [polypeptide binding]; other site 265072001737 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 265072001738 DNA binding residues [nucleotide binding] 265072001739 dimerization interface [polypeptide binding]; other site 265072001740 putative membrane-bound dehydrogenase domain; Region: Piru_Ver_Nterm; TIGR02604 265072001741 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 265072001742 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 265072001743 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 265072001744 N-terminal plug; other site 265072001745 ligand-binding site [chemical binding]; other site 265072001746 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 265072001747 rRNA binding site [nucleotide binding]; other site 265072001748 predicted 30S ribosome binding site; other site 265072001749 Helix-turn-helix domain; Region: HTH_18; pfam12833 265072001750 Protein of unknown function DUF86; Region: DUF86; cl01031 265072001751 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 265072001752 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 265072001753 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 265072001754 Helix-turn-helix domain; Region: HTH_18; pfam12833 265072001755 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 265072001756 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 265072001757 methylamine dehydrogenase (amicyanin) heavy chain; Region: TTQ_MADH_Hv; TIGR02658 265072001758 Methylamine utilisation protein MauE; Region: MauE; pfam07291 265072001759 Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for...; Region: mauD; cd02967 265072001760 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072001761 catalytic residues [active] 265072001762 methylamine dehydrogenase (amicyanin) light chain; Region: TTQ_MADH_Lt; TIGR02659 265072001763 tryptophan tryptophylquinone biosynthesis enzyme MauG; Region: TTQ_mauG; TIGR03791 265072001764 MauM/NapG family ferredoxin-type protein; Region: mauM_napG; TIGR00397 265072001765 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 265072001766 4Fe-4S binding domain; Region: Fer4_5; pfam12801 265072001767 azurin; Region: azurin; TIGR02695 265072001768 aromatic amino acid exporter; Provisional; Region: PRK11689 265072001769 EamA-like transporter family; Region: EamA; pfam00892 265072001770 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 265072001771 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 265072001772 active site 265072001773 DNA binding site [nucleotide binding] 265072001774 Int/Topo IB signature motif; other site 265072001775 catalytic residues [active] 265072001776 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 265072001777 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 265072001778 putative dimer interface [polypeptide binding]; other site 265072001779 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 265072001780 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 265072001781 FeS/SAM binding site; other site 265072001782 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 265072001783 ferredoxin-NADP+ reductase; Region: PLN02852 265072001784 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 265072001785 Ferredoxin [Energy production and conversion]; Region: COG1146 265072001786 4Fe-4S binding domain; Region: Fer4; pfam00037 265072001787 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 265072001788 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 265072001789 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 265072001790 putative [4Fe-4S] binding site [ion binding]; other site 265072001791 putative molybdopterin cofactor binding site [chemical binding]; other site 265072001792 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 265072001793 putative molybdopterin cofactor binding site; other site 265072001794 Putative lumazine-binding; Region: Lumazine_bd_2; pfam12893 265072001795 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 265072001796 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 265072001797 DNA-binding site [nucleotide binding]; DNA binding site 265072001798 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 265072001799 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072001800 homodimer interface [polypeptide binding]; other site 265072001801 catalytic residue [active] 265072001802 aspartate kinase; Reviewed; Region: PRK06635 265072001803 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 265072001804 putative nucleotide binding site [chemical binding]; other site 265072001805 putative catalytic residues [active] 265072001806 putative Mg ion binding site [ion binding]; other site 265072001807 putative aspartate binding site [chemical binding]; other site 265072001808 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 265072001809 putative allosteric regulatory site; other site 265072001810 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 265072001811 putative allosteric regulatory residue; other site 265072001812 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 265072001813 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 265072001814 motif 1; other site 265072001815 active site 265072001816 motif 2; other site 265072001817 motif 3; other site 265072001818 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 265072001819 recombination regulator RecX; Reviewed; Region: recX; PRK00117 265072001820 recombinase A; Provisional; Region: recA; PRK09354 265072001821 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 265072001822 hexamer interface [polypeptide binding]; other site 265072001823 Walker A motif; other site 265072001824 ATP binding site [chemical binding]; other site 265072001825 Walker B motif; other site 265072001826 Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only]; Region: CinA; COG1546 265072001827 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 265072001828 tetramer interfaces [polypeptide binding]; other site 265072001829 binuclear metal-binding site [ion binding]; other site 265072001830 thiamine monophosphate kinase; Provisional; Region: PRK05731 265072001831 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 265072001832 ATP binding site [chemical binding]; other site 265072001833 dimerization interface [polypeptide binding]; other site 265072001834 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 265072001835 MPT binding site; other site 265072001836 trimer interface [polypeptide binding]; other site 265072001837 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 265072001838 protein binding site [polypeptide binding]; other site 265072001839 Site-specific recombinase; Region: SpecificRecomb; pfam10136 265072001840 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12671 265072001841 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 265072001842 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 265072001843 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 265072001844 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 265072001845 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 265072001846 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 265072001847 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 265072001848 Domain of unknown function (DUF4040); Region: DUF4040; pfam13244 265072001849 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12573 265072001850 hypothetical protein; Provisional; Region: PRK05255 265072001851 peptidase PmbA; Provisional; Region: PRK11040 265072001852 VacJ like lipoprotein; Region: VacJ; cl01073 265072001853 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 265072001854 AMP binding site [chemical binding]; other site 265072001855 metal binding site [ion binding]; metal-binding site 265072001856 active site 265072001857 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 265072001858 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 265072001859 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 265072001860 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072001861 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 265072001862 NAD(P) binding site [chemical binding]; other site 265072001863 active site 265072001864 short chain dehydrogenase; Provisional; Region: PRK06180 265072001865 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 265072001866 NADP binding site [chemical binding]; other site 265072001867 active site 265072001868 steroid binding site; other site 265072001869 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 265072001870 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 265072001871 DNA photolyase; Region: DNA_photolyase; pfam00875 265072001872 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 265072001873 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 265072001874 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 265072001875 tetramerization interface [polypeptide binding]; other site 265072001876 active site 265072001877 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 265072001878 Pantoate-beta-alanine ligase; Region: PanC; cd00560 265072001879 pantoate--beta-alanine ligase; Region: panC; TIGR00018 265072001880 active site 265072001881 ATP-binding site [chemical binding]; other site 265072001882 pantoate-binding site; other site 265072001883 HXXH motif; other site 265072001884 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 265072001885 oligomerization interface [polypeptide binding]; other site 265072001886 active site 265072001887 metal binding site [ion binding]; metal-binding site 265072001888 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 265072001889 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 265072001890 Substrate-binding site [chemical binding]; other site 265072001891 Substrate specificity [chemical binding]; other site 265072001892 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 265072001893 catalytic center binding site [active] 265072001894 ATP binding site [chemical binding]; other site 265072001895 poly(A) polymerase; Region: pcnB; TIGR01942 265072001896 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 265072001897 active site 265072001898 NTP binding site [chemical binding]; other site 265072001899 metal binding triad [ion binding]; metal-binding site 265072001900 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 265072001901 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 265072001902 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 265072001903 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 265072001904 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 265072001905 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 265072001906 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-C; cd09651 265072001907 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cd09757 265072001908 CRISPR-associated protein Cas7/Csd2, subtype I-C/DVULG; Region: cas_Csd2; TIGR02589 265072001909 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cd09637 265072001910 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-C; cd09721 265072001911 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 265072001912 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 265072001913 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 265072001914 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 265072001915 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 265072001916 Walker A/P-loop; other site 265072001917 ATP binding site [chemical binding]; other site 265072001918 Q-loop/lid; other site 265072001919 ABC transporter signature motif; other site 265072001920 Walker B; other site 265072001921 D-loop; other site 265072001922 H-loop/switch region; other site 265072001923 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 265072001924 active site 265072001925 catalytic site [active] 265072001926 TOBE-like domain; Region: TOBE_3; pfam12857 265072001927 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 265072001928 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 265072001929 dimer interface [polypeptide binding]; other site 265072001930 conserved gate region; other site 265072001931 putative PBP binding loops; other site 265072001932 ABC-ATPase subunit interface; other site 265072001933 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 265072001934 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 265072001935 dimer interface [polypeptide binding]; other site 265072001936 conserved gate region; other site 265072001937 putative PBP binding loops; other site 265072001938 ABC-ATPase subunit interface; other site 265072001939 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 265072001940 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 265072001941 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 265072001942 serine O-acetyltransferase; Region: cysE; TIGR01172 265072001943 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 265072001944 trimer interface [polypeptide binding]; other site 265072001945 active site 265072001946 substrate binding site [chemical binding]; other site 265072001947 CoA binding site [chemical binding]; other site 265072001948 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 265072001949 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 265072001950 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072001951 catalytic residue [active] 265072001952 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 265072001953 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 265072001954 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 265072001955 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 265072001956 Uncharacterized small protein (DUF2292); Region: DUF2292; pfam10055 265072001957 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 265072001958 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 265072001959 glutamate racemase; Provisional; Region: PRK00865 265072001960 Zinc-finger domain; Region: zf-CHCC; cl01821 265072001961 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 265072001962 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 265072001963 homodimer interface [polypeptide binding]; other site 265072001964 substrate-cofactor binding pocket; other site 265072001965 catalytic residue [active] 265072001966 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 265072001967 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 265072001968 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 265072001969 Cu(I) binding site [ion binding]; other site 265072001970 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 265072001971 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 265072001972 Low-spin heme binding site [chemical binding]; other site 265072001973 Putative water exit pathway; other site 265072001974 Binuclear center (active site) [active] 265072001975 Putative proton exit pathway; other site 265072001976 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 265072001977 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 265072001978 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 265072001979 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 265072001980 G5 domain; Region: G5; pfam07501 265072001981 Cytochrome c; Region: Cytochrom_C; pfam00034 265072001982 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 265072001983 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 265072001984 4Fe-4S binding domain; Region: Fer4_5; pfam12801 265072001985 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 265072001986 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 265072001987 YtkA-like; Region: YtkA; pfam13115 265072001988 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 265072001989 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 265072001990 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 265072001991 metal-binding site [ion binding] 265072001992 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 265072001993 Soluble P-type ATPase [General function prediction only]; Region: COG4087 265072001994 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 265072001995 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 265072001996 heme binding site [chemical binding]; other site 265072001997 ferroxidase pore; other site 265072001998 ferroxidase diiron center [ion binding]; other site 265072001999 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 265072002000 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 265072002001 heme binding site [chemical binding]; other site 265072002002 ferroxidase pore; other site 265072002003 ferroxidase diiron center [ion binding]; other site 265072002004 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 265072002005 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 265072002006 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 265072002007 heme-binding site [chemical binding]; other site 265072002008 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 265072002009 FAD binding pocket [chemical binding]; other site 265072002010 FAD binding motif [chemical binding]; other site 265072002011 phosphate binding motif [ion binding]; other site 265072002012 beta-alpha-beta structure motif; other site 265072002013 NAD binding pocket [chemical binding]; other site 265072002014 Heme binding pocket [chemical binding]; other site 265072002015 Predicted transcriptional regulator [Transcription]; Region: COG1959 265072002016 Transcriptional regulator; Region: Rrf2; cl17282 265072002017 Protein of unknown function DUF45; Region: DUF45; pfam01863 265072002018 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 265072002019 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 265072002020 putative acyl-acceptor binding pocket; other site 265072002021 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 265072002022 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 265072002023 active site 265072002024 motif I; other site 265072002025 motif II; other site 265072002026 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 265072002027 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 265072002028 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 265072002029 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 265072002030 motif 1; other site 265072002031 dimer interface [polypeptide binding]; other site 265072002032 active site 265072002033 motif 2; other site 265072002034 motif 3; other site 265072002035 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 265072002036 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 265072002037 putative active site [active] 265072002038 catalytic triad [active] 265072002039 putative dimer interface [polypeptide binding]; other site 265072002040 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 265072002041 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 265072002042 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 265072002043 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 265072002044 Transporter associated domain; Region: CorC_HlyC; smart01091 265072002045 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 265072002046 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 265072002047 PhoH-like protein; Region: PhoH; pfam02562 265072002048 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 265072002049 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 265072002050 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 265072002051 FeS/SAM binding site; other site 265072002052 TRAM domain; Region: TRAM; pfam01938 265072002053 siroheme synthase; Provisional; Region: cysG; PRK10637 265072002054 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 265072002055 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 265072002056 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 265072002057 active site 265072002058 SAM binding site [chemical binding]; other site 265072002059 homodimer interface [polypeptide binding]; other site 265072002060 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072002061 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 265072002062 dimerization interface [polypeptide binding]; other site 265072002063 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 265072002064 dimer interface [polypeptide binding]; other site 265072002065 phosphorylation site [posttranslational modification] 265072002066 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002067 ATP binding site [chemical binding]; other site 265072002068 Mg2+ binding site [ion binding]; other site 265072002069 G-X-G motif; other site 265072002070 osmolarity response regulator; Provisional; Region: ompR; PRK09468 265072002071 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072002072 active site 265072002073 phosphorylation site [posttranslational modification] 265072002074 intermolecular recognition site; other site 265072002075 dimerization interface [polypeptide binding]; other site 265072002076 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 265072002077 DNA binding site [nucleotide binding] 265072002078 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 265072002079 EF-hand domain pair; Region: EF_hand_5; pfam13499 265072002080 Ca2+ binding site [ion binding]; other site 265072002081 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 265072002082 Protein of unknown function, DUF482; Region: DUF482; pfam04339 265072002083 putative cation:proton antiport protein; Provisional; Region: PRK10669 265072002084 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 265072002085 TrkA-N domain; Region: TrkA_N; pfam02254 265072002086 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_8; cd07817 265072002087 putative hydrophobic ligand binding site [chemical binding]; other site 265072002088 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 265072002089 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 265072002090 putative active site [active] 265072002091 catalytic site [active] 265072002092 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 265072002093 putative active site [active] 265072002094 catalytic site [active] 265072002095 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 265072002096 GAF domain; Region: GAF; pfam01590 265072002097 PAS domain S-box; Region: sensory_box; TIGR00229 265072002098 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072002099 putative active site [active] 265072002100 heme pocket [chemical binding]; other site 265072002101 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072002102 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072002103 metal binding site [ion binding]; metal-binding site 265072002104 active site 265072002105 I-site; other site 265072002106 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 265072002107 BssS protein family; Region: BssS; pfam13991 265072002108 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 265072002109 GAF domain; Region: GAF; cl17456 265072002110 PAS domain S-box; Region: sensory_box; TIGR00229 265072002111 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072002112 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 265072002113 dimer interface [polypeptide binding]; other site 265072002114 phosphorylation site [posttranslational modification] 265072002115 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002116 ATP binding site [chemical binding]; other site 265072002117 Mg2+ binding site [ion binding]; other site 265072002118 G-X-G motif; other site 265072002119 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 265072002120 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072002121 active site 265072002122 phosphorylation site [posttranslational modification] 265072002123 intermolecular recognition site; other site 265072002124 dimerization interface [polypeptide binding]; other site 265072002125 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 265072002126 Predicted membrane protein [Function unknown]; Region: COG2323 265072002127 GTP-binding protein YchF; Reviewed; Region: PRK09601 265072002128 YchF GTPase; Region: YchF; cd01900 265072002129 G1 box; other site 265072002130 GTP/Mg2+ binding site [chemical binding]; other site 265072002131 Switch I region; other site 265072002132 G2 box; other site 265072002133 Switch II region; other site 265072002134 G3 box; other site 265072002135 G4 box; other site 265072002136 G5 box; other site 265072002137 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 265072002138 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 265072002139 putative active site [active] 265072002140 catalytic residue [active] 265072002141 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 265072002142 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 265072002143 5S rRNA interface [nucleotide binding]; other site 265072002144 CTC domain interface [polypeptide binding]; other site 265072002145 L16 interface [polypeptide binding]; other site 265072002146 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 265072002147 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 265072002148 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072002149 active site 265072002150 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 265072002151 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 265072002152 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 265072002153 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 265072002154 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 265072002155 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 265072002156 binding surface 265072002157 TPR motif; other site 265072002158 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 265072002159 TPR motif; other site 265072002160 binding surface 265072002161 Tetratricopeptide repeat; Region: TPR_12; pfam13424 265072002162 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 265072002163 binding surface 265072002164 TPR motif; other site 265072002165 TPR repeat; Region: TPR_11; pfam13414 265072002166 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 265072002167 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 265072002168 Walker A/P-loop; other site 265072002169 ATP binding site [chemical binding]; other site 265072002170 Q-loop/lid; other site 265072002171 ABC transporter signature motif; other site 265072002172 Walker B; other site 265072002173 D-loop; other site 265072002174 H-loop/switch region; other site 265072002175 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 265072002176 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 265072002177 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 265072002178 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 265072002179 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 265072002180 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 265072002181 DNA binding site [nucleotide binding] 265072002182 catalytic residue [active] 265072002183 H2TH interface [polypeptide binding]; other site 265072002184 putative catalytic residues [active] 265072002185 turnover-facilitating residue; other site 265072002186 intercalation triad [nucleotide binding]; other site 265072002187 8OG recognition residue [nucleotide binding]; other site 265072002188 putative reading head residues; other site 265072002189 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 265072002190 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 265072002191 MoxR-like ATPases [General function prediction only]; Region: COG0714 265072002192 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 265072002193 Walker A motif; other site 265072002194 ATP binding site [chemical binding]; other site 265072002195 Walker B motif; other site 265072002196 arginine finger; other site 265072002197 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 265072002198 Protein of unknown function DUF58; Region: DUF58; pfam01882 265072002199 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 265072002200 metal ion-dependent adhesion site (MIDAS); other site 265072002201 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 265072002202 metal ion-dependent adhesion site (MIDAS); other site 265072002203 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 265072002204 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 265072002205 DNA binding residues [nucleotide binding] 265072002206 dimer interface [polypeptide binding]; other site 265072002207 putative metal binding site [ion binding]; other site 265072002208 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 265072002209 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 265072002210 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 265072002211 Na binding site [ion binding]; other site 265072002212 putative glycosylation site [posttranslational modification]; other site 265072002213 putative glycosylation site [posttranslational modification]; other site 265072002214 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 265072002215 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 265072002216 active site 265072002217 substrate binding site [chemical binding]; other site 265072002218 ATP binding site [chemical binding]; other site 265072002219 SCP-2 sterol transfer family; Region: SCP2; pfam02036 265072002220 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 265072002221 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 265072002222 S-adenosylmethionine binding site [chemical binding]; other site 265072002223 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 265072002224 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 265072002225 Dynamin family; Region: Dynamin_N; pfam00350 265072002226 G1 box; other site 265072002227 GTP/Mg2+ binding site [chemical binding]; other site 265072002228 G2 box; other site 265072002229 Switch I region; other site 265072002230 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 265072002231 G3 box; other site 265072002232 Switch II region; other site 265072002233 GTP/Mg2+ binding site [chemical binding]; other site 265072002234 G4 box; other site 265072002235 G5 box; other site 265072002236 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 265072002237 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 265072002238 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 265072002239 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072002240 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 265072002241 DNA binding residues [nucleotide binding] 265072002242 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 265072002243 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 265072002244 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 265072002245 FtsX-like permease family; Region: FtsX; pfam02687 265072002246 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 265072002247 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 265072002248 Walker A/P-loop; other site 265072002249 ATP binding site [chemical binding]; other site 265072002250 Q-loop/lid; other site 265072002251 ABC transporter signature motif; other site 265072002252 Walker B; other site 265072002253 D-loop; other site 265072002254 H-loop/switch region; other site 265072002255 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 265072002256 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 265072002257 ZIP Zinc transporter; Region: Zip; pfam02535 265072002258 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072002259 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072002260 PEP-CTERM motif; Region: VPEP; pfam07589 265072002261 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 265072002262 protein structure with unknown function; Region: DUF4144; pfam13642 265072002263 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 265072002264 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 265072002265 dimerization interface [polypeptide binding]; other site 265072002266 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 265072002267 dimer interface [polypeptide binding]; other site 265072002268 phosphorylation site [posttranslational modification] 265072002269 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002270 ATP binding site [chemical binding]; other site 265072002271 Mg2+ binding site [ion binding]; other site 265072002272 G-X-G motif; other site 265072002273 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 265072002274 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072002275 active site 265072002276 phosphorylation site [posttranslational modification] 265072002277 intermolecular recognition site; other site 265072002278 dimerization interface [polypeptide binding]; other site 265072002279 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 265072002280 DNA binding site [nucleotide binding] 265072002281 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 265072002282 dimer interface [polypeptide binding]; other site 265072002283 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 265072002284 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 265072002285 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 265072002286 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 265072002287 catalytic loop [active] 265072002288 iron binding site [ion binding]; other site 265072002289 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 265072002290 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 265072002291 [4Fe-4S] binding site [ion binding]; other site 265072002292 molybdopterin cofactor binding site; other site 265072002293 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 265072002294 molybdopterin cofactor binding site; other site 265072002295 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 265072002296 putative dimer interface [polypeptide binding]; other site 265072002297 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 265072002298 SLBB domain; Region: SLBB; pfam10531 265072002299 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 265072002300 formate dehydrogenase subunit gamma; Validated; Region: PRK05988 265072002301 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a...; Region: TRX_Fd_NuoE_FDH_gamma; cd03081 265072002302 putative dimer interface [polypeptide binding]; other site 265072002303 [2Fe-2S] cluster binding site [ion binding]; other site 265072002304 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 265072002305 FAD binding domain; Region: FAD_binding_4; pfam01565 265072002306 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 265072002307 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 265072002308 ligand binding site [chemical binding]; other site 265072002309 NAD binding site [chemical binding]; other site 265072002310 tetramer interface [polypeptide binding]; other site 265072002311 catalytic site [active] 265072002312 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 265072002313 L-serine binding site [chemical binding]; other site 265072002314 ACT domain interface; other site 265072002315 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 265072002316 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 265072002317 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 265072002318 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 265072002319 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072002320 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 265072002321 putative dimerization interface [polypeptide binding]; other site 265072002322 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 265072002323 Ligand binding site [chemical binding]; other site 265072002324 Electron transfer flavoprotein domain; Region: ETF; pfam01012 265072002325 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 265072002326 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 265072002327 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 265072002328 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 265072002329 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 265072002330 FAD binding pocket [chemical binding]; other site 265072002331 FAD binding motif [chemical binding]; other site 265072002332 phosphate binding motif [ion binding]; other site 265072002333 beta-alpha-beta structure motif; other site 265072002334 NAD binding pocket [chemical binding]; other site 265072002335 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 265072002336 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 265072002337 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 265072002338 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072002339 Walker A/P-loop; other site 265072002340 ATP binding site [chemical binding]; other site 265072002341 Q-loop/lid; other site 265072002342 ABC transporter signature motif; other site 265072002343 Walker B; other site 265072002344 D-loop; other site 265072002345 H-loop/switch region; other site 265072002346 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 265072002347 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 265072002348 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 265072002349 P loop; other site 265072002350 GTP binding site [chemical binding]; other site 265072002351 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 265072002352 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 265072002353 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 265072002354 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 265072002355 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 265072002356 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 265072002357 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 265072002358 S-adenosylmethionine binding site [chemical binding]; other site 265072002359 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 265072002360 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 265072002361 active site 265072002362 (T/H)XGH motif; other site 265072002363 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 265072002364 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 265072002365 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 265072002366 dimer interface [polypeptide binding]; other site 265072002367 active site 265072002368 metal binding site [ion binding]; metal-binding site 265072002369 glutathione binding site [chemical binding]; other site 265072002370 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 265072002371 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 265072002372 Acetate kinase [Energy production and conversion]; Region: ackA; COG0282 265072002373 propionate/acetate kinase; Provisional; Region: PRK12379 265072002374 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072002375 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 265072002376 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072002377 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 265072002378 Protein export membrane protein; Region: SecD_SecF; cl14618 265072002379 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 265072002380 Protein export membrane protein; Region: SecD_SecF; cl14618 265072002381 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072002382 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 265072002383 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 265072002384 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 265072002385 2-isopropylmalate synthase; Validated; Region: PRK03739 265072002386 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 265072002387 active site 265072002388 catalytic residues [active] 265072002389 metal binding site [ion binding]; metal-binding site 265072002390 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 265072002391 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 265072002392 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 265072002393 putative substrate translocation pore; other site 265072002394 chaperone protein DnaJ; Provisional; Region: PRK10767 265072002395 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 265072002396 HSP70 interaction site [polypeptide binding]; other site 265072002397 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 265072002398 substrate binding site [polypeptide binding]; other site 265072002399 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 265072002400 Zn binding sites [ion binding]; other site 265072002401 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 265072002402 dimer interface [polypeptide binding]; other site 265072002403 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 265072002404 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 265072002405 nucleotide binding site [chemical binding]; other site 265072002406 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 265072002407 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 265072002408 dimer interface [polypeptide binding]; other site 265072002409 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 265072002410 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 265072002411 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 265072002412 putative active site [active] 265072002413 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072002414 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 265072002415 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 265072002416 hypothetical protein; Provisional; Region: PRK10649 265072002417 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 265072002418 Sulfatase; Region: Sulfatase; pfam00884 265072002419 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 265072002420 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 265072002421 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 265072002422 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 265072002423 phosphogluconate dehydratase; Validated; Region: PRK09054 265072002424 6-phosphogluconate dehydratase; Region: edd; TIGR01196 265072002425 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 265072002426 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 265072002427 active site 265072002428 intersubunit interface [polypeptide binding]; other site 265072002429 catalytic residue [active] 265072002430 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 265072002431 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 265072002432 active site 265072002433 ATP binding site [chemical binding]; other site 265072002434 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 265072002435 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072002436 putative ADP-binding pocket [chemical binding]; other site 265072002437 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 265072002438 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 265072002439 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 265072002440 putative active site [active] 265072002441 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 265072002442 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 265072002443 putative ribose interaction site [chemical binding]; other site 265072002444 putative ADP binding site [chemical binding]; other site 265072002445 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 265072002446 active site 265072002447 nucleotide binding site [chemical binding]; other site 265072002448 HIGH motif; other site 265072002449 KMSKS motif; other site 265072002450 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 265072002451 dimer interface [polypeptide binding]; other site 265072002452 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 265072002453 active site 265072002454 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 265072002455 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 265072002456 NADP binding site [chemical binding]; other site 265072002457 homopentamer interface [polypeptide binding]; other site 265072002458 substrate binding site [chemical binding]; other site 265072002459 active site 265072002460 ferrochelatase; Reviewed; Region: hemH; PRK00035 265072002461 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 265072002462 C-terminal domain interface [polypeptide binding]; other site 265072002463 active site 265072002464 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 265072002465 active site 265072002466 N-terminal domain interface [polypeptide binding]; other site 265072002467 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 265072002468 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 265072002469 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 265072002470 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 265072002471 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 265072002472 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 265072002473 Walker A/P-loop; other site 265072002474 ATP binding site [chemical binding]; other site 265072002475 Q-loop/lid; other site 265072002476 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 265072002477 ABC transporter signature motif; other site 265072002478 Walker B; other site 265072002479 D-loop; other site 265072002480 H-loop/switch region; other site 265072002481 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 265072002482 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 265072002483 dihydrodipicolinate reductase; Provisional; Region: PRK00048 265072002484 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 265072002485 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 265072002486 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 265072002487 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 265072002488 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 265072002489 catalytic site [active] 265072002490 subunit interface [polypeptide binding]; other site 265072002491 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 265072002492 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 265072002493 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 265072002494 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 265072002495 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 265072002496 ATP-grasp domain; Region: ATP-grasp_4; cl17255 265072002497 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 265072002498 IMP binding site; other site 265072002499 dimer interface [polypeptide binding]; other site 265072002500 interdomain contacts; other site 265072002501 partial ornithine binding site; other site 265072002502 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 265072002503 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 265072002504 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 265072002505 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 265072002506 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 265072002507 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 265072002508 S-adenosylmethionine binding site [chemical binding]; other site 265072002509 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 265072002510 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 265072002511 Walker A motif; other site 265072002512 ATP binding site [chemical binding]; other site 265072002513 Walker B motif; other site 265072002514 arginine finger; other site 265072002515 Peptidase family M41; Region: Peptidase_M41; pfam01434 265072002516 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 265072002517 dihydropteroate synthase; Region: DHPS; TIGR01496 265072002518 substrate binding pocket [chemical binding]; other site 265072002519 dimer interface [polypeptide binding]; other site 265072002520 inhibitor binding site; inhibition site 265072002521 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 265072002522 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 265072002523 active site 265072002524 substrate binding site [chemical binding]; other site 265072002525 metal binding site [ion binding]; metal-binding site 265072002526 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 265072002527 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 265072002528 active site 265072002529 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; pfam00882 265072002530 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 265072002531 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072002532 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 265072002533 putative ADP-binding pocket [chemical binding]; other site 265072002534 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 265072002535 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 265072002536 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 265072002537 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 265072002538 Walker A/P-loop; other site 265072002539 ATP binding site [chemical binding]; other site 265072002540 Q-loop/lid; other site 265072002541 ABC transporter signature motif; other site 265072002542 Walker B; other site 265072002543 D-loop; other site 265072002544 H-loop/switch region; other site 265072002545 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 265072002546 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 265072002547 dimer interface [polypeptide binding]; other site 265072002548 conserved gate region; other site 265072002549 putative PBP binding loops; other site 265072002550 ABC-ATPase subunit interface; other site 265072002551 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 265072002552 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 265072002553 dimer interface [polypeptide binding]; other site 265072002554 conserved gate region; other site 265072002555 putative PBP binding loops; other site 265072002556 ABC-ATPase subunit interface; other site 265072002557 phosphate binding protein; Region: ptsS_2; TIGR02136 265072002558 peptide chain release factor 2; Validated; Region: prfB; PRK00578 265072002559 This domain is found in peptide chain release factors; Region: PCRF; smart00937 265072002560 RF-1 domain; Region: RF-1; pfam00472 265072002561 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 265072002562 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 265072002563 dimer interface [polypeptide binding]; other site 265072002564 putative anticodon binding site; other site 265072002565 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 265072002566 motif 1; other site 265072002567 active site 265072002568 motif 2; other site 265072002569 motif 3; other site 265072002570 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 265072002571 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 265072002572 Sulfate transporter family; Region: Sulfate_transp; pfam00916 265072002573 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 265072002574 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeC; cd03378 265072002575 active site clefts [active] 265072002576 zinc binding site [ion binding]; other site 265072002577 dimer interface [polypeptide binding]; other site 265072002578 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 265072002579 putative diguanylate cyclase; Provisional; Region: PRK09776 265072002580 MASE1; Region: MASE1; cl17823 265072002581 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072002582 putative active site [active] 265072002583 heme pocket [chemical binding]; other site 265072002584 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072002585 putative active site [active] 265072002586 heme pocket [chemical binding]; other site 265072002587 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072002588 putative active site [active] 265072002589 heme pocket [chemical binding]; other site 265072002590 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072002591 metal binding site [ion binding]; metal-binding site 265072002592 active site 265072002593 I-site; other site 265072002594 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 265072002595 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 265072002596 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 265072002597 catalytic loop [active] 265072002598 iron binding site [ion binding]; other site 265072002599 chaperone protein HscA; Provisional; Region: hscA; PRK05183 265072002600 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 265072002601 nucleotide binding site [chemical binding]; other site 265072002602 putative NEF/HSP70 interaction site [polypeptide binding]; other site 265072002603 SBD interface [polypeptide binding]; other site 265072002604 co-chaperone HscB; Provisional; Region: hscB; PRK03578 265072002605 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 265072002606 HSP70 interaction site [polypeptide binding]; other site 265072002607 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 265072002608 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 265072002609 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 265072002610 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 265072002611 trimerization site [polypeptide binding]; other site 265072002612 active site 265072002613 cysteine desulfurase; Provisional; Region: PRK14012 265072002614 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 265072002615 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072002616 catalytic residue [active] 265072002617 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 265072002618 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 265072002619 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072002620 catalytic residue [active] 265072002621 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 265072002622 Rrf2 family protein; Region: rrf2_super; TIGR00738 265072002623 serine O-acetyltransferase; Region: cysE; TIGR01172 265072002624 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 265072002625 trimer interface [polypeptide binding]; other site 265072002626 active site 265072002627 substrate binding site [chemical binding]; other site 265072002628 CoA binding site [chemical binding]; other site 265072002629 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 265072002630 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 265072002631 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 265072002632 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 265072002633 active site 265072002634 dimerization interface [polypeptide binding]; other site 265072002635 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 265072002636 dimerization interface [polypeptide binding]; other site 265072002637 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 265072002638 Histidine kinase; Region: HisKA_3; pfam07730 265072002639 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002640 ATP binding site [chemical binding]; other site 265072002641 Mg2+ binding site [ion binding]; other site 265072002642 G-X-G motif; other site 265072002643 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072002644 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072002645 active site 265072002646 phosphorylation site [posttranslational modification] 265072002647 intermolecular recognition site; other site 265072002648 dimerization interface [polypeptide binding]; other site 265072002649 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 265072002650 DNA binding residues [nucleotide binding] 265072002651 dimerization interface [polypeptide binding]; other site 265072002652 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072002653 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072002654 active site 265072002655 phosphorylation site [posttranslational modification] 265072002656 intermolecular recognition site; other site 265072002657 dimerization interface [polypeptide binding]; other site 265072002658 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 265072002659 DNA binding residues [nucleotide binding] 265072002660 dimerization interface [polypeptide binding]; other site 265072002661 PAS domain S-box; Region: sensory_box; TIGR00229 265072002662 Histidine kinase; Region: HisKA_3; pfam07730 265072002663 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002664 ATP binding site [chemical binding]; other site 265072002665 Mg2+ binding site [ion binding]; other site 265072002666 G-X-G motif; other site 265072002667 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072002668 Phage protein; Region: DUF3653; pfam12375 265072002669 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 265072002670 catalytic residues [active] 265072002671 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; pfam05840 265072002672 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072002673 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 265072002674 MutS domain I; Region: MutS_I; pfam01624 265072002675 MutS domain II; Region: MutS_II; pfam05188 265072002676 MutS domain III; Region: MutS_III; pfam05192 265072002677 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 265072002678 Walker A/P-loop; other site 265072002679 ATP binding site [chemical binding]; other site 265072002680 Q-loop/lid; other site 265072002681 ABC transporter signature motif; other site 265072002682 Walker B; other site 265072002683 D-loop; other site 265072002684 H-loop/switch region; other site 265072002685 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 265072002686 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 265072002687 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 265072002688 catalytic triad [active] 265072002689 Uncharacterized conserved protein [Function unknown]; Region: COG2850 265072002690 Cupin domain; Region: Cupin_2; cl17218 265072002691 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 265072002692 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072002693 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 265072002694 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 265072002695 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 265072002696 dihydrodipicolinate synthase; Region: dapA; TIGR00674 265072002697 dimer interface [polypeptide binding]; other site 265072002698 active site 265072002699 catalytic residue [active] 265072002700 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 265072002701 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 265072002702 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 265072002703 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 265072002704 active site 265072002705 motif I; other site 265072002706 motif II; other site 265072002707 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 265072002708 Flagellar protein YcgR; Region: YcgR_2; pfam12945 265072002709 PilZ domain; Region: PilZ; pfam07238 265072002710 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 265072002711 ferredoxin; Provisional; Region: PRK08764 265072002712 Putative Fe-S cluster; Region: FeS; pfam04060 265072002713 4Fe-4S binding domain; Region: Fer4; pfam00037 265072002714 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 265072002715 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 265072002716 minor groove reading motif; other site 265072002717 helix-hairpin-helix signature motif; other site 265072002718 substrate binding pocket [chemical binding]; other site 265072002719 active site 265072002720 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 265072002721 FIST C domain; Region: FIST_C; pfam10442 265072002722 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 265072002723 dimer interface [polypeptide binding]; other site 265072002724 substrate binding site [chemical binding]; other site 265072002725 ATP binding site [chemical binding]; other site 265072002726 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 265072002727 L-aspartate oxidase; Provisional; Region: PRK09077 265072002728 L-aspartate oxidase; Provisional; Region: PRK06175 265072002729 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 265072002730 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 265072002731 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072002732 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 265072002733 DNA binding residues [nucleotide binding] 265072002734 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 265072002735 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 265072002736 anti-sigma E factor; Provisional; Region: rseB; PRK09455 265072002737 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 265072002738 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 265072002739 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 265072002740 protein binding site [polypeptide binding]; other site 265072002741 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 265072002742 protein binding site [polypeptide binding]; other site 265072002743 GTP-binding protein LepA; Provisional; Region: PRK05433 265072002744 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 265072002745 G1 box; other site 265072002746 putative GEF interaction site [polypeptide binding]; other site 265072002747 GTP/Mg2+ binding site [chemical binding]; other site 265072002748 Switch I region; other site 265072002749 G2 box; other site 265072002750 G3 box; other site 265072002751 Switch II region; other site 265072002752 G4 box; other site 265072002753 G5 box; other site 265072002754 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 265072002755 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 265072002756 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 265072002757 signal peptidase I; Provisional; Region: PRK10861 265072002758 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 265072002759 Catalytic site [active] 265072002760 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 265072002761 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 265072002762 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 265072002763 dimerization interface [polypeptide binding]; other site 265072002764 active site 265072002765 metal binding site [ion binding]; metal-binding site 265072002766 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 265072002767 dsRNA binding site [nucleotide binding]; other site 265072002768 GTPase Era; Reviewed; Region: era; PRK00089 265072002769 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 265072002770 G1 box; other site 265072002771 GTP/Mg2+ binding site [chemical binding]; other site 265072002772 Switch I region; other site 265072002773 G2 box; other site 265072002774 Switch II region; other site 265072002775 G3 box; other site 265072002776 G4 box; other site 265072002777 G5 box; other site 265072002778 KH domain; Region: KH_2; pfam07650 265072002779 phospholipid:lipid A palmitoyltransferase; Provisional; Region: pagP; PRK11045 265072002780 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 265072002781 Recombination protein O N terminal; Region: RecO_N; pfam11967 265072002782 Recombination protein O C terminal; Region: RecO_C; pfam02565 265072002783 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 265072002784 active site 265072002785 hydrophilic channel; other site 265072002786 dimerization interface [polypeptide binding]; other site 265072002787 catalytic residues [active] 265072002788 active site lid [active] 265072002789 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 265072002790 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 265072002791 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 265072002792 putative ATP binding site [chemical binding]; other site 265072002793 putative substrate interface [chemical binding]; other site 265072002794 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072002795 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 265072002796 N-terminal plug; other site 265072002797 ligand-binding site [chemical binding]; other site 265072002798 heat shock protein 90; Provisional; Region: PRK05218 265072002799 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002800 ATP binding site [chemical binding]; other site 265072002801 Mg2+ binding site [ion binding]; other site 265072002802 G-X-G motif; other site 265072002803 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 265072002804 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 265072002805 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 265072002806 RNA binding surface [nucleotide binding]; other site 265072002807 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 265072002808 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 265072002809 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 265072002810 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072002811 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 265072002812 homodimer interface [polypeptide binding]; other site 265072002813 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 265072002814 active site pocket [active] 265072002815 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 265072002816 Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]; Region: COG3545 265072002817 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 265072002818 Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm; Region: BLMA_like; cd08349 265072002819 dimer interface [polypeptide binding]; other site 265072002820 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 265072002821 ligand binding site [chemical binding]; other site 265072002822 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 265072002823 emp24/gp25L/p24 family/GOLD; Region: EMP24_GP25L; pfam01105 265072002824 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 265072002825 putative catalytic site [active] 265072002826 putative metal binding site [ion binding]; other site 265072002827 putative phosphate binding site [ion binding]; other site 265072002828 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072002829 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072002830 metal binding site [ion binding]; metal-binding site 265072002831 active site 265072002832 I-site; other site 265072002833 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 265072002834 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 265072002835 dimerization interface [polypeptide binding]; other site 265072002836 ATP binding site [chemical binding]; other site 265072002837 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 265072002838 dimerization interface [polypeptide binding]; other site 265072002839 ATP binding site [chemical binding]; other site 265072002840 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 265072002841 putative active site [active] 265072002842 catalytic triad [active] 265072002843 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 265072002844 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 265072002845 putative membrane-bound dehydrogenase domain; Region: Piru_Ver_Nterm; TIGR02604 265072002846 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 265072002847 cyanate transporter; Region: CynX; TIGR00896 265072002848 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 265072002849 putative substrate translocation pore; other site 265072002850 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 265072002851 putative phosphoketolase; Provisional; Region: PRK05261 265072002852 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 265072002853 TPP-binding site; other site 265072002854 XFP C-terminal domain; Region: XFP_C; pfam09363 265072002855 PAAR motif; Region: PAAR_motif; pfam05488 265072002856 Rhs element Vgr protein; Region: vgr_GE; TIGR01646 265072002857 Phage protein D [General function prediction only]; Region: COG3500 265072002858 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 265072002859 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 265072002860 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 265072002861 dinuclear metal binding motif [ion binding]; other site 265072002862 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 265072002863 GAF domain; Region: GAF; pfam01590 265072002864 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 265072002865 Walker A motif; other site 265072002866 ATP binding site [chemical binding]; other site 265072002867 Walker B motif; other site 265072002868 arginine finger; other site 265072002869 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 265072002870 DNA-binding interface [nucleotide binding]; DNA binding site 265072002871 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 265072002872 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 265072002873 active site 265072002874 metal binding site [ion binding]; metal-binding site 265072002875 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 265072002876 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 265072002877 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 265072002878 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 265072002879 aminotransferase AlaT; Validated; Region: PRK09265 265072002880 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 265072002881 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072002882 homodimer interface [polypeptide binding]; other site 265072002883 catalytic residue [active] 265072002884 homoserine dehydrogenase; Provisional; Region: PRK06349 265072002885 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 265072002886 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 265072002887 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 265072002888 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 265072002889 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 265072002890 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072002891 catalytic residue [active] 265072002892 thymidylate synthase; Reviewed; Region: thyA; PRK01827 265072002893 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 265072002894 dimerization interface [polypeptide binding]; other site 265072002895 active site 265072002896 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072002897 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072002898 metal binding site [ion binding]; metal-binding site 265072002899 active site 265072002900 I-site; other site 265072002901 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 265072002902 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 265072002903 Predicted membrane protein [Function unknown]; Region: COG3212 265072002904 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 265072002905 Putative motility protein; Region: YjfB_motility; pfam14070 265072002906 response regulator GlrR; Provisional; Region: PRK15115 265072002907 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072002908 active site 265072002909 phosphorylation site [posttranslational modification] 265072002910 intermolecular recognition site; other site 265072002911 dimerization interface [polypeptide binding]; other site 265072002912 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 265072002913 Walker A motif; other site 265072002914 ATP binding site [chemical binding]; other site 265072002915 Walker B motif; other site 265072002916 arginine finger; other site 265072002917 CHASE3 domain; Region: CHASE3; cl05000 265072002918 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072002919 HAMP domain; Region: HAMP; pfam00672 265072002920 dimerization interface [polypeptide binding]; other site 265072002921 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 265072002922 dimer interface [polypeptide binding]; other site 265072002923 phosphorylation site [posttranslational modification] 265072002924 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072002925 ATP binding site [chemical binding]; other site 265072002926 Mg2+ binding site [ion binding]; other site 265072002927 G-X-G motif; other site 265072002928 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 265072002929 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 265072002930 folate binding site [chemical binding]; other site 265072002931 NADP+ binding site [chemical binding]; other site 265072002932 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 265072002933 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 265072002934 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 265072002935 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072002936 catalytic residue [active] 265072002937 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 265072002938 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 265072002939 trimer interface [polypeptide binding]; other site 265072002940 active site 265072002941 glucose-6-phosphate 1-dehydrogenase; Provisional; Region: PRK12853 265072002942 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 265072002943 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 265072002944 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 265072002945 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 265072002946 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 265072002947 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 265072002948 putative active site [active] 265072002949 antiporter inner membrane protein; Provisional; Region: PRK11670 265072002950 Domain of unknown function DUF59; Region: DUF59; pfam01883 265072002951 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 265072002952 Walker A motif; other site 265072002953 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 265072002954 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 265072002955 active site 265072002956 HIGH motif; other site 265072002957 KMSKS motif; other site 265072002958 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 265072002959 tRNA binding surface [nucleotide binding]; other site 265072002960 anticodon binding site; other site 265072002961 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 265072002962 dimer interface [polypeptide binding]; other site 265072002963 putative tRNA-binding site [nucleotide binding]; other site 265072002964 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 265072002965 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 265072002966 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 265072002967 active site 265072002968 dimer interface [polypeptide binding]; other site 265072002969 tetratricopeptide repeat protein; Provisional; Region: PRK11788 265072002970 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 265072002971 binding surface 265072002972 TPR motif; other site 265072002973 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 265072002974 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 265072002975 IHF dimer interface [polypeptide binding]; other site 265072002976 IHF - DNA interface [nucleotide binding]; other site 265072002977 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 265072002978 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 265072002979 RNA binding site [nucleotide binding]; other site 265072002980 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 265072002981 RNA binding site [nucleotide binding]; other site 265072002982 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 265072002983 RNA binding site [nucleotide binding]; other site 265072002984 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 265072002985 RNA binding site [nucleotide binding]; other site 265072002986 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 265072002987 RNA binding site [nucleotide binding]; other site 265072002988 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 265072002989 RNA binding site [nucleotide binding]; other site 265072002990 cytidylate kinase; Provisional; Region: cmk; PRK00023 265072002991 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 265072002992 CMP-binding site; other site 265072002993 The sites determining sugar specificity; other site 265072002994 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 265072002995 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 265072002996 hinge; other site 265072002997 active site 265072002998 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 265072002999 prephenate dehydrogenase; Validated; Region: PRK08507 265072003000 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 265072003001 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 265072003002 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 265072003003 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 265072003004 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 265072003005 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 265072003006 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 265072003007 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 265072003008 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 265072003009 metal-binding site [ion binding] 265072003010 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 265072003011 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 265072003012 metal-binding site [ion binding] 265072003013 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 265072003014 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 265072003015 motif II; other site 265072003016 hypothetical protein; Provisional; Region: PRK01254 265072003017 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 265072003018 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 265072003019 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 265072003020 TraB family; Region: TraB; cl12050 265072003021 TraB family; Region: TraB; pfam01963 265072003022 spermidine N1-acetyltransferase; Provisional; Region: PRK15130 265072003023 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 265072003024 Coenzyme A binding pocket [chemical binding]; other site 265072003025 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 265072003026 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 265072003027 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 265072003028 Response regulator receiver domain; Region: Response_reg; pfam00072 265072003029 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003030 active site 265072003031 phosphorylation site [posttranslational modification] 265072003032 intermolecular recognition site; other site 265072003033 dimerization interface [polypeptide binding]; other site 265072003034 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072003035 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003036 active site 265072003037 phosphorylation site [posttranslational modification] 265072003038 intermolecular recognition site; other site 265072003039 dimerization interface [polypeptide binding]; other site 265072003040 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 265072003041 DNA binding residues [nucleotide binding] 265072003042 dimerization interface [polypeptide binding]; other site 265072003043 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 265072003044 CHASE3 domain; Region: CHASE3; pfam05227 265072003045 Histidine kinase; Region: HisKA_3; pfam07730 265072003046 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 265072003047 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072003048 ATP binding site [chemical binding]; other site 265072003049 Mg2+ binding site [ion binding]; other site 265072003050 G-X-G motif; other site 265072003051 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 265072003052 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 265072003053 EF-hand domain pair; Region: EF_hand_5; pfam13499 265072003054 Ca2+ binding site [ion binding]; other site 265072003055 BON domain; Region: BON; pfam04972 265072003056 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 265072003057 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 265072003058 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 265072003059 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 265072003060 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 265072003061 ATP binding site [chemical binding]; other site 265072003062 putative Mg++ binding site [ion binding]; other site 265072003063 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 265072003064 nucleotide binding region [chemical binding]; other site 265072003065 ATP-binding site [chemical binding]; other site 265072003066 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 265072003067 HRDC domain; Region: HRDC; pfam00570 265072003068 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 265072003069 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 265072003070 ATP binding site [chemical binding]; other site 265072003071 Mg++ binding site [ion binding]; other site 265072003072 motif III; other site 265072003073 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 265072003074 nucleotide binding region [chemical binding]; other site 265072003075 ATP-binding site [chemical binding]; other site 265072003076 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 265072003077 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 265072003078 RNA binding surface [nucleotide binding]; other site 265072003079 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 265072003080 active site 265072003081 uracil binding [chemical binding]; other site 265072003082 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 265072003083 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 265072003084 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 265072003085 PhnA protein; Region: PhnA; pfam03831 265072003086 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 265072003087 dimer interface [polypeptide binding]; other site 265072003088 putative tRNA-binding site [nucleotide binding]; other site 265072003089 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481 265072003090 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 265072003091 DAK2 domain; Region: Dak2; cl03685 265072003092 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 265072003093 tetramer (dimer of dimers) interface [polypeptide binding]; other site 265072003094 active site 265072003095 dimer interface [polypeptide binding]; other site 265072003096 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 265072003097 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 265072003098 catalytic residues [active] 265072003099 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; pfam05840 265072003100 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072003101 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 265072003102 MutS domain I; Region: MutS_I; pfam01624 265072003103 MutS domain II; Region: MutS_II; pfam05188 265072003104 MutS domain III; Region: MutS_III; pfam05192 265072003105 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 265072003106 Walker A/P-loop; other site 265072003107 ATP binding site [chemical binding]; other site 265072003108 Q-loop/lid; other site 265072003109 ABC transporter signature motif; other site 265072003110 Walker B; other site 265072003111 D-loop; other site 265072003112 H-loop/switch region; other site 265072003113 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 265072003114 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 265072003115 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 265072003116 catalytic triad [active] 265072003117 Uncharacterized conserved protein [Function unknown]; Region: COG2850 265072003118 Cupin domain; Region: Cupin_2; cl17218 265072003119 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 265072003120 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072003121 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 265072003122 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 265072003123 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 265072003124 dihydrodipicolinate synthase; Region: dapA; TIGR00674 265072003125 dimer interface [polypeptide binding]; other site 265072003126 active site 265072003127 catalytic residue [active] 265072003128 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 265072003129 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 265072003130 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 265072003131 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 265072003132 active site 265072003133 motif I; other site 265072003134 motif II; other site 265072003135 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 265072003136 Flagellar protein YcgR; Region: YcgR_2; pfam12945 265072003137 PilZ domain; Region: PilZ; pfam07238 265072003138 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 265072003139 ferredoxin; Provisional; Region: PRK08764 265072003140 Putative Fe-S cluster; Region: FeS; pfam04060 265072003141 4Fe-4S binding domain; Region: Fer4; pfam00037 265072003142 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 265072003143 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 265072003144 minor groove reading motif; other site 265072003145 helix-hairpin-helix signature motif; other site 265072003146 substrate binding pocket [chemical binding]; other site 265072003147 active site 265072003148 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 265072003149 FIST C domain; Region: FIST_C; pfam10442 265072003150 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 265072003151 dimer interface [polypeptide binding]; other site 265072003152 substrate binding site [chemical binding]; other site 265072003153 ATP binding site [chemical binding]; other site 265072003154 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 265072003155 L-aspartate oxidase; Provisional; Region: PRK09077 265072003156 L-aspartate oxidase; Provisional; Region: PRK06175 265072003157 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 265072003158 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 265072003159 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072003160 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 265072003161 DNA binding residues [nucleotide binding] 265072003162 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 265072003163 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 265072003164 anti-sigma E factor; Provisional; Region: rseB; PRK09455 265072003165 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 265072003166 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 265072003167 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 265072003168 protein binding site [polypeptide binding]; other site 265072003169 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 265072003170 protein binding site [polypeptide binding]; other site 265072003171 GTP-binding protein LepA; Provisional; Region: PRK05433 265072003172 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 265072003173 G1 box; other site 265072003174 putative GEF interaction site [polypeptide binding]; other site 265072003175 GTP/Mg2+ binding site [chemical binding]; other site 265072003176 Switch I region; other site 265072003177 G2 box; other site 265072003178 G3 box; other site 265072003179 Switch II region; other site 265072003180 G4 box; other site 265072003181 G5 box; other site 265072003182 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 265072003183 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 265072003184 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 265072003185 signal peptidase I; Provisional; Region: PRK10861 265072003186 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 265072003187 Catalytic site [active] 265072003188 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 265072003189 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 265072003190 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 265072003191 dimerization interface [polypeptide binding]; other site 265072003192 active site 265072003193 metal binding site [ion binding]; metal-binding site 265072003194 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 265072003195 dsRNA binding site [nucleotide binding]; other site 265072003196 GTPase Era; Reviewed; Region: era; PRK00089 265072003197 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 265072003198 G1 box; other site 265072003199 GTP/Mg2+ binding site [chemical binding]; other site 265072003200 Switch I region; other site 265072003201 G2 box; other site 265072003202 Switch II region; other site 265072003203 G3 box; other site 265072003204 G4 box; other site 265072003205 G5 box; other site 265072003206 KH domain; Region: KH_2; pfam07650 265072003207 phospholipid:lipid A palmitoyltransferase; Provisional; Region: pagP; PRK11045 265072003208 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 265072003209 Recombination protein O N terminal; Region: RecO_N; pfam11967 265072003210 Recombination protein O C terminal; Region: RecO_C; pfam02565 265072003211 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 265072003212 active site 265072003213 hydrophilic channel; other site 265072003214 dimerization interface [polypeptide binding]; other site 265072003215 catalytic residues [active] 265072003216 active site lid [active] 265072003217 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 265072003218 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 265072003219 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 265072003220 putative ATP binding site [chemical binding]; other site 265072003221 putative substrate interface [chemical binding]; other site 265072003222 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072003223 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 265072003224 N-terminal plug; other site 265072003225 ligand-binding site [chemical binding]; other site 265072003226 heat shock protein 90; Provisional; Region: PRK05218 265072003227 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072003228 ATP binding site [chemical binding]; other site 265072003229 Mg2+ binding site [ion binding]; other site 265072003230 G-X-G motif; other site 265072003231 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 265072003232 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 265072003233 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 265072003234 RNA binding surface [nucleotide binding]; other site 265072003235 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 265072003236 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 265072003237 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 265072003238 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072003239 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 265072003240 homodimer interface [polypeptide binding]; other site 265072003241 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 265072003242 active site pocket [active] 265072003243 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 265072003244 Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]; Region: COG3545 265072003245 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 265072003246 Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm; Region: BLMA_like; cd08349 265072003247 dimer interface [polypeptide binding]; other site 265072003248 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 265072003249 ligand binding site [chemical binding]; other site 265072003250 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 265072003251 emp24/gp25L/p24 family/GOLD; Region: EMP24_GP25L; pfam01105 265072003252 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 265072003253 putative catalytic site [active] 265072003254 putative metal binding site [ion binding]; other site 265072003255 putative phosphate binding site [ion binding]; other site 265072003256 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072003257 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072003258 metal binding site [ion binding]; metal-binding site 265072003259 active site 265072003260 I-site; other site 265072003261 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 265072003262 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 265072003263 dimerization interface [polypeptide binding]; other site 265072003264 ATP binding site [chemical binding]; other site 265072003265 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 265072003266 dimerization interface [polypeptide binding]; other site 265072003267 ATP binding site [chemical binding]; other site 265072003268 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 265072003269 putative active site [active] 265072003270 catalytic triad [active] 265072003271 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 265072003272 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 265072003273 putative membrane-bound dehydrogenase domain; Region: Piru_Ver_Nterm; TIGR02604 265072003274 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 265072003275 cyanate transporter; Region: CynX; TIGR00896 265072003276 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 265072003277 putative substrate translocation pore; other site 265072003278 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 265072003279 putative phosphoketolase; Provisional; Region: PRK05261 265072003280 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 265072003281 TPP-binding site; other site 265072003282 XFP C-terminal domain; Region: XFP_C; pfam09363 265072003283 PAAR motif; Region: PAAR_motif; pfam05488 265072003284 Rhs element Vgr protein; Region: vgr_GE; TIGR01646 265072003285 Phage protein D [General function prediction only]; Region: COG3500 265072003286 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 265072003287 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 265072003288 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 265072003289 dinuclear metal binding motif [ion binding]; other site 265072003290 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 265072003291 GAF domain; Region: GAF; pfam01590 265072003292 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 265072003293 Walker A motif; other site 265072003294 ATP binding site [chemical binding]; other site 265072003295 Walker B motif; other site 265072003296 arginine finger; other site 265072003297 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 265072003298 DNA-binding interface [nucleotide binding]; DNA binding site 265072003299 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 265072003300 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 265072003301 active site 265072003302 metal binding site [ion binding]; metal-binding site 265072003303 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 265072003304 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 265072003305 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 265072003306 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 265072003307 aminotransferase AlaT; Validated; Region: PRK09265 265072003308 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 265072003309 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072003310 homodimer interface [polypeptide binding]; other site 265072003311 catalytic residue [active] 265072003312 homoserine dehydrogenase; Provisional; Region: PRK06349 265072003313 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 265072003314 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 265072003315 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 265072003316 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 265072003317 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 265072003318 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072003319 catalytic residue [active] 265072003320 thymidylate synthase; Reviewed; Region: thyA; PRK01827 265072003321 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 265072003322 dimerization interface [polypeptide binding]; other site 265072003323 active site 265072003324 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072003325 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072003326 metal binding site [ion binding]; metal-binding site 265072003327 active site 265072003328 I-site; other site 265072003329 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 265072003330 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 265072003331 Predicted membrane protein [Function unknown]; Region: COG3212 265072003332 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 265072003333 Putative motility protein; Region: YjfB_motility; pfam14070 265072003334 response regulator GlrR; Provisional; Region: PRK15115 265072003335 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003336 active site 265072003337 phosphorylation site [posttranslational modification] 265072003338 intermolecular recognition site; other site 265072003339 dimerization interface [polypeptide binding]; other site 265072003340 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 265072003341 Walker A motif; other site 265072003342 ATP binding site [chemical binding]; other site 265072003343 Walker B motif; other site 265072003344 arginine finger; other site 265072003345 CHASE3 domain; Region: CHASE3; cl05000 265072003346 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072003347 HAMP domain; Region: HAMP; pfam00672 265072003348 dimerization interface [polypeptide binding]; other site 265072003349 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 265072003350 dimer interface [polypeptide binding]; other site 265072003351 phosphorylation site [posttranslational modification] 265072003352 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072003353 ATP binding site [chemical binding]; other site 265072003354 Mg2+ binding site [ion binding]; other site 265072003355 G-X-G motif; other site 265072003356 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 265072003357 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 265072003358 folate binding site [chemical binding]; other site 265072003359 NADP+ binding site [chemical binding]; other site 265072003360 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 265072003361 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 265072003362 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 265072003363 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072003364 catalytic residue [active] 265072003365 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 265072003366 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 265072003367 trimer interface [polypeptide binding]; other site 265072003368 active site 265072003369 glucose-6-phosphate 1-dehydrogenase; Provisional; Region: PRK12853 265072003370 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 265072003371 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 265072003372 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 265072003373 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 265072003374 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 265072003375 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 265072003376 putative active site [active] 265072003377 antiporter inner membrane protein; Provisional; Region: PRK11670 265072003378 Domain of unknown function DUF59; Region: DUF59; pfam01883 265072003379 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 265072003380 Walker A motif; other site 265072003381 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 265072003382 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 265072003383 active site 265072003384 HIGH motif; other site 265072003385 KMSKS motif; other site 265072003386 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 265072003387 tRNA binding surface [nucleotide binding]; other site 265072003388 anticodon binding site; other site 265072003389 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 265072003390 dimer interface [polypeptide binding]; other site 265072003391 putative tRNA-binding site [nucleotide binding]; other site 265072003392 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 265072003393 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 265072003394 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 265072003395 active site 265072003396 dimer interface [polypeptide binding]; other site 265072003397 tetratricopeptide repeat protein; Provisional; Region: PRK11788 265072003398 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 265072003399 binding surface 265072003400 TPR motif; other site 265072003401 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 265072003402 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 265072003403 IHF dimer interface [polypeptide binding]; other site 265072003404 IHF - DNA interface [nucleotide binding]; other site 265072003405 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 265072003406 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 265072003407 RNA binding site [nucleotide binding]; other site 265072003408 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 265072003409 RNA binding site [nucleotide binding]; other site 265072003410 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 265072003411 RNA binding site [nucleotide binding]; other site 265072003412 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 265072003413 RNA binding site [nucleotide binding]; other site 265072003414 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 265072003415 RNA binding site [nucleotide binding]; other site 265072003416 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 265072003417 RNA binding site [nucleotide binding]; other site 265072003418 cytidylate kinase; Provisional; Region: cmk; PRK00023 265072003419 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 265072003420 CMP-binding site; other site 265072003421 The sites determining sugar specificity; other site 265072003422 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 265072003423 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 265072003424 hinge; other site 265072003425 active site 265072003426 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 265072003427 prephenate dehydrogenase; Validated; Region: PRK08507 265072003428 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 265072003429 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 265072003430 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 265072003431 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 265072003432 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 265072003433 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 265072003434 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 265072003435 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 265072003436 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 265072003437 metal-binding site [ion binding] 265072003438 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 265072003439 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 265072003440 metal-binding site [ion binding] 265072003441 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 265072003442 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 265072003443 motif II; other site 265072003444 hypothetical protein; Provisional; Region: PRK01254 265072003445 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 265072003446 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 265072003447 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 265072003448 TraB family; Region: TraB; cl12050 265072003449 TraB family; Region: TraB; pfam01963 265072003450 spermidine N1-acetyltransferase; Provisional; Region: PRK15130 265072003451 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 265072003452 Coenzyme A binding pocket [chemical binding]; other site 265072003453 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 265072003454 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 265072003455 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 265072003456 Response regulator receiver domain; Region: Response_reg; pfam00072 265072003457 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003458 active site 265072003459 phosphorylation site [posttranslational modification] 265072003460 intermolecular recognition site; other site 265072003461 dimerization interface [polypeptide binding]; other site 265072003462 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072003463 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003464 active site 265072003465 phosphorylation site [posttranslational modification] 265072003466 intermolecular recognition site; other site 265072003467 dimerization interface [polypeptide binding]; other site 265072003468 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 265072003469 DNA binding residues [nucleotide binding] 265072003470 dimerization interface [polypeptide binding]; other site 265072003471 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 265072003472 CHASE3 domain; Region: CHASE3; pfam05227 265072003473 Histidine kinase; Region: HisKA_3; pfam07730 265072003474 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 265072003475 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072003476 ATP binding site [chemical binding]; other site 265072003477 Mg2+ binding site [ion binding]; other site 265072003478 G-X-G motif; other site 265072003479 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 265072003480 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 265072003481 EF-hand domain pair; Region: EF_hand_5; pfam13499 265072003482 Ca2+ binding site [ion binding]; other site 265072003483 BON domain; Region: BON; pfam04972 265072003484 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 265072003485 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 265072003486 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 265072003487 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 265072003488 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 265072003489 ATP binding site [chemical binding]; other site 265072003490 putative Mg++ binding site [ion binding]; other site 265072003491 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 265072003492 nucleotide binding region [chemical binding]; other site 265072003493 ATP-binding site [chemical binding]; other site 265072003494 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 265072003495 HRDC domain; Region: HRDC; pfam00570 265072003496 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 265072003497 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 265072003498 ATP binding site [chemical binding]; other site 265072003499 Mg++ binding site [ion binding]; other site 265072003500 motif III; other site 265072003501 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 265072003502 nucleotide binding region [chemical binding]; other site 265072003503 ATP-binding site [chemical binding]; other site 265072003504 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 265072003505 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 265072003506 RNA binding surface [nucleotide binding]; other site 265072003507 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 265072003508 active site 265072003509 uracil binding [chemical binding]; other site 265072003510 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 265072003511 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 265072003512 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 265072003513 PhnA protein; Region: PhnA; pfam03831 265072003514 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 265072003515 dimer interface [polypeptide binding]; other site 265072003516 putative tRNA-binding site [nucleotide binding]; other site 265072003517 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481 265072003518 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 265072003519 DAK2 domain; Region: Dak2; cl03685 265072003520 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 265072003521 tetramer (dimer of dimers) interface [polypeptide binding]; other site 265072003522 active site 265072003523 dimer interface [polypeptide binding]; other site 265072003524 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 265072003525 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 265072003526 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 265072003527 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 265072003528 dimerization interface [polypeptide binding]; other site 265072003529 domain crossover interface; other site 265072003530 redox-dependent activation switch; other site 265072003531 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 265072003532 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 265072003533 active site 265072003534 HIGH motif; other site 265072003535 nucleotide binding site [chemical binding]; other site 265072003536 active site 265072003537 KMSKS motif; other site 265072003538 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 265072003539 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 265072003540 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 265072003541 Walker A motif; other site 265072003542 ATP binding site [chemical binding]; other site 265072003543 Walker B motif; other site 265072003544 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 265072003545 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 265072003546 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 265072003547 PAS fold; Region: PAS_4; pfam08448 265072003548 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072003549 PAS domain; Region: PAS_9; pfam13426 265072003550 putative active site [active] 265072003551 heme pocket [chemical binding]; other site 265072003552 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072003553 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072003554 metal binding site [ion binding]; metal-binding site 265072003555 active site 265072003556 I-site; other site 265072003557 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 265072003558 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 265072003559 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 265072003560 substrate binding site; other site 265072003561 dimer interface; other site 265072003562 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 265072003563 homotrimer interaction site [polypeptide binding]; other site 265072003564 zinc binding site [ion binding]; other site 265072003565 CDP-binding sites; other site 265072003566 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 265072003567 Smr domain; Region: Smr; pfam01713 265072003568 thioredoxin reductase; Provisional; Region: PRK10262 265072003569 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 265072003570 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072003571 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 265072003572 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 265072003573 dimerization interface [polypeptide binding]; other site 265072003574 DPS ferroxidase diiron center [ion binding]; other site 265072003575 ion pore; other site 265072003576 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 265072003577 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 265072003578 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 265072003579 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 265072003580 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 265072003581 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 265072003582 binding surface 265072003583 TPR motif; other site 265072003584 Tetratricopeptide repeat; Region: TPR_16; pfam13432 265072003585 Protein of unknown function (DUF560); Region: DUF560; pfam04575 265072003586 FecR protein; Region: FecR; pfam04773 265072003587 recombination factor protein RarA; Reviewed; Region: PRK13342 265072003588 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 265072003589 Walker A motif; other site 265072003590 ATP binding site [chemical binding]; other site 265072003591 Walker B motif; other site 265072003592 arginine finger; other site 265072003593 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 265072003594 seryl-tRNA synthetase; Provisional; Region: PRK05431 265072003595 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 265072003596 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 265072003597 dimer interface [polypeptide binding]; other site 265072003598 active site 265072003599 motif 1; other site 265072003600 motif 2; other site 265072003601 motif 3; other site 265072003602 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 265072003603 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 265072003604 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 265072003605 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 265072003606 substrate binding pocket [chemical binding]; other site 265072003607 membrane-bound complex binding site; other site 265072003608 hinge residues; other site 265072003609 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 265072003610 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 265072003611 N-acetyl-D-glucosamine binding site [chemical binding]; other site 265072003612 catalytic residue [active] 265072003613 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 265072003614 EamA-like transporter family; Region: EamA; pfam00892 265072003615 putative chaperone; Provisional; Region: PRK11678 265072003616 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 265072003617 nucleotide binding site [chemical binding]; other site 265072003618 putative NEF/HSP70 interaction site [polypeptide binding]; other site 265072003619 SBD interface [polypeptide binding]; other site 265072003620 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 265072003621 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072003622 Walker A/P-loop; other site 265072003623 ATP binding site [chemical binding]; other site 265072003624 Q-loop/lid; other site 265072003625 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072003626 ABC transporter signature motif; other site 265072003627 Walker B; other site 265072003628 D-loop; other site 265072003629 ABC transporter; Region: ABC_tran_2; pfam12848 265072003630 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072003631 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 265072003632 dimer interface [polypeptide binding]; other site 265072003633 FMN binding site [chemical binding]; other site 265072003634 transcription elongation factor regulatory protein; Validated; Region: PRK06342 265072003635 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 265072003636 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 265072003637 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 265072003638 active site 265072003639 HIGH motif; other site 265072003640 dimer interface [polypeptide binding]; other site 265072003641 KMSKS motif; other site 265072003642 GMP synthase; Reviewed; Region: guaA; PRK00074 265072003643 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 265072003644 AMP/PPi binding site [chemical binding]; other site 265072003645 candidate oxyanion hole; other site 265072003646 catalytic triad [active] 265072003647 potential glutamine specificity residues [chemical binding]; other site 265072003648 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 265072003649 ATP Binding subdomain [chemical binding]; other site 265072003650 Ligand Binding sites [chemical binding]; other site 265072003651 Dimerization subdomain; other site 265072003652 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 265072003653 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 265072003654 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 265072003655 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 265072003656 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 265072003657 active site 265072003658 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 265072003659 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2914 265072003660 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 265072003661 putative coenzyme Q binding site [chemical binding]; other site 265072003662 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 265072003663 SmpB-tmRNA interface; other site 265072003664 Staphylococcal nuclease homologues; Region: SNc; smart00318 265072003665 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 265072003666 Catalytic site; other site 265072003667 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 265072003668 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072003669 NAD(P) binding site [chemical binding]; other site 265072003670 active site 265072003671 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072003672 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072003673 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 265072003674 putative effector binding pocket; other site 265072003675 dimerization interface [polypeptide binding]; other site 265072003676 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 265072003677 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 265072003678 catalytic residues [active] 265072003679 catalytic nucleophile [active] 265072003680 Presynaptic Site I dimer interface [polypeptide binding]; other site 265072003681 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 265072003682 Synaptic Flat tetramer interface [polypeptide binding]; other site 265072003683 Synaptic Site I dimer interface [polypeptide binding]; other site 265072003684 DNA binding site [nucleotide binding] 265072003685 Recombinase; Region: Recombinase; pfam07508 265072003686 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 265072003687 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 265072003688 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 265072003689 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 265072003690 protein binding site [polypeptide binding]; other site 265072003691 Peptidase family M48; Region: Peptidase_M48; cl12018 265072003692 thioredoxin 2; Provisional; Region: PRK10996 265072003693 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 265072003694 catalytic residues [active] 265072003695 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 265072003696 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 265072003697 YfdX protein; Region: YfdX; pfam10938 265072003698 YfdX protein; Region: YfdX; pfam10938 265072003699 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 265072003700 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 265072003701 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 265072003702 FtsH Extracellular; Region: FtsH_ext; pfam06480 265072003703 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 265072003704 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 265072003705 Walker A motif; other site 265072003706 ATP binding site [chemical binding]; other site 265072003707 Walker B motif; other site 265072003708 arginine finger; other site 265072003709 Peptidase family M41; Region: Peptidase_M41; pfam01434 265072003710 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 265072003711 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 265072003712 putative active site [active] 265072003713 catalytic site [active] 265072003714 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 265072003715 putative active site [active] 265072003716 catalytic site [active] 265072003717 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 265072003718 Clp amino terminal domain; Region: Clp_N; pfam02861 265072003719 Clp amino terminal domain; Region: Clp_N; pfam02861 265072003720 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 265072003721 Walker A motif; other site 265072003722 ATP binding site [chemical binding]; other site 265072003723 Walker B motif; other site 265072003724 arginine finger; other site 265072003725 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 265072003726 Walker A motif; other site 265072003727 ATP binding site [chemical binding]; other site 265072003728 Walker B motif; other site 265072003729 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 265072003730 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 265072003731 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 265072003732 putative dimer interface [polypeptide binding]; other site 265072003733 Helix-turn-helix domain; Region: HTH_17; pfam12728 265072003734 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 265072003735 PLD-like domain; Region: PLDc_2; pfam13091 265072003736 homodimer interface [polypeptide binding]; other site 265072003737 putative active site [active] 265072003738 catalytic site [active] 265072003739 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 265072003740 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 265072003741 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 265072003742 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 265072003743 ATP binding site [chemical binding]; other site 265072003744 putative Mg++ binding site [ion binding]; other site 265072003745 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 265072003746 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 265072003747 HsdM N-terminal domain; Region: HsdM_N; pfam12161 265072003748 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 265072003749 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 265072003750 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 265072003751 conserved cys residue [active] 265072003752 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 265072003753 Helix-turn-helix domain; Region: HTH_17; pfam12728 265072003754 Fic family protein [Function unknown]; Region: COG3177 265072003755 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 265072003756 Fic/DOC family; Region: Fic; pfam02661 265072003757 Response regulator receiver domain; Region: Response_reg; pfam00072 265072003758 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003759 active site 265072003760 phosphorylation site [posttranslational modification] 265072003761 intermolecular recognition site; other site 265072003762 dimerization interface [polypeptide binding]; other site 265072003763 PAS domain S-box; Region: sensory_box; TIGR00229 265072003764 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072003765 putative active site [active] 265072003766 heme pocket [chemical binding]; other site 265072003767 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072003768 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072003769 metal binding site [ion binding]; metal-binding site 265072003770 active site 265072003771 I-site; other site 265072003772 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 265072003773 HDOD domain; Region: HDOD; pfam08668 265072003774 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072003775 Zn2+ binding site [ion binding]; other site 265072003776 Mg2+ binding site [ion binding]; other site 265072003777 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072003778 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 265072003779 dimer interface [polypeptide binding]; other site 265072003780 phosphorylation site [posttranslational modification] 265072003781 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072003782 ATP binding site [chemical binding]; other site 265072003783 Mg2+ binding site [ion binding]; other site 265072003784 G-X-G motif; other site 265072003785 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 265072003786 catalytic residues [active] 265072003787 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 265072003788 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 265072003789 catalytic triad [active] 265072003790 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 265072003791 DNA-binding site [nucleotide binding]; DNA binding site 265072003792 RNA-binding motif; other site 265072003793 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 265072003794 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 265072003795 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 265072003796 active site 265072003797 catalytic site [active] 265072003798 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 265072003799 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072003800 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072003801 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072003802 Walker A/P-loop; other site 265072003803 ATP binding site [chemical binding]; other site 265072003804 Q-loop/lid; other site 265072003805 ABC transporter signature motif; other site 265072003806 Walker B; other site 265072003807 D-loop; other site 265072003808 H-loop/switch region; other site 265072003809 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 265072003810 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 265072003811 UDP-galactopyranose mutase; Region: GLF; pfam03275 265072003812 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: GT1_like_1; cd04950 265072003813 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072003814 putative homodimer interface [polypeptide binding]; other site 265072003815 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 265072003816 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 265072003817 catalytic residue [active] 265072003818 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 265072003819 catalytic residues [active] 265072003820 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 265072003821 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072003822 peroxiredoxin; Region: AhpC; TIGR03137 265072003823 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 265072003824 dimer interface [polypeptide binding]; other site 265072003825 decamer (pentamer of dimers) interface [polypeptide binding]; other site 265072003826 catalytic triad [active] 265072003827 peroxidatic and resolving cysteines [active] 265072003828 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072003829 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072003830 metal binding site [ion binding]; metal-binding site 265072003831 active site 265072003832 I-site; other site 265072003833 ABC transporter ATPase component; Reviewed; Region: PRK11147 265072003834 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072003835 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072003836 ABC transporter; Region: ABC_tran_2; pfam12848 265072003837 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072003838 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 265072003839 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 265072003840 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 265072003841 Major Facilitator Superfamily; Region: MFS_1; pfam07690 265072003842 putative substrate translocation pore; other site 265072003843 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 265072003844 Part of AAA domain; Region: AAA_19; pfam13245 265072003845 Family description; Region: UvrD_C_2; pfam13538 265072003846 PEP-CTERM motif; Region: VPEP; pfam07589 265072003847 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 265072003848 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 265072003849 GTP/Mg2+ binding site [chemical binding]; other site 265072003850 G4 box; other site 265072003851 G5 box; other site 265072003852 G1 box; other site 265072003853 Switch I region; other site 265072003854 G2 box; other site 265072003855 G3 box; other site 265072003856 Switch II region; other site 265072003857 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 265072003858 dimer interface [polypeptide binding]; other site 265072003859 Alkaline phosphatase homologues; Region: alkPPc; smart00098 265072003860 active site 265072003861 Methyltransferase domain; Region: Methyltransf_32; pfam13679 265072003862 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 265072003863 Protein of unknown function (DUF461); Region: DUF461; pfam04314 265072003864 DEAD-like helicases superfamily; Region: DEXDc; smart00487 265072003865 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 265072003866 ATP binding site [chemical binding]; other site 265072003867 putative Mg++ binding site [ion binding]; other site 265072003868 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 265072003869 nucleotide binding region [chemical binding]; other site 265072003870 Helicase associated domain (HA2); Region: HA2; pfam04408 265072003871 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 265072003872 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 265072003873 Transglycosylase SLT domain; Region: SLT_2; pfam13406 265072003874 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 265072003875 N-acetyl-D-glucosamine binding site [chemical binding]; other site 265072003876 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 265072003877 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 265072003878 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 265072003879 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 265072003880 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 265072003881 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 265072003882 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 265072003883 ATP binding site [chemical binding]; other site 265072003884 putative Mg++ binding site [ion binding]; other site 265072003885 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 265072003886 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 265072003887 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 265072003888 Superfamily II helicase [General function prediction only]; Region: COG1204 265072003889 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 265072003890 ATP binding site [chemical binding]; other site 265072003891 putative Mg++ binding site [ion binding]; other site 265072003892 helicase superfamily c-terminal domain; Region: HELICc; smart00490 265072003893 AAA domain; Region: AAA_13; pfam13166 265072003894 HsdM N-terminal domain; Region: HsdM_N; pfam12161 265072003895 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 265072003896 Methyltransferase domain; Region: Methyltransf_26; pfam13659 265072003897 S-adenosylmethionine binding site [chemical binding]; other site 265072003898 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 265072003899 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 265072003900 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072003901 catalytic residues [active] 265072003902 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 265072003903 ATP cone domain; Region: ATP-cone; pfam03477 265072003904 Class I ribonucleotide reductase; Region: RNR_I; cd01679 265072003905 active site 265072003906 dimer interface [polypeptide binding]; other site 265072003907 catalytic residues [active] 265072003908 effector binding site; other site 265072003909 R2 peptide binding site; other site 265072003910 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 265072003911 dimer interface [polypeptide binding]; other site 265072003912 putative radical transfer pathway; other site 265072003913 diiron center [ion binding]; other site 265072003914 tyrosyl radical; other site 265072003915 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 265072003916 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 265072003917 catalytic loop [active] 265072003918 iron binding site [ion binding]; other site 265072003919 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 265072003920 Domain of unknown function DUF20; Region: UPF0118; pfam01594 265072003921 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 265072003922 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 265072003923 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 265072003924 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072003925 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 265072003926 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 265072003927 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072003928 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 265072003929 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 265072003930 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 265072003931 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 265072003932 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 265072003933 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 265072003934 metal binding site 2 [ion binding]; metal-binding site 265072003935 putative DNA binding helix; other site 265072003936 metal binding site 1 [ion binding]; metal-binding site 265072003937 dimer interface [polypeptide binding]; other site 265072003938 structural Zn2+ binding site [ion binding]; other site 265072003939 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 265072003940 RNB domain; Region: RNB; pfam00773 265072003941 spermidine synthase; Provisional; Region: PRK04457 265072003942 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 265072003943 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 265072003944 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 265072003945 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 265072003946 homodimer interface [polypeptide binding]; other site 265072003947 chemical substrate binding site [chemical binding]; other site 265072003948 oligomer interface [polypeptide binding]; other site 265072003949 metal binding site [ion binding]; metal-binding site 265072003950 aminopeptidase N; Provisional; Region: pepN; PRK14015 265072003951 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 265072003952 active site 265072003953 Zn binding site [ion binding]; other site 265072003954 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 265072003955 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 265072003956 dimer interface [polypeptide binding]; other site 265072003957 catalytic triad [active] 265072003958 peroxidatic and resolving cysteines [active] 265072003959 Uncharacterized conserved protein [Function unknown]; Region: COG3287 265072003960 FIST N domain; Region: FIST; pfam08495 265072003961 FIST C domain; Region: FIST_C; pfam10442 265072003962 Response regulator receiver domain; Region: Response_reg; pfam00072 265072003963 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003964 active site 265072003965 phosphorylation site [posttranslational modification] 265072003966 intermolecular recognition site; other site 265072003967 dimerization interface [polypeptide binding]; other site 265072003968 Response regulator receiver domain; Region: Response_reg; pfam00072 265072003969 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003970 active site 265072003971 phosphorylation site [posttranslational modification] 265072003972 intermolecular recognition site; other site 265072003973 dimerization interface [polypeptide binding]; other site 265072003974 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 265072003975 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 265072003976 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072003977 dimer interface [polypeptide binding]; other site 265072003978 putative CheW interface [polypeptide binding]; other site 265072003979 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 265072003980 putative binding surface; other site 265072003981 active site 265072003982 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 265072003983 putative binding surface; other site 265072003984 active site 265072003985 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 265072003986 putative binding surface; other site 265072003987 active site 265072003988 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 265072003989 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 265072003990 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072003991 ATP binding site [chemical binding]; other site 265072003992 Mg2+ binding site [ion binding]; other site 265072003993 G-X-G motif; other site 265072003994 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 265072003995 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 265072003996 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072003997 active site 265072003998 phosphorylation site [posttranslational modification] 265072003999 intermolecular recognition site; other site 265072004000 dimerization interface [polypeptide binding]; other site 265072004001 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 265072004002 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 265072004003 putative active site [active] 265072004004 putative PHP Thumb interface [polypeptide binding]; other site 265072004005 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 265072004006 generic binding surface II; other site 265072004007 generic binding surface I; other site 265072004008 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 265072004009 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 265072004010 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 265072004011 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 265072004012 Ligand Binding Site [chemical binding]; other site 265072004013 TilS substrate binding domain; Region: TilS; pfam09179 265072004014 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 265072004015 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 265072004016 active site 265072004017 catalytic triad [active] 265072004018 oxyanion hole [active] 265072004019 switch loop; other site 265072004020 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 265072004021 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 265072004022 Walker A/P-loop; other site 265072004023 ATP binding site [chemical binding]; other site 265072004024 Q-loop/lid; other site 265072004025 ABC transporter signature motif; other site 265072004026 Walker B; other site 265072004027 D-loop; other site 265072004028 H-loop/switch region; other site 265072004029 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 265072004030 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 265072004031 FtsX-like permease family; Region: FtsX; pfam02687 265072004032 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 265072004033 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 265072004034 N-terminal plug; other site 265072004035 ligand-binding site [chemical binding]; other site 265072004036 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 265072004037 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072004038 active site 265072004039 phosphorylation site [posttranslational modification] 265072004040 intermolecular recognition site; other site 265072004041 dimerization interface [polypeptide binding]; other site 265072004042 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 265072004043 Walker A motif; other site 265072004044 ATP binding site [chemical binding]; other site 265072004045 Walker B motif; other site 265072004046 arginine finger; other site 265072004047 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072004048 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 265072004049 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072004050 NAD(P) binding site [chemical binding]; other site 265072004051 ATP-grasp domain; Region: ATP-grasp; pfam02222 265072004052 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 265072004053 apolar tunnel; other site 265072004054 heme binding site [chemical binding]; other site 265072004055 dimerization interface [polypeptide binding]; other site 265072004056 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 265072004057 DEAD-like helicases superfamily; Region: DEXDc; smart00487 265072004058 ATP binding site [chemical binding]; other site 265072004059 Mg++ binding site [ion binding]; other site 265072004060 motif III; other site 265072004061 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 265072004062 nucleotide binding region [chemical binding]; other site 265072004063 ATP-binding site [chemical binding]; other site 265072004064 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 265072004065 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 265072004066 ATP binding site [chemical binding]; other site 265072004067 Mg++ binding site [ion binding]; other site 265072004068 motif III; other site 265072004069 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 265072004070 nucleotide binding region [chemical binding]; other site 265072004071 ATP-binding site [chemical binding]; other site 265072004072 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 265072004073 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 265072004074 G1 box; other site 265072004075 putative GEF interaction site [polypeptide binding]; other site 265072004076 GTP/Mg2+ binding site [chemical binding]; other site 265072004077 Switch I region; other site 265072004078 G2 box; other site 265072004079 G3 box; other site 265072004080 Switch II region; other site 265072004081 G4 box; other site 265072004082 G5 box; other site 265072004083 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 265072004084 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 265072004085 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 265072004086 binding surface 265072004087 TPR motif; other site 265072004088 TPR repeat; Region: TPR_11; pfam13414 265072004089 TPR repeat; Region: TPR_11; pfam13414 265072004090 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 265072004091 binding surface 265072004092 TPR motif; other site 265072004093 TPR repeat; Region: TPR_11; pfam13414 265072004094 TPR repeat; Region: TPR_11; pfam13414 265072004095 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 265072004096 binding surface 265072004097 TPR motif; other site 265072004098 Tetratricopeptide repeat; Region: TPR_16; pfam13432 265072004099 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; pfam13759 265072004100 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 265072004101 RmuC family; Region: RmuC; pfam02646 265072004102 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 265072004103 MoaE interaction surface [polypeptide binding]; other site 265072004104 MoeB interaction surface [polypeptide binding]; other site 265072004105 thiocarboxylated glycine; other site 265072004106 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 265072004107 MoaE homodimer interface [polypeptide binding]; other site 265072004108 MoaD interaction [polypeptide binding]; other site 265072004109 active site residues [active] 265072004110 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 265072004111 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 265072004112 RNA binding surface [nucleotide binding]; other site 265072004113 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 265072004114 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 265072004115 FeS/SAM binding site; other site 265072004116 C factor cell-cell signaling protein; Provisional; Region: PRK09009 265072004117 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 265072004118 NADP binding site [chemical binding]; other site 265072004119 homodimer interface [polypeptide binding]; other site 265072004120 active site 265072004121 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 265072004122 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 265072004123 Substrate binding site; other site 265072004124 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 265072004125 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 265072004126 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 265072004127 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 265072004128 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 265072004129 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 265072004130 NADP-binding site; other site 265072004131 homotetramer interface [polypeptide binding]; other site 265072004132 substrate binding site [chemical binding]; other site 265072004133 homodimer interface [polypeptide binding]; other site 265072004134 active site 265072004135 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072004136 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 265072004137 NAD(P) binding site [chemical binding]; other site 265072004138 active site 265072004139 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 265072004140 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072004141 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 265072004142 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 265072004143 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_4; cd03795 265072004144 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072004145 putative ADP-binding pocket [chemical binding]; other site 265072004146 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 265072004147 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 265072004148 putative NAD(P) binding site [chemical binding]; other site 265072004149 active site 265072004150 putative substrate binding site [chemical binding]; other site 265072004151 Bacterial sugar transferase; Region: Bac_transf; pfam02397 265072004152 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 265072004153 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 265072004154 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 265072004155 NAD(P) binding site [chemical binding]; other site 265072004156 homodimer interface [polypeptide binding]; other site 265072004157 substrate binding site [chemical binding]; other site 265072004158 active site 265072004159 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 265072004160 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 265072004161 active site 265072004162 tetramer interface; other site 265072004163 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072004164 active site 265072004165 Response regulator receiver domain; Region: Response_reg; pfam00072 265072004166 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072004167 active site 265072004168 phosphorylation site [posttranslational modification] 265072004169 intermolecular recognition site; other site 265072004170 dimerization interface [polypeptide binding]; other site 265072004171 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072004172 Response regulator receiver domain; Region: Response_reg; pfam00072 265072004173 active site 265072004174 phosphorylation site [posttranslational modification] 265072004175 intermolecular recognition site; other site 265072004176 dimerization interface [polypeptide binding]; other site 265072004177 Heme NO binding associated; Region: HNOBA; pfam07701 265072004178 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072004179 PAS domain; Region: PAS_9; pfam13426 265072004180 putative active site [active] 265072004181 heme pocket [chemical binding]; other site 265072004182 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 265072004183 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 265072004184 putative active site [active] 265072004185 heme pocket [chemical binding]; other site 265072004186 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 265072004187 dimer interface [polypeptide binding]; other site 265072004188 phosphorylation site [posttranslational modification] 265072004189 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072004190 ATP binding site [chemical binding]; other site 265072004191 Mg2+ binding site [ion binding]; other site 265072004192 G-X-G motif; other site 265072004193 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 265072004194 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 265072004195 glutamate dehydrogenase; Provisional; Region: PRK09414 265072004196 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 265072004197 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 265072004198 NAD(P) binding site [chemical binding]; other site 265072004199 serine/threonine protein kinase; Provisional; Region: PRK11768 265072004200 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 265072004201 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 265072004202 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 265072004203 protoheme IX farnesyltransferase; Provisional; Region: PRK13362 265072004204 UbiA prenyltransferase family; Region: UbiA; pfam01040 265072004205 cytochrome o ubiquinol oxidase subunit IV; Provisional; Region: PRK10582 265072004206 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 265072004207 Subunit I/III interface [polypeptide binding]; other site 265072004208 Subunit III/IV interface [polypeptide binding]; other site 265072004209 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 265072004210 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 265072004211 D-pathway; other site 265072004212 Putative ubiquinol binding site [chemical binding]; other site 265072004213 Low-spin heme (heme b) binding site [chemical binding]; other site 265072004214 Putative water exit pathway; other site 265072004215 Binuclear center (heme o3/CuB) [ion binding]; other site 265072004216 K-pathway; other site 265072004217 Putative proton exit pathway; other site 265072004218 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 265072004219 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 265072004220 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 265072004221 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 265072004222 secondary substrate binding site; other site 265072004223 primary substrate binding site; other site 265072004224 inhibition loop; other site 265072004225 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 265072004226 HD domain; Region: HD_4; pfam13328 265072004227 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 265072004228 synthetase active site [active] 265072004229 NTP binding site [chemical binding]; other site 265072004230 metal binding site [ion binding]; metal-binding site 265072004231 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 265072004232 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 265072004233 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 265072004234 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 265072004235 helix-hairpin-helix signature motif; other site 265072004236 substrate binding pocket [chemical binding]; other site 265072004237 active site 265072004238 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 265072004239 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 265072004240 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 265072004241 catalytic triad [active] 265072004242 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 265072004243 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 265072004244 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 265072004245 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072004246 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072004247 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072004248 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 265072004249 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 265072004250 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072004251 active site 265072004252 phosphorylation site [posttranslational modification] 265072004253 intermolecular recognition site; other site 265072004254 dimerization interface [polypeptide binding]; other site 265072004255 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 265072004256 DNA binding site [nucleotide binding] 265072004257 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 265072004258 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072004259 HAMP domain; Region: HAMP; pfam00672 265072004260 dimerization interface [polypeptide binding]; other site 265072004261 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 265072004262 dimer interface [polypeptide binding]; other site 265072004263 phosphorylation site [posttranslational modification] 265072004264 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072004265 ATP binding site [chemical binding]; other site 265072004266 Mg2+ binding site [ion binding]; other site 265072004267 G-X-G motif; other site 265072004268 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 265072004269 Integrase core domain; Region: rve; pfam00665 265072004270 Integrase core domain; Region: rve_3; pfam13683 265072004271 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 265072004272 Protein of unknown function (DUF2283); Region: DUF2283; pfam10049 265072004273 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 265072004274 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 265072004275 DNA binding site [nucleotide binding] 265072004276 Int/Topo IB signature motif; other site 265072004277 active site 265072004278 MltA-interacting protein MipA; Region: MipA; cl01504 265072004279 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 265072004280 aspartate aminotransferase; Provisional; Region: PRK05764 265072004281 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 265072004282 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072004283 homodimer interface [polypeptide binding]; other site 265072004284 catalytic residue [active] 265072004285 excinuclease ABC subunit B; Provisional; Region: PRK05298 265072004286 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 265072004287 ATP binding site [chemical binding]; other site 265072004288 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 265072004289 putative Mg++ binding site [ion binding]; other site 265072004290 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 265072004291 nucleotide binding region [chemical binding]; other site 265072004292 ATP-binding site [chemical binding]; other site 265072004293 Ultra-violet resistance protein B; Region: UvrB; pfam12344 265072004294 UvrB/uvrC motif; Region: UVR; pfam02151 265072004295 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 265072004296 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 265072004297 homodimer interface [polypeptide binding]; other site 265072004298 oligonucleotide binding site [chemical binding]; other site 265072004299 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 265072004300 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 265072004301 RNA binding surface [nucleotide binding]; other site 265072004302 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 265072004303 active site 265072004304 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 265072004305 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 265072004306 motif II; other site 265072004307 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 265072004308 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 265072004309 oligomer interface [polypeptide binding]; other site 265072004310 tandem repeat interface [polypeptide binding]; other site 265072004311 active site residues [active] 265072004312 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 265072004313 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 265072004314 active site 265072004315 dimer interface [polypeptide binding]; other site 265072004316 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 265072004317 dimer interface [polypeptide binding]; other site 265072004318 active site 265072004319 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 265072004320 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 265072004321 generic binding surface I; other site 265072004322 generic binding surface II; other site 265072004323 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 265072004324 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 265072004325 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 265072004326 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 265072004327 replicative DNA helicase; Region: DnaB; TIGR00665 265072004328 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 265072004329 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 265072004330 Walker A motif; other site 265072004331 ATP binding site [chemical binding]; other site 265072004332 Walker B motif; other site 265072004333 DNA binding loops [nucleotide binding] 265072004334 alanine racemase; Reviewed; Region: dadX; PRK03646 265072004335 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 265072004336 active site 265072004337 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 265072004338 substrate binding site [chemical binding]; other site 265072004339 catalytic residues [active] 265072004340 dimer interface [polypeptide binding]; other site 265072004341 DNA repair protein RadA; Provisional; Region: PRK11823 265072004342 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 265072004343 Walker A motif/ATP binding site; other site 265072004344 ATP binding site [chemical binding]; other site 265072004345 Walker B motif; other site 265072004346 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 265072004347 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 265072004348 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 265072004349 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 265072004350 Tetratricopeptide repeat; Region: TPR_16; pfam13432 265072004351 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 265072004352 Secretin and TonB N terminus short domain; Region: STN; smart00965 265072004353 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 265072004354 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072004355 phosphomevalonate kinase, ERG8-type, eukaryotic branch; Region: Pmev_kin_ERG8; TIGR01219 265072004356 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 265072004357 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 265072004358 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 265072004359 Walker A motif; other site 265072004360 ATP binding site [chemical binding]; other site 265072004361 Walker B motif; other site 265072004362 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 265072004363 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072004364 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072004365 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 265072004366 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 265072004367 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 265072004368 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 265072004369 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 265072004370 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072004371 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072004372 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 265072004373 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072004374 Walker A/P-loop; other site 265072004375 ATP binding site [chemical binding]; other site 265072004376 Q-loop/lid; other site 265072004377 ABC transporter signature motif; other site 265072004378 Walker B; other site 265072004379 D-loop; other site 265072004380 H-loop/switch region; other site 265072004381 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 265072004382 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 265072004383 Walker A/P-loop; other site 265072004384 ATP binding site [chemical binding]; other site 265072004385 Q-loop/lid; other site 265072004386 ABC transporter signature motif; other site 265072004387 Walker B; other site 265072004388 D-loop; other site 265072004389 H-loop/switch region; other site 265072004390 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 265072004391 Secretin and TonB N terminus short domain; Region: STN; smart00965 265072004392 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 265072004393 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072004394 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072004395 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 265072004396 FecR protein; Region: FecR; pfam04773 265072004397 RNA polymerase sigma factor, SigM family; Region: SigM_subfam; TIGR02950 265072004398 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 265072004399 DNA binding residues [nucleotide binding] 265072004400 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 265072004401 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily; Region: M14_ASTE_ASPA_like; cd06230 265072004402 active site 265072004403 Zn binding site [ion binding]; other site 265072004404 YceI-like domain; Region: YceI; pfam04264 265072004405 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 265072004406 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 265072004407 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 265072004408 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 265072004409 dimerization interface [polypeptide binding]; other site 265072004410 active site 265072004411 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 265072004412 multidrug efflux protein; Reviewed; Region: PRK09577 265072004413 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 265072004414 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 265072004415 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072004416 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 265072004417 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072004418 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 265072004419 Domain of unknown function DUF; Region: DUF204; pfam02659 265072004420 Domain of unknown function DUF; Region: DUF204; pfam02659 265072004421 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 265072004422 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 265072004423 glycogen branching enzyme; Provisional; Region: PRK05402 265072004424 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 265072004425 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 265072004426 active site 265072004427 catalytic site [active] 265072004428 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 265072004429 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 265072004430 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 265072004431 ligand binding site; other site 265072004432 oligomer interface; other site 265072004433 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 265072004434 dimer interface [polypeptide binding]; other site 265072004435 N-terminal domain interface [polypeptide binding]; other site 265072004436 sulfate 1 binding site; other site 265072004437 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 265072004438 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 265072004439 putative active site [active] 265072004440 catalytic site [active] 265072004441 N-terminal catalytic domain of 4-alpha-glucanotransferase; glycoside hydrolase family 57 (GH57); Region: GH57N_TLGT_like; cd10793 265072004442 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 265072004443 active site 265072004444 catalytic site [active] 265072004445 homodimer interface [polypeptide binding]; other site 265072004446 Lid 1; other site 265072004447 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 265072004448 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 265072004449 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 265072004450 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 265072004451 nucleotide binding site [chemical binding]; other site 265072004452 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 265072004453 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 265072004454 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 265072004455 active site 265072004456 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 265072004457 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 265072004458 putative active site [active] 265072004459 YdjC motif; other site 265072004460 Mg binding site [ion binding]; other site 265072004461 putative homodimer interface [polypeptide binding]; other site 265072004462 GtrA-like protein; Region: GtrA; pfam04138 265072004463 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 265072004464 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 265072004465 Ligand binding site; other site 265072004466 Putative Catalytic site; other site 265072004467 DXD motif; other site 265072004468 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 265072004469 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 265072004470 epoxyqueuosine reductase; Region: TIGR00276 265072004471 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 265072004472 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 265072004473 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 265072004474 AMIN domain; Region: AMIN; pfam11741 265072004475 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 265072004476 active site 265072004477 metal binding site [ion binding]; metal-binding site 265072004478 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 265072004479 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 265072004480 Beta-Casp domain; Region: Beta-Casp; smart01027 265072004481 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 265072004482 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 265072004483 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 265072004484 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072004485 ATP binding site [chemical binding]; other site 265072004486 Mg2+ binding site [ion binding]; other site 265072004487 G-X-G motif; other site 265072004488 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 265072004489 ATP binding site [chemical binding]; other site 265072004490 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 265072004491 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 265072004492 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 265072004493 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 265072004494 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 265072004495 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072004496 homodimer interface [polypeptide binding]; other site 265072004497 catalytic residue [active] 265072004498 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 265072004499 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 265072004500 Walker A motif; other site 265072004501 ATP binding site [chemical binding]; other site 265072004502 Walker B motif; other site 265072004503 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 265072004504 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 265072004505 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072004506 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072004507 metal binding site [ion binding]; metal-binding site 265072004508 active site 265072004509 I-site; other site 265072004510 Cache domain; Region: Cache_1; pfam02743 265072004511 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 265072004512 TPR motif; other site 265072004513 TPR repeat; Region: TPR_11; pfam13414 265072004514 binding surface 265072004515 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 265072004516 binding surface 265072004517 TPR repeat; Region: TPR_11; pfam13414 265072004518 TPR motif; other site 265072004519 TPR repeat; Region: TPR_11; pfam13414 265072004520 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 265072004521 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 265072004522 Uncharacterized conserved protein [Function unknown]; Region: COG4121 265072004523 hydroxyglutarate oxidase; Provisional; Region: PRK11728 265072004524 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 265072004525 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 265072004526 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 265072004527 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 265072004528 dimer interface [polypeptide binding]; other site 265072004529 conserved gate region; other site 265072004530 putative PBP binding loops; other site 265072004531 ABC-ATPase subunit interface; other site 265072004532 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072004533 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 265072004534 Walker A/P-loop; other site 265072004535 ATP binding site [chemical binding]; other site 265072004536 Q-loop/lid; other site 265072004537 ABC transporter signature motif; other site 265072004538 Walker B; other site 265072004539 D-loop; other site 265072004540 H-loop/switch region; other site 265072004541 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 265072004542 S-adenosylmethionine binding site [chemical binding]; other site 265072004543 Predicted transcriptional regulator [Transcription]; Region: COG2932 265072004544 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 265072004545 Catalytic site [active] 265072004546 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 265072004547 dimerization interface [polypeptide binding]; other site 265072004548 substrate binding site [chemical binding]; other site 265072004549 active site 265072004550 calcium binding site [ion binding]; other site 265072004551 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 265072004552 Sulfatase; Region: Sulfatase; pfam00884 265072004553 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 265072004554 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 265072004555 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 265072004556 Walker A/P-loop; other site 265072004557 ATP binding site [chemical binding]; other site 265072004558 Q-loop/lid; other site 265072004559 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 265072004560 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 265072004561 ABC transporter signature motif; other site 265072004562 Walker B; other site 265072004563 D-loop; other site 265072004564 H-loop/switch region; other site 265072004565 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 265072004566 FtsZ protein binding site [polypeptide binding]; other site 265072004567 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 265072004568 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 265072004569 nucleotide binding pocket [chemical binding]; other site 265072004570 K-X-D-G motif; other site 265072004571 catalytic site [active] 265072004572 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 265072004573 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 265072004574 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 265072004575 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 265072004576 Dimer interface [polypeptide binding]; other site 265072004577 BRCT sequence motif; other site 265072004578 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 265072004579 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 265072004580 active site 265072004581 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 265072004582 TPR motif; other site 265072004583 binding surface 265072004584 Conserved TM helix; Region: TM_helix; pfam05552 265072004585 Conserved TM helix; Region: TM_helix; pfam05552 265072004586 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 265072004587 DNA-binding site [nucleotide binding]; DNA binding site 265072004588 RNA-binding motif; other site 265072004589 trigger factor; Provisional; Region: tig; PRK01490 265072004590 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 265072004591 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 265072004592 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 265072004593 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 265072004594 oligomer interface [polypeptide binding]; other site 265072004595 active site residues [active] 265072004596 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 265072004597 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 265072004598 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 265072004599 Walker A motif; other site 265072004600 ATP binding site [chemical binding]; other site 265072004601 Walker B motif; other site 265072004602 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 265072004603 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 265072004604 Found in ATP-dependent protease La (LON); Region: LON; smart00464 265072004605 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 265072004606 Walker A motif; other site 265072004607 ATP binding site [chemical binding]; other site 265072004608 Walker B motif; other site 265072004609 arginine finger; other site 265072004610 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 265072004611 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 265072004612 IHF dimer interface [polypeptide binding]; other site 265072004613 IHF - DNA interface [nucleotide binding]; other site 265072004614 periplasmic folding chaperone; Provisional; Region: PRK10788 265072004615 SurA N-terminal domain; Region: SurA_N_3; cl07813 265072004616 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 265072004617 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 265072004618 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 265072004619 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 265072004620 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 265072004621 active site 265072004622 catalytic site [active] 265072004623 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 265072004624 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 265072004625 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 265072004626 catalytic site [active] 265072004627 active site 265072004628 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 265072004629 trehalose synthase; Region: treS_nterm; TIGR02456 265072004630 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 265072004631 active site 265072004632 catalytic site [active] 265072004633 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 265072004634 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 265072004635 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 265072004636 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 265072004637 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 265072004638 active site 265072004639 homodimer interface [polypeptide binding]; other site 265072004640 catalytic site [active] 265072004641 acceptor binding site [chemical binding]; other site 265072004642 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 265072004643 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_1; cd09140 265072004644 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 265072004645 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 265072004646 putative active site [active] 265072004647 putative active site [active] 265072004648 catalytic site [active] 265072004649 catalytic site [active] 265072004650 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_2; cd09143 265072004651 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 265072004652 putative active site [active] 265072004653 putative active site [active] 265072004654 catalytic site [active] 265072004655 catalytic site [active] 265072004656 Uncharacterized conserved protein [Function unknown]; Region: COG0398 265072004657 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 265072004658 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 265072004659 putative catalytic site [active] 265072004660 putative metal binding site [ion binding]; other site 265072004661 putative phosphate binding site [ion binding]; other site 265072004662 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 265072004663 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 265072004664 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 265072004665 S-adenosylmethionine binding site [chemical binding]; other site 265072004666 short chain dehydrogenase; Provisional; Region: PRK06701 265072004667 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 265072004668 NAD binding site [chemical binding]; other site 265072004669 metal binding site [ion binding]; metal-binding site 265072004670 active site 265072004671 Predicted membrane protein (DUF2231); Region: DUF2231; pfam09990 265072004672 CopC domain; Region: CopC; pfam04234 265072004673 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 265072004674 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 265072004675 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 265072004676 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 265072004677 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 265072004678 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 265072004679 Low-spin heme binding site [chemical binding]; other site 265072004680 D-pathway; other site 265072004681 Putative water exit pathway; other site 265072004682 Binuclear center (active site) [active] 265072004683 K-pathway; other site 265072004684 Putative proton exit pathway; other site 265072004685 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 265072004686 dimanganese center [ion binding]; other site 265072004687 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 265072004688 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 265072004689 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 265072004690 putative NAD(P) binding site [chemical binding]; other site 265072004691 active site 265072004692 DoxX-like family; Region: DoxX_3; pfam13781 265072004693 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 265072004694 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 265072004695 NAD binding site [chemical binding]; other site 265072004696 catalytic Zn binding site [ion binding]; other site 265072004697 structural Zn binding site [ion binding]; other site 265072004698 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 265072004699 Cytochrome P450; Region: p450; cl12078 265072004700 Domain of unknown function (DUF336); Region: DUF336; pfam03928 265072004701 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; pfam09678 265072004702 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cd00386 265072004703 Subunit I/III interface [polypeptide binding]; other site 265072004704 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 265072004705 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 265072004706 D-pathway; other site 265072004707 Putative ubiquinol binding site [chemical binding]; other site 265072004708 Low-spin heme (heme b) binding site [chemical binding]; other site 265072004709 Putative water exit pathway; other site 265072004710 Binuclear center (heme o3/CuB) [ion binding]; other site 265072004711 K-pathway; other site 265072004712 Putative proton exit pathway; other site 265072004713 Cytochrome c oxidase subunit IV; Region: Cyt_c_ox_IV; pfam12270 265072004714 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 265072004715 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 265072004716 Cytochrome c; Region: Cytochrom_C; pfam00034 265072004717 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 265072004718 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 265072004719 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 265072004720 Trp docking motif [polypeptide binding]; other site 265072004721 dimer interface [polypeptide binding]; other site 265072004722 active site 265072004723 small subunit binding site [polypeptide binding]; other site 265072004724 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 265072004725 Mechanosensitive ion channel; Region: MS_channel; pfam00924 265072004726 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072004727 Zonular occludens toxin (Zot); Region: Zot; cl17485 265072004728 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 265072004729 active site 265072004730 catalytic residues [active] 265072004731 metal binding site [ion binding]; metal-binding site 265072004732 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 265072004733 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 265072004734 active site lid residues [active] 265072004735 substrate binding pocket [chemical binding]; other site 265072004736 catalytic residues [active] 265072004737 substrate-Mg2+ binding site; other site 265072004738 aspartate-rich region 1; other site 265072004739 aspartate-rich region 2; other site 265072004740 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 265072004741 active site lid residues [active] 265072004742 substrate binding pocket [chemical binding]; other site 265072004743 catalytic residues [active] 265072004744 substrate-Mg2+ binding site; other site 265072004745 aspartate-rich region 1; other site 265072004746 aspartate-rich region 2; other site 265072004747 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 265072004748 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 265072004749 Membrane protein of unknown function; Region: DUF360; pfam04020 265072004750 glycogen synthase; Provisional; Region: glgA; PRK00654 265072004751 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 265072004752 ADP-binding pocket [chemical binding]; other site 265072004753 homodimer interface [polypeptide binding]; other site 265072004754 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 265072004755 catalytic site [active] 265072004756 putative active site [active] 265072004757 putative substrate binding site [chemical binding]; other site 265072004758 dimer interface [polypeptide binding]; other site 265072004759 Peptidase family M48; Region: Peptidase_M48; pfam01435 265072004760 GTPase RsgA; Reviewed; Region: PRK00098 265072004761 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 265072004762 RNA binding site [nucleotide binding]; other site 265072004763 homodimer interface [polypeptide binding]; other site 265072004764 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 265072004765 GTPase/Zn-binding domain interface [polypeptide binding]; other site 265072004766 GTP/Mg2+ binding site [chemical binding]; other site 265072004767 G4 box; other site 265072004768 G5 box; other site 265072004769 G1 box; other site 265072004770 Switch I region; other site 265072004771 G2 box; other site 265072004772 G3 box; other site 265072004773 Switch II region; other site 265072004774 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 265072004775 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 265072004776 putative active site [active] 265072004777 Zn binding site [ion binding]; other site 265072004778 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 265072004779 active site 265072004780 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 265072004781 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 265072004782 active site 265072004783 catalytic site [active] 265072004784 substrate binding site [chemical binding]; other site 265072004785 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 265072004786 RNA/DNA hybrid binding site [nucleotide binding]; other site 265072004787 active site 265072004788 Methyltransferase domain; Region: Methyltransf_11; pfam08241 265072004789 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 265072004790 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 265072004791 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 265072004792 N-acetyl-D-glucosamine binding site [chemical binding]; other site 265072004793 catalytic residue [active] 265072004794 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072004795 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 265072004796 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072004797 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 265072004798 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072004799 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 265072004800 The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold; Region: PBP2_AppA_like; cd08514 265072004801 peptide binding site [polypeptide binding]; other site 265072004802 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 265072004803 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 265072004804 dimer interface [polypeptide binding]; other site 265072004805 conserved gate region; other site 265072004806 putative PBP binding loops; other site 265072004807 ABC-ATPase subunit interface; other site 265072004808 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 265072004809 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 265072004810 dimer interface [polypeptide binding]; other site 265072004811 conserved gate region; other site 265072004812 putative PBP binding loops; other site 265072004813 ABC-ATPase subunit interface; other site 265072004814 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 265072004815 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 265072004816 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 265072004817 arsenical pump membrane protein; Provisional; Region: PRK15445 265072004818 transmembrane helices; other site 265072004819 FOG: CBS domain [General function prediction only]; Region: COG0517 265072004820 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 265072004821 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 265072004822 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 265072004823 P loop; other site 265072004824 Nucleotide binding site [chemical binding]; other site 265072004825 DTAP/Switch II; other site 265072004826 Switch I; other site 265072004827 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 265072004828 P loop; other site 265072004829 Nucleotide binding site [chemical binding]; other site 265072004830 DTAP/Switch II; other site 265072004831 Switch I; other site 265072004832 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 265072004833 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 265072004834 dimerization interface [polypeptide binding]; other site 265072004835 putative DNA binding site [nucleotide binding]; other site 265072004836 putative Zn2+ binding site [ion binding]; other site 265072004837 Low molecular weight phosphatase family; Region: LMWPc; cd00115 265072004838 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 265072004839 active site 265072004840 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 265072004841 multiple promoter invertase; Provisional; Region: mpi; PRK13413 265072004842 catalytic residues [active] 265072004843 catalytic nucleophile [active] 265072004844 Presynaptic Site I dimer interface [polypeptide binding]; other site 265072004845 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 265072004846 Synaptic Flat tetramer interface [polypeptide binding]; other site 265072004847 Synaptic Site I dimer interface [polypeptide binding]; other site 265072004848 DNA binding site [nucleotide binding] 265072004849 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 265072004850 DNA-binding interface [nucleotide binding]; DNA binding site 265072004851 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 265072004852 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 265072004853 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 265072004854 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 265072004855 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 265072004856 active site 265072004857 PilZ domain; Region: PilZ; cl01260 265072004858 DNA polymerase III subunit delta'; Validated; Region: PRK06964 265072004859 DNA polymerase III subunit delta'; Validated; Region: PRK08485 265072004860 thymidylate kinase; Validated; Region: tmk; PRK00698 265072004861 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 265072004862 TMP-binding site; other site 265072004863 ATP-binding site [chemical binding]; other site 265072004864 YceG-like family; Region: YceG; pfam02618 265072004865 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 265072004866 dimerization interface [polypeptide binding]; other site 265072004867 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 265072004868 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 265072004869 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072004870 catalytic residue [active] 265072004871 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 265072004872 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 265072004873 dimer interface [polypeptide binding]; other site 265072004874 active site 265072004875 acyl carrier protein; Provisional; Region: acpP; PRK00982 265072004876 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 265072004877 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 265072004878 NAD(P) binding site [chemical binding]; other site 265072004879 homotetramer interface [polypeptide binding]; other site 265072004880 homodimer interface [polypeptide binding]; other site 265072004881 active site 265072004882 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 265072004883 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 265072004884 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 265072004885 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 265072004886 dimer interface [polypeptide binding]; other site 265072004887 active site 265072004888 CoA binding pocket [chemical binding]; other site 265072004889 putative phosphate acyltransferase; Provisional; Region: PRK05331 265072004890 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 265072004891 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 265072004892 pyruvate carboxylase subunit A; Validated; Region: PRK07178 265072004893 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 265072004894 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 265072004895 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 265072004896 pyruvate carboxylase subunit B; Validated; Region: PRK09282 265072004897 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 265072004898 active site 265072004899 catalytic residues [active] 265072004900 metal binding site [ion binding]; metal-binding site 265072004901 homodimer binding site [polypeptide binding]; other site 265072004902 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 265072004903 carboxyltransferase (CT) interaction site; other site 265072004904 biotinylation site [posttranslational modification]; other site 265072004905 Maf-like protein; Region: Maf; pfam02545 265072004906 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 265072004907 active site 265072004908 dimer interface [polypeptide binding]; other site 265072004909 Uncharacterized conserved protein [Function unknown]; Region: COG5316 265072004910 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 265072004911 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 265072004912 putative SAM binding site [chemical binding]; other site 265072004913 homodimer interface [polypeptide binding]; other site 265072004914 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 265072004915 RNA/DNA hybrid binding site [nucleotide binding]; other site 265072004916 active site 265072004917 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 265072004918 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 265072004919 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 265072004920 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 265072004921 active site 265072004922 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 265072004923 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 265072004924 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 265072004925 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 265072004926 trimer interface [polypeptide binding]; other site 265072004927 active site 265072004928 UDP-GlcNAc binding site [chemical binding]; other site 265072004929 lipid binding site [chemical binding]; lipid-binding site 265072004930 periplasmic chaperone; Provisional; Region: PRK10780 265072004931 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 265072004932 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 265072004933 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 265072004934 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 265072004935 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 265072004936 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 265072004937 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 265072004938 Surface antigen; Region: Bac_surface_Ag; pfam01103 265072004939 zinc metallopeptidase RseP; Provisional; Region: PRK10779 265072004940 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 265072004941 active site 265072004942 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 265072004943 protein binding site [polypeptide binding]; other site 265072004944 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 265072004945 protein binding site [polypeptide binding]; other site 265072004946 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 265072004947 putative substrate binding region [chemical binding]; other site 265072004948 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 265072004949 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 265072004950 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 265072004951 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 265072004952 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 265072004953 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 265072004954 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 265072004955 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 265072004956 catalytic residue [active] 265072004957 putative FPP diphosphate binding site; other site 265072004958 putative FPP binding hydrophobic cleft; other site 265072004959 dimer interface [polypeptide binding]; other site 265072004960 putative IPP diphosphate binding site; other site 265072004961 ribosome recycling factor; Reviewed; Region: frr; PRK00083 265072004962 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 265072004963 hinge region; other site 265072004964 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 265072004965 putative nucleotide binding site [chemical binding]; other site 265072004966 uridine monophosphate binding site [chemical binding]; other site 265072004967 homohexameric interface [polypeptide binding]; other site 265072004968 elongation factor Ts; Provisional; Region: tsf; PRK09377 265072004969 UBA/TS-N domain; Region: UBA; pfam00627 265072004970 Elongation factor TS; Region: EF_TS; pfam00889 265072004971 Elongation factor TS; Region: EF_TS; pfam00889 265072004972 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 265072004973 rRNA interaction site [nucleotide binding]; other site 265072004974 S8 interaction site; other site 265072004975 putative laminin-1 binding site; other site 265072004976 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 265072004977 active site 265072004978 PII uridylyl-transferase; Provisional; Region: PRK03059 265072004979 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 265072004980 metal binding triad; other site 265072004981 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 265072004982 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072004983 Zn2+ binding site [ion binding]; other site 265072004984 Mg2+ binding site [ion binding]; other site 265072004985 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 265072004986 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 265072004987 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 265072004988 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 265072004989 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 265072004990 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 265072004991 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 265072004992 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 265072004993 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 265072004994 motif II; other site 265072004995 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 265072004996 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 265072004997 putative FMN binding site [chemical binding]; other site 265072004998 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 265072004999 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_14; cd08497 265072005000 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 265072005001 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 265072005002 Walker A/P-loop; other site 265072005003 ATP binding site [chemical binding]; other site 265072005004 Q-loop/lid; other site 265072005005 ABC transporter signature motif; other site 265072005006 Walker B; other site 265072005007 D-loop; other site 265072005008 H-loop/switch region; other site 265072005009 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 265072005010 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 265072005011 Walker A/P-loop; other site 265072005012 ATP binding site [chemical binding]; other site 265072005013 Q-loop/lid; other site 265072005014 ABC transporter signature motif; other site 265072005015 Walker B; other site 265072005016 D-loop; other site 265072005017 H-loop/switch region; other site 265072005018 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 265072005019 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 265072005020 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 265072005021 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 265072005022 dimer interface [polypeptide binding]; other site 265072005023 conserved gate region; other site 265072005024 putative PBP binding loops; other site 265072005025 ABC-ATPase subunit interface; other site 265072005026 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 265072005027 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 265072005028 dimer interface [polypeptide binding]; other site 265072005029 conserved gate region; other site 265072005030 ABC-ATPase subunit interface; other site 265072005031 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 265072005032 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 265072005033 motif II; other site 265072005034 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 265072005035 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 265072005036 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 265072005037 active site 265072005038 non-prolyl cis peptide bond; other site 265072005039 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; smart01007 265072005040 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 265072005041 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 265072005042 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072005043 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 265072005044 N-terminal plug; other site 265072005045 ligand-binding site [chemical binding]; other site 265072005046 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072005047 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072005048 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072005049 Walker A/P-loop; other site 265072005050 ATP binding site [chemical binding]; other site 265072005051 Q-loop/lid; other site 265072005052 ABC transporter signature motif; other site 265072005053 Walker B; other site 265072005054 D-loop; other site 265072005055 H-loop/switch region; other site 265072005056 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072005057 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072005058 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 265072005059 Walker A/P-loop; other site 265072005060 ATP binding site [chemical binding]; other site 265072005061 Q-loop/lid; other site 265072005062 ABC transporter signature motif; other site 265072005063 Walker B; other site 265072005064 D-loop; other site 265072005065 H-loop/switch region; other site 265072005066 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 265072005067 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 265072005068 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 265072005069 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 265072005070 dimer interface [polypeptide binding]; other site 265072005071 decamer (pentamer of dimers) interface [polypeptide binding]; other site 265072005072 catalytic triad [active] 265072005073 Predicted permeases [General function prediction only]; Region: COG0730 265072005074 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 265072005075 active site 265072005076 catalytic site [active] 265072005077 substrate binding site [chemical binding]; other site 265072005078 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 265072005079 GIY-YIG motif/motif A; other site 265072005080 active site 265072005081 catalytic site [active] 265072005082 putative DNA binding site [nucleotide binding]; other site 265072005083 metal binding site [ion binding]; metal-binding site 265072005084 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072005085 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072005086 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 265072005087 Walker A/P-loop; other site 265072005088 ATP binding site [chemical binding]; other site 265072005089 Q-loop/lid; other site 265072005090 ABC transporter signature motif; other site 265072005091 Walker B; other site 265072005092 D-loop; other site 265072005093 H-loop/switch region; other site 265072005094 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072005095 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072005096 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072005097 Walker A/P-loop; other site 265072005098 ATP binding site [chemical binding]; other site 265072005099 Q-loop/lid; other site 265072005100 ABC transporter signature motif; other site 265072005101 Walker B; other site 265072005102 D-loop; other site 265072005103 H-loop/switch region; other site 265072005104 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 265072005105 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 265072005106 putative PBP binding loops; other site 265072005107 ABC-ATPase subunit interface; other site 265072005108 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 265072005109 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 265072005110 dimer interface [polypeptide binding]; other site 265072005111 conserved gate region; other site 265072005112 putative PBP binding loops; other site 265072005113 ABC-ATPase subunit interface; other site 265072005114 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072005115 TolR protein; Region: tolR; TIGR02801 265072005116 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 265072005117 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 265072005118 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 265072005119 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 265072005120 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 265072005121 Walker A/P-loop; other site 265072005122 ATP binding site [chemical binding]; other site 265072005123 Q-loop/lid; other site 265072005124 ABC transporter signature motif; other site 265072005125 Walker B; other site 265072005126 D-loop; other site 265072005127 H-loop/switch region; other site 265072005128 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 265072005129 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 265072005130 substrate binding pocket [chemical binding]; other site 265072005131 membrane-bound complex binding site; other site 265072005132 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 265072005133 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 265072005134 substrate binding pocket [chemical binding]; other site 265072005135 membrane-bound complex binding site; other site 265072005136 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 265072005137 active site 265072005138 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; smart01007 265072005139 intersubunit interface [polypeptide binding]; other site 265072005140 Zn2+ binding site [ion binding]; other site 265072005141 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 265072005142 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 265072005143 Walker A motif; other site 265072005144 ATP binding site [chemical binding]; other site 265072005145 Walker B motif; other site 265072005146 arginine finger; other site 265072005147 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 265072005148 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 265072005149 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 265072005150 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cd00181 265072005151 ligand binding site [chemical binding]; other site 265072005152 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 265072005153 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072005154 dimer interface [polypeptide binding]; other site 265072005155 putative CheW interface [polypeptide binding]; other site 265072005156 Heme NO binding associated; Region: HNOBA; pfam07701 265072005157 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 265072005158 cyclase homology domain; Region: CHD; cd07302 265072005159 nucleotidyl binding site; other site 265072005160 metal binding site [ion binding]; metal-binding site 265072005161 dimer interface [polypeptide binding]; other site 265072005162 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 265072005163 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 265072005164 Walker A motif; other site 265072005165 ATP binding site [chemical binding]; other site 265072005166 Walker B motif; other site 265072005167 arginine finger; other site 265072005168 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 265072005169 hypothetical protein; Validated; Region: PRK00153 265072005170 recombination protein RecR; Reviewed; Region: recR; PRK00076 265072005171 RecR protein; Region: RecR; pfam02132 265072005172 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 265072005173 putative active site [active] 265072005174 putative metal-binding site [ion binding]; other site 265072005175 tetramer interface [polypeptide binding]; other site 265072005176 phosphoglycolate phosphatase; Provisional; Region: PRK13222 265072005177 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 265072005178 motif II; other site 265072005179 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 265072005180 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 265072005181 S-adenosylmethionine binding site [chemical binding]; other site 265072005182 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 265072005183 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 265072005184 active site 265072005185 putative substrate binding pocket [chemical binding]; other site 265072005186 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 265072005187 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 265072005188 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 265072005189 ligand binding site [chemical binding]; other site 265072005190 hypothetical protein; Provisional; Region: PRK02227 265072005191 Protein of unknown function (DUF447); Region: DUF447; pfam04289 265072005192 dihydropteroate synthase-related protein; Region: TIGR00284 265072005193 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 265072005194 substrate binding pocket [chemical binding]; other site 265072005195 dimer interface [polypeptide binding]; other site 265072005196 inhibitor binding site; inhibition site 265072005197 Archaeal flavoproteins [Energy production and conversion]; Region: COG1036 265072005198 Flavoprotein; Region: Flavoprotein; pfam02441 265072005199 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 265072005200 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 265072005201 GDP-binding site [chemical binding]; other site 265072005202 ACT binding site; other site 265072005203 IMP binding site; other site 265072005204 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 265072005205 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 265072005206 dimer interface [polypeptide binding]; other site 265072005207 motif 1; other site 265072005208 active site 265072005209 motif 2; other site 265072005210 motif 3; other site 265072005211 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 265072005212 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 265072005213 HflC protein; Region: hflC; TIGR01932 265072005214 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 265072005215 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 265072005216 HflK protein; Region: hflK; TIGR01933 265072005217 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 265072005218 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 265072005219 HflX GTPase family; Region: HflX; cd01878 265072005220 G1 box; other site 265072005221 GTP/Mg2+ binding site [chemical binding]; other site 265072005222 Switch I region; other site 265072005223 G2 box; other site 265072005224 G3 box; other site 265072005225 Switch II region; other site 265072005226 G4 box; other site 265072005227 G5 box; other site 265072005228 bacterial Hfq-like; Region: Hfq; cd01716 265072005229 hexamer interface [polypeptide binding]; other site 265072005230 Sm1 motif; other site 265072005231 RNA binding site [nucleotide binding]; other site 265072005232 Sm2 motif; other site 265072005233 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 265072005234 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 265072005235 HIGH motif; other site 265072005236 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 265072005237 active site 265072005238 KMSKS motif; other site 265072005239 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072005240 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 265072005241 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072005242 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072005243 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072005244 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072005245 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072005246 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 265072005247 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 265072005248 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 265072005249 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 265072005250 FeS/SAM binding site; other site 265072005251 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 265072005252 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 265072005253 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 265072005254 N-terminal plug; other site 265072005255 ligand-binding site [chemical binding]; other site 265072005256 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 265072005257 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072005258 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 265072005259 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 265072005260 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 265072005261 ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ChuT; COG4558 265072005262 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 265072005263 intersubunit interface [polypeptide binding]; other site 265072005264 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 265072005265 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 265072005266 ABC-ATPase subunit interface; other site 265072005267 dimer interface [polypeptide binding]; other site 265072005268 putative PBP binding regions; other site 265072005269 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 265072005270 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 265072005271 Walker A/P-loop; other site 265072005272 ATP binding site [chemical binding]; other site 265072005273 Q-loop/lid; other site 265072005274 ABC transporter signature motif; other site 265072005275 Walker B; other site 265072005276 D-loop; other site 265072005277 H-loop/switch region; other site 265072005278 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 265072005279 active site 265072005280 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 265072005281 Cupin domain; Region: Cupin_2; pfam07883 265072005282 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 265072005283 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 265072005284 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 265072005285 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 265072005286 RNA binding surface [nucleotide binding]; other site 265072005287 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 265072005288 active site 265072005289 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 265072005290 GTP-binding protein Der; Reviewed; Region: PRK00093 265072005291 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 265072005292 G1 box; other site 265072005293 GTP/Mg2+ binding site [chemical binding]; other site 265072005294 Switch I region; other site 265072005295 G2 box; other site 265072005296 Switch II region; other site 265072005297 G3 box; other site 265072005298 G4 box; other site 265072005299 G5 box; other site 265072005300 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 265072005301 G1 box; other site 265072005302 GTP/Mg2+ binding site [chemical binding]; other site 265072005303 Switch I region; other site 265072005304 G2 box; other site 265072005305 G3 box; other site 265072005306 Switch II region; other site 265072005307 G4 box; other site 265072005308 G5 box; other site 265072005309 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 265072005310 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 265072005311 Trp docking motif [polypeptide binding]; other site 265072005312 active site 265072005313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 265072005314 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 265072005315 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 265072005316 Walker A/P-loop; other site 265072005317 ATP binding site [chemical binding]; other site 265072005318 Q-loop/lid; other site 265072005319 ABC transporter signature motif; other site 265072005320 Walker B; other site 265072005321 D-loop; other site 265072005322 H-loop/switch region; other site 265072005323 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 265072005324 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 265072005325 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 265072005326 Walker A/P-loop; other site 265072005327 ATP binding site [chemical binding]; other site 265072005328 Q-loop/lid; other site 265072005329 ABC transporter signature motif; other site 265072005330 Walker B; other site 265072005331 D-loop; other site 265072005332 H-loop/switch region; other site 265072005333 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 265072005334 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 265072005335 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 265072005336 dimer interface [polypeptide binding]; other site 265072005337 motif 1; other site 265072005338 active site 265072005339 motif 2; other site 265072005340 motif 3; other site 265072005341 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 265072005342 anticodon binding site; other site 265072005343 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 265072005344 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 265072005345 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 265072005346 Helix-turn-helix domain; Region: HTH_25; pfam13413 265072005347 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 265072005348 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 265072005349 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 265072005350 binding surface 265072005351 TPR motif; other site 265072005352 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 265072005353 binding surface 265072005354 TPR motif; other site 265072005355 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 265072005356 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 265072005357 FeS/SAM binding site; other site 265072005358 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 265072005359 active site 265072005360 multimer interface [polypeptide binding]; other site 265072005361 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 265072005362 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 265072005363 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 265072005364 ribonuclease R; Region: RNase_R; TIGR02063 265072005365 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 265072005366 RNB domain; Region: RNB; pfam00773 265072005367 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 265072005368 RNA binding site [nucleotide binding]; other site 265072005369 Outer membrane efflux protein; Region: OEP; pfam02321 265072005370 Outer membrane efflux protein; Region: OEP; pfam02321 265072005371 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072005372 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 265072005373 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 265072005374 Predicted membrane protein [Function unknown]; Region: COG4655 265072005375 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 265072005376 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 265072005377 binding surface 265072005378 TPR motif; other site 265072005379 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 265072005380 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072005381 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 265072005382 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072005383 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 265072005384 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 265072005385 ATP binding site [chemical binding]; other site 265072005386 Walker A motif; other site 265072005387 hexamer interface [polypeptide binding]; other site 265072005388 Walker B motif; other site 265072005389 AAA domain; Region: AAA_31; pfam13614 265072005390 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072005391 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 265072005392 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 265072005393 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072005394 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 265072005395 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 265072005396 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 265072005397 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cd00488 265072005398 aromatic arch; other site 265072005399 DCoH dimer interaction site [polypeptide binding]; other site 265072005400 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 265072005401 DCoH tetramer interaction site [polypeptide binding]; other site 265072005402 substrate binding site [chemical binding]; other site 265072005403 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 265072005404 substrate binding site [chemical binding]; other site 265072005405 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 265072005406 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 265072005407 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 265072005408 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: COG1548; cl00668 265072005409 ATP-grasp domain; Region: ATP-grasp_3; pfam02655 265072005410 hisA/hisF family protein; Region: hisAF_rel; TIGR00734 265072005411 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an...; Region: HisA_HisF; cd04723 265072005412 active site 265072005413 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 265072005414 Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with...; Region: SIS_PHI; cd05005 265072005415 tetramer interface [polypeptide binding]; other site 265072005416 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 265072005417 active site 265072005418 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 265072005419 active site 265072005420 dimer interface [polypeptide binding]; other site 265072005421 magnesium binding site [ion binding]; other site 265072005422 transaldolase-like protein; Provisional; Region: PTZ00411 265072005423 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 265072005424 active site 265072005425 dimer interface [polypeptide binding]; other site 265072005426 catalytic residue [active] 265072005427 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; pfam01874 265072005428 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 265072005429 ATP-grasp domain; Region: ATP-grasp_4; cl17255 265072005430 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional; Region: PRK02264 265072005431 Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5), N...; Region: MCH; cd00545 265072005432 trimer interface I [polypeptide binding]; other site 265072005433 putative substrate binding pocket [chemical binding]; other site 265072005434 trimer interface II [polypeptide binding]; other site 265072005435 Predicted ATP-dependent carboligase related to biotin carboxylase [General function prediction only]; Region: COG2232 265072005436 ATP-grasp domain; Region: ATP-grasp_4; cl17255 265072005437 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; Region: Mpt_N; pfam09176 265072005438 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 265072005439 NAD(P) binding pocket [chemical binding]; other site 265072005440 Predicted archaeal sugar kinases [General function prediction only]; Region: COG1907 265072005441 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 265072005442 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 265072005443 The MopB_FmdB-FwdB CD contains the molybdenum/tungsten formylmethanofuran dehydrogenases, subunit B (FmdB/FwdB), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea...; Region: MopB_FmdB-FwdB; cd02761 265072005444 formylmethanofuran dehydrogenase subunit B; Region: one_C_dehyd_B; TIGR03129 265072005445 putative [4Fe-4S] binding site [ion binding]; other site 265072005446 putative molybdopterin cofactor binding site [chemical binding]; other site 265072005447 formylmethanofuran dehydrogenase subunit A; Region: one_C_dehyd_A; TIGR03121 265072005448 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 265072005449 active site 265072005450 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional; Region: PRK02114 265072005451 Formylmethanofuran-tetrahydromethanopterin formyltransferase; Region: FTR; pfam01913 265072005452 FTR, proximal lobe; Region: FTR_C; pfam02741 265072005453 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 265072005454 domain_subunit interface; other site 265072005455 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 265072005456 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 265072005457 ligand binding site [chemical binding]; other site 265072005458 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 265072005459 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 265072005460 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 265072005461 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 265072005462 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072005463 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 265072005464 substrate binding site [chemical binding]; other site 265072005465 dimerization interface [polypeptide binding]; other site 265072005466 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 265072005467 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 265072005468 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 265072005469 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 265072005470 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 265072005471 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 265072005472 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 265072005473 Active Sites [active] 265072005474 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 265072005475 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 265072005476 CysD dimerization site [polypeptide binding]; other site 265072005477 G1 box; other site 265072005478 putative GEF interaction site [polypeptide binding]; other site 265072005479 GTP/Mg2+ binding site [chemical binding]; other site 265072005480 Switch I region; other site 265072005481 G2 box; other site 265072005482 G3 box; other site 265072005483 Switch II region; other site 265072005484 G4 box; other site 265072005485 G5 box; other site 265072005486 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 265072005487 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 265072005488 Ferredoxin [Energy production and conversion]; Region: COG1146 265072005489 4Fe-4S binding domain; Region: Fer4; cl02805 265072005490 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 265072005491 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 265072005492 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 265072005493 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 265072005494 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 265072005495 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 265072005496 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 265072005497 putative substrate translocation pore; other site 265072005498 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 265072005499 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 265072005500 S-adenosylmethionine binding site [chemical binding]; other site 265072005501 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 265072005502 Active Sites [active] 265072005503 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 265072005504 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 265072005505 FeS/SAM binding site; other site 265072005506 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 265072005507 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 265072005508 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 265072005509 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 265072005510 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 265072005511 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 265072005512 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 265072005513 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072005514 homodimer interface [polypeptide binding]; other site 265072005515 catalytic residue [active] 265072005516 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 265072005517 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072005518 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072005519 metal binding site [ion binding]; metal-binding site 265072005520 active site 265072005521 I-site; other site 265072005522 Chorismate mutase type II; Region: CM_2; smart00830 265072005523 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 265072005524 Prephenate dehydratase; Region: PDT; pfam00800 265072005525 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 265072005526 putative L-Phe binding site [chemical binding]; other site 265072005527 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 265072005528 homodimer interface [polypeptide binding]; other site 265072005529 substrate-cofactor binding pocket; other site 265072005530 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072005531 catalytic residue [active] 265072005532 DNA gyrase subunit A; Validated; Region: PRK05560 265072005533 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 265072005534 CAP-like domain; other site 265072005535 active site 265072005536 primary dimer interface [polypeptide binding]; other site 265072005537 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 265072005538 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 265072005539 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 265072005540 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 265072005541 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 265072005542 peroxidase; Provisional; Region: PRK15000 265072005543 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 265072005544 dimer interface [polypeptide binding]; other site 265072005545 decamer (pentamer of dimers) interface [polypeptide binding]; other site 265072005546 catalytic triad [active] 265072005547 peroxidatic and resolving cysteines [active] 265072005548 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 265072005549 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 265072005550 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 265072005551 homodimer interface [polypeptide binding]; other site 265072005552 substrate-cofactor binding pocket; other site 265072005553 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072005554 catalytic residue [active] 265072005555 amidophosphoribosyltransferase; Provisional; Region: PRK09246 265072005556 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 265072005557 active site 265072005558 tetramer interface [polypeptide binding]; other site 265072005559 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072005560 active site 265072005561 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 265072005562 Colicin V production protein; Region: Colicin_V; pfam02674 265072005563 cell division protein DedD; Provisional; Region: PRK11633 265072005564 Sporulation related domain; Region: SPOR; pfam05036 265072005565 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 265072005566 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 265072005567 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 265072005568 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 265072005569 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 265072005570 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 265072005571 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 265072005572 substrate binding site [chemical binding]; other site 265072005573 active site 265072005574 catalytic residues [active] 265072005575 heterodimer interface [polypeptide binding]; other site 265072005576 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 265072005577 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 265072005578 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072005579 catalytic residue [active] 265072005580 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 265072005581 active site 265072005582 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 265072005583 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 265072005584 dimerization interface 3.5A [polypeptide binding]; other site 265072005585 active site 265072005586 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 265072005587 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072005588 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 265072005589 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 265072005590 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 265072005591 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 265072005592 tartrate dehydrogenase; Region: TTC; TIGR02089 265072005593 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 265072005594 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 265072005595 substrate binding site [chemical binding]; other site 265072005596 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 265072005597 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 265072005598 substrate binding site [chemical binding]; other site 265072005599 ligand binding site [chemical binding]; other site 265072005600 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 265072005601 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 265072005602 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 265072005603 argininosuccinate synthase; Provisional; Region: PRK13820 265072005604 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 265072005605 ANP binding site [chemical binding]; other site 265072005606 Substrate Binding Site II [chemical binding]; other site 265072005607 Substrate Binding Site I [chemical binding]; other site 265072005608 ornithine carbamoyltransferase; Provisional; Region: PRK00779 265072005609 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 265072005610 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 265072005611 acetylornithine aminotransferase; Provisional; Region: PRK02627 265072005612 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 265072005613 inhibitor-cofactor binding pocket; inhibition site 265072005614 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072005615 catalytic residue [active] 265072005616 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 265072005617 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 265072005618 [2Fe-2S] cluster binding site [ion binding]; other site 265072005619 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 265072005620 alpha subunit interface [polypeptide binding]; other site 265072005621 active site 265072005622 substrate binding site [chemical binding]; other site 265072005623 Fe binding site [ion binding]; other site 265072005624 EamA-like transporter family; Region: EamA; pfam00892 265072005625 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 265072005626 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072005627 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072005628 active site 265072005629 phosphorylation site [posttranslational modification] 265072005630 intermolecular recognition site; other site 265072005631 dimerization interface [polypeptide binding]; other site 265072005632 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 265072005633 DNA binding residues [nucleotide binding] 265072005634 dimerization interface [polypeptide binding]; other site 265072005635 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 265072005636 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 265072005637 dimerization interface [polypeptide binding]; other site 265072005638 PAS domain S-box; Region: sensory_box; TIGR00229 265072005639 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072005640 putative active site [active] 265072005641 heme pocket [chemical binding]; other site 265072005642 Histidine kinase; Region: HisKA_3; pfam07730 265072005643 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072005644 ATP binding site [chemical binding]; other site 265072005645 Mg2+ binding site [ion binding]; other site 265072005646 G-X-G motif; other site 265072005647 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 265072005648 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 265072005649 Trp docking motif [polypeptide binding]; other site 265072005650 dimer interface [polypeptide binding]; other site 265072005651 active site 265072005652 small subunit binding site [polypeptide binding]; other site 265072005653 PEP-CTERM motif; Region: VPEP; pfam07589 265072005654 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 265072005655 Na/Pi-cotransporter; Region: NaPi_cotrn_rel; TIGR00704 265072005656 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 265072005657 Methyltransferase domain; Region: Methyltransf_23; pfam13489 265072005658 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 265072005659 S-adenosylmethionine binding site [chemical binding]; other site 265072005660 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 265072005661 putative lipoprotein; Provisional; Region: PRK10533 265072005662 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072005663 Zn2+ binding site [ion binding]; other site 265072005664 Mg2+ binding site [ion binding]; other site 265072005665 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 265072005666 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 265072005667 metal binding triad; other site 265072005668 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 265072005669 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 265072005670 metal binding triad; other site 265072005671 acetyl-CoA synthetase; Provisional; Region: PRK00174 265072005672 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 265072005673 active site 265072005674 CoA binding site [chemical binding]; other site 265072005675 acyl-activating enzyme (AAE) consensus motif; other site 265072005676 AMP binding site [chemical binding]; other site 265072005677 acetate binding site [chemical binding]; other site 265072005678 Putative phosphatase (DUF442); Region: DUF442; cl17385 265072005679 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 265072005680 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 265072005681 motif II; other site 265072005682 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 265072005683 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 265072005684 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 265072005685 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 265072005686 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 265072005687 NAD(P) binding site [chemical binding]; other site 265072005688 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 265072005689 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 265072005690 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 265072005691 ligand binding site [chemical binding]; other site 265072005692 flexible hinge region; other site 265072005693 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 265072005694 putative switch regulator; other site 265072005695 non-specific DNA interactions [nucleotide binding]; other site 265072005696 putative cAMP binding site [chemical binding]; other site 265072005697 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072005698 Response regulator receiver domain; Region: Response_reg; pfam00072 265072005699 active site 265072005700 phosphorylation site [posttranslational modification] 265072005701 intermolecular recognition site; other site 265072005702 dimerization interface [polypeptide binding]; other site 265072005703 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 265072005704 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 265072005705 G1 box; other site 265072005706 putative GEF interaction site [polypeptide binding]; other site 265072005707 GTP/Mg2+ binding site [chemical binding]; other site 265072005708 Switch I region; other site 265072005709 G2 box; other site 265072005710 G3 box; other site 265072005711 Switch II region; other site 265072005712 G4 box; other site 265072005713 G5 box; other site 265072005714 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 265072005715 hypothetical protein; Provisional; Region: PRK01842 265072005716 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072005717 This family is most closely related to the GT1 family of glycosyltransferases. ExpC in Rhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucan (exopolysaccharide II); Region: GT1_ExpC_like; cd03818 265072005718 putative ADP-binding pocket [chemical binding]; other site 265072005719 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 265072005720 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072005721 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072005722 ABC transporter; Region: ABC_tran_2; pfam12848 265072005723 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 265072005724 TIGR02099 family protein; Region: TIGR02099 265072005725 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 265072005726 nitrilase; Region: PLN02798 265072005727 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 265072005728 putative active site [active] 265072005729 catalytic triad [active] 265072005730 dimer interface [polypeptide binding]; other site 265072005731 protease TldD; Provisional; Region: tldD; PRK10735 265072005732 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 265072005733 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 265072005734 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 265072005735 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 265072005736 ATP binding site [chemical binding]; other site 265072005737 putative Mg++ binding site [ion binding]; other site 265072005738 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 265072005739 nucleotide binding region [chemical binding]; other site 265072005740 ATP-binding site [chemical binding]; other site 265072005741 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 265072005742 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 265072005743 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 265072005744 choice-of-anchor A domain; Region: choice_anch_A; TIGR04215 265072005745 PEP-CTERM motif; Region: VPEP; pfam07589 265072005746 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 265072005747 Family description; Region: UvrD_C_2; pfam13538 265072005748 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 265072005749 probable DNA repair protein; Region: TIGR03623 265072005750 Actin depolymerization factor/cofilin- and gelsolin-like domains; Region: ADF_gelsolin; cl15697 265072005751 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 265072005752 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 265072005753 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 265072005754 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 265072005755 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 265072005756 conserved hypothetical protein, PP_1857 family; Region: efp_adjacent_2; TIGR03837 265072005757 elongation factor P; Validated; Region: PRK00529 265072005758 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 265072005759 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 265072005760 RNA binding site [nucleotide binding]; other site 265072005761 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 265072005762 RNA binding site [nucleotide binding]; other site 265072005763 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 265072005764 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 265072005765 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 265072005766 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 265072005767 FeS/SAM binding site; other site 265072005768 CheW-like domain; Region: CheW; pfam01584 265072005769 Response regulator receiver domain; Region: Response_reg; pfam00072 265072005770 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072005771 active site 265072005772 phosphorylation site [posttranslational modification] 265072005773 intermolecular recognition site; other site 265072005774 dimerization interface [polypeptide binding]; other site 265072005775 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 265072005776 DNA binding residues [nucleotide binding] 265072005777 dimerization interface [polypeptide binding]; other site 265072005778 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 265072005779 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072005780 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 265072005781 dimer interface [polypeptide binding]; other site 265072005782 phosphorylation site [posttranslational modification] 265072005783 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072005784 ATP binding site [chemical binding]; other site 265072005785 Mg2+ binding site [ion binding]; other site 265072005786 G-X-G motif; other site 265072005787 Response regulator receiver domain; Region: Response_reg; pfam00072 265072005788 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072005789 active site 265072005790 phosphorylation site [posttranslational modification] 265072005791 intermolecular recognition site; other site 265072005792 dimerization interface [polypeptide binding]; other site 265072005793 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 265072005794 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072005795 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 265072005796 UreF; Region: UreF; pfam01730 265072005797 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 265072005798 dimer interface [polypeptide binding]; other site 265072005799 catalytic residues [active] 265072005800 urease subunit alpha; Reviewed; Region: ureC; PRK13207 265072005801 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 265072005802 subunit interactions [polypeptide binding]; other site 265072005803 active site 265072005804 flap region; other site 265072005805 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 265072005806 gamma-beta subunit interface [polypeptide binding]; other site 265072005807 alpha-beta subunit interface [polypeptide binding]; other site 265072005808 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 265072005809 alpha-gamma subunit interface [polypeptide binding]; other site 265072005810 beta-gamma subunit interface [polypeptide binding]; other site 265072005811 UreD urease accessory protein; Region: UreD; pfam01774 265072005812 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 265072005813 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 265072005814 Walker A/P-loop; other site 265072005815 ATP binding site [chemical binding]; other site 265072005816 Q-loop/lid; other site 265072005817 ABC transporter signature motif; other site 265072005818 Walker B; other site 265072005819 D-loop; other site 265072005820 H-loop/switch region; other site 265072005821 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 265072005822 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 265072005823 Walker A/P-loop; other site 265072005824 ATP binding site [chemical binding]; other site 265072005825 Q-loop/lid; other site 265072005826 ABC transporter signature motif; other site 265072005827 Walker B; other site 265072005828 D-loop; other site 265072005829 H-loop/switch region; other site 265072005830 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 265072005831 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 265072005832 TM-ABC transporter signature motif; other site 265072005833 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 265072005834 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 265072005835 TM-ABC transporter signature motif; other site 265072005836 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 265072005837 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 265072005838 putative ligand binding site [chemical binding]; other site 265072005839 Putative regulatory protein; Region: CxxC_CXXC_SSSS; smart00834 265072005840 Acetamidase/Formamidase family; Region: FmdA_AmdA; pfam03069 265072005841 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 265072005842 SOS regulatory protein LexA; Region: lexA; TIGR00498 265072005843 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 265072005844 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 265072005845 Catalytic site [active] 265072005846 Predicted membrane protein [Function unknown]; Region: COG3174 265072005847 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 265072005848 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 265072005849 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 265072005850 active site 265072005851 non-prolyl cis peptide bond; other site 265072005852 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08642 265072005853 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072005854 NAD(P) binding site [chemical binding]; other site 265072005855 active site 265072005856 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 265072005857 Na binding site [ion binding]; other site 265072005858 Conserved TM helix; Region: TM_helix; pfam05552 265072005859 Conserved TM helix; Region: TM_helix; pfam05552 265072005860 Conserved TM helix; Region: TM_helix; pfam05552 265072005861 Uncharacterized conserved protein [Function unknown]; Region: COG0397 265072005862 hypothetical protein; Validated; Region: PRK00029 265072005863 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 265072005864 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 265072005865 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 265072005866 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072005867 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072005868 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 265072005869 putative effector binding pocket; other site 265072005870 putative dimerization interface [polypeptide binding]; other site 265072005871 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 265072005872 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072005873 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072005874 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072005875 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 265072005876 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072005877 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 265072005878 BON domain; Region: BON; pfam04972 265072005879 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 265072005880 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 265072005881 active site 265072005882 catalytic tetrad [active] 265072005883 TLC ATP/ADP transporter; Region: TLC; cl03940 265072005884 TLC ATP/ADP transporter; Region: TLC; cl03940 265072005885 Predicted transcriptional regulators [Transcription]; Region: COG1733 265072005886 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 265072005887 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 265072005888 NADH(P)-binding; Region: NAD_binding_10; pfam13460 265072005889 NAD binding site [chemical binding]; other site 265072005890 substrate binding site [chemical binding]; other site 265072005891 putative active site [active] 265072005892 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 265072005893 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072005894 NAD(P) binding site [chemical binding]; other site 265072005895 active site 265072005896 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 265072005897 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 265072005898 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 265072005899 GIY-YIG motif/motif A; other site 265072005900 active site 265072005901 catalytic site [active] 265072005902 putative DNA binding site [nucleotide binding]; other site 265072005903 metal binding site [ion binding]; metal-binding site 265072005904 UvrB/uvrC motif; Region: UVR; pfam02151 265072005905 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 265072005906 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 265072005907 active site 1 [active] 265072005908 dimer interface [polypeptide binding]; other site 265072005909 hexamer interface [polypeptide binding]; other site 265072005910 active site 2 [active] 265072005911 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 265072005912 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 265072005913 hypothetical protein; Provisional; Region: PRK05208 265072005914 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 265072005915 Predicted transporter component [General function prediction only]; Region: COG2391 265072005916 Sulphur transport; Region: Sulf_transp; pfam04143 265072005917 Predicted transporter component [General function prediction only]; Region: COG2391 265072005918 Sulphur transport; Region: Sulf_transp; pfam04143 265072005919 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 265072005920 Putative phosphatase (DUF442); Region: DUF442; cl17385 265072005921 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 265072005922 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 265072005923 PAS domain; Region: PAS_9; pfam13426 265072005924 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 265072005925 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 265072005926 Walker A motif; other site 265072005927 ATP binding site [chemical binding]; other site 265072005928 Walker B motif; other site 265072005929 arginine finger; other site 265072005930 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072005931 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 265072005932 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 265072005933 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 265072005934 substrate binding site [chemical binding]; other site 265072005935 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 265072005936 substrate binding site [chemical binding]; other site 265072005937 ligand binding site [chemical binding]; other site 265072005938 adenylosuccinate lyase; Provisional; Region: PRK09285 265072005939 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 265072005940 tetramer interface [polypeptide binding]; other site 265072005941 active site 265072005942 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 265072005943 Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; Region: SPEC; cl02488 265072005944 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 265072005945 Surface antigen; Region: Bac_surface_Ag; pfam01103 265072005946 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 265072005947 Family of unknown function (DUF490); Region: DUF490; pfam04357 265072005948 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 265072005949 putative metal binding site [ion binding]; other site 265072005950 Uncharacterized conserved protein [Function unknown]; Region: COG1432 265072005951 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 265072005952 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 265072005953 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 265072005954 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 265072005955 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 265072005956 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 265072005957 S-adenosylmethionine binding site [chemical binding]; other site 265072005958 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 265072005959 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072005960 Peptidase family M23; Region: Peptidase_M23; pfam01551 265072005961 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 265072005962 catalytic residues [active] 265072005963 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 265072005964 putative FMN binding site [chemical binding]; other site 265072005965 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 265072005966 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 265072005967 FMN binding site [chemical binding]; other site 265072005968 active site 265072005969 substrate binding site [chemical binding]; other site 265072005970 catalytic residue [active] 265072005971 Uncharacterized conserved protein [Function unknown]; Region: COG2353 265072005972 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 265072005973 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 265072005974 Pirin-related protein [General function prediction only]; Region: COG1741 265072005975 Pirin; Region: Pirin; pfam02678 265072005976 putative sulfate transport protein CysZ; Validated; Region: PRK04949 265072005977 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 265072005978 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072005979 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 265072005980 dimerization interface [polypeptide binding]; other site 265072005981 MoxR-like ATPases [General function prediction only]; Region: COG0714 265072005982 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 265072005983 Walker A motif; other site 265072005984 ATP binding site [chemical binding]; other site 265072005985 Walker B motif; other site 265072005986 arginine finger; other site 265072005987 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 265072005988 Protein of unknown function DUF58; Region: DUF58; pfam01882 265072005989 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 265072005990 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 265072005991 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 265072005992 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 265072005993 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 265072005994 nucleoside/Zn binding site; other site 265072005995 dimer interface [polypeptide binding]; other site 265072005996 catalytic motif [active] 265072005997 Rhomboid family; Region: Rhomboid; pfam01694 265072005998 BAX inhibitor (BI)-1/YccA-like protein family; Region: BI-1-like; cl00473 265072005999 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 265072006000 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 265072006001 beta-hexosaminidase; Provisional; Region: PRK05337 265072006002 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 265072006003 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 265072006004 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 265072006005 dimer interface [polypeptide binding]; other site 265072006006 conserved gate region; other site 265072006007 putative PBP binding loops; other site 265072006008 ABC-ATPase subunit interface; other site 265072006009 glutathione ABC transporter permease GsiC; Provisional; Region: PRK15081 265072006010 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 265072006011 putative PBP binding loops; other site 265072006012 dimer interface [polypeptide binding]; other site 265072006013 ABC-ATPase subunit interface; other site 265072006014 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 265072006015 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 265072006016 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 265072006017 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 265072006018 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 265072006019 TRAM domain; Region: TRAM; pfam01938 265072006020 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 265072006021 S-adenosylmethionine binding site [chemical binding]; other site 265072006022 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 265072006023 active site 265072006024 catalytic site [active] 265072006025 substrate binding site [chemical binding]; other site 265072006026 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 265072006027 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 265072006028 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 265072006029 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 265072006030 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 265072006031 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 265072006032 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 265072006033 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 265072006034 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 265072006035 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 265072006036 Walker A/P-loop; other site 265072006037 ATP binding site [chemical binding]; other site 265072006038 Q-loop/lid; other site 265072006039 ABC transporter signature motif; other site 265072006040 Walker B; other site 265072006041 D-loop; other site 265072006042 H-loop/switch region; other site 265072006043 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 265072006044 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 265072006045 dimer interface [polypeptide binding]; other site 265072006046 conserved gate region; other site 265072006047 putative PBP binding loops; other site 265072006048 ABC-ATPase subunit interface; other site 265072006049 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 265072006050 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 265072006051 substrate binding pocket [chemical binding]; other site 265072006052 membrane-bound complex binding site; other site 265072006053 cysteine synthase B; Region: cysM; TIGR01138 265072006054 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 265072006055 dimer interface [polypeptide binding]; other site 265072006056 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072006057 catalytic residue [active] 265072006058 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 265072006059 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 265072006060 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 265072006061 generic binding surface II; other site 265072006062 generic binding surface I; other site 265072006063 TfoX N-terminal domain; Region: TfoX_N; pfam04993 265072006064 Peptidase family M48; Region: Peptidase_M48; pfam01435 265072006065 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 265072006066 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 265072006067 trimer interface [polypeptide binding]; other site 265072006068 active site 265072006069 substrate binding site [chemical binding]; other site 265072006070 CoA binding site [chemical binding]; other site 265072006071 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 265072006072 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 265072006073 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 265072006074 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072006075 metal binding site [ion binding]; metal-binding site 265072006076 active site 265072006077 I-site; other site 265072006078 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 265072006079 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 265072006080 ArsC family; Region: ArsC; pfam03960 265072006081 putative catalytic residues [active] 265072006082 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 265072006083 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 265072006084 metal binding site [ion binding]; metal-binding site 265072006085 dimer interface [polypeptide binding]; other site 265072006086 HemK family putative methylases; Region: hemK_fam; TIGR00536 265072006087 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 265072006088 S-adenosylmethionine binding site [chemical binding]; other site 265072006089 Domain of unknown function (DUF202); Region: DUF202; pfam02656 265072006090 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 265072006091 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 265072006092 RNA binding surface [nucleotide binding]; other site 265072006093 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 265072006094 probable active site [active] 265072006095 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 265072006096 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 265072006097 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 265072006098 Peptidase family M50; Region: Peptidase_M50; pfam02163 265072006099 active site 265072006100 putative substrate binding region [chemical binding]; other site 265072006101 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 265072006102 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 265072006103 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 265072006104 active site 265072006105 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 265072006106 intracellular septation protein A; Reviewed; Region: PRK00259 265072006107 YciI-like protein; Reviewed; Region: PRK11370 265072006108 BolA-like protein; Region: BolA; pfam01722 265072006109 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 265072006110 SurA N-terminal domain; Region: SurA_N_3; cl07813 265072006111 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 265072006112 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 265072006113 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 265072006114 Cytochrome c; Region: Cytochrom_C; pfam00034 265072006115 Iron permease FTR1 family; Region: FTR1; cl00475 265072006116 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 265072006117 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_9; cd07245 265072006118 dimer interface [polypeptide binding]; other site 265072006119 putative metal binding site [ion binding]; other site 265072006120 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 265072006121 Nitrogen regulatory protein P-II; Region: P-II; smart00938 265072006122 NAD synthetase; Provisional; Region: PRK13981 265072006123 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 265072006124 multimer interface [polypeptide binding]; other site 265072006125 active site 265072006126 catalytic triad [active] 265072006127 protein interface 1 [polypeptide binding]; other site 265072006128 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 265072006129 homodimer interface [polypeptide binding]; other site 265072006130 NAD binding pocket [chemical binding]; other site 265072006131 ATP binding pocket [chemical binding]; other site 265072006132 Mg binding site [ion binding]; other site 265072006133 active-site loop [active] 265072006134 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 265072006135 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 265072006136 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 265072006137 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 265072006138 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 265072006139 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 265072006140 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 265072006141 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 265072006142 CoA binding domain; Region: CoA_binding; smart00881 265072006143 CoA-ligase; Region: Ligase_CoA; pfam00549 265072006144 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 265072006145 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 265072006146 CoA-ligase; Region: Ligase_CoA; pfam00549 265072006147 phosphoserine phosphatase SerB; Region: serB; TIGR00338 265072006148 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 265072006149 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 265072006150 motif II; other site 265072006151 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 265072006152 active site 265072006153 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 265072006154 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 265072006155 DNA-binding site [nucleotide binding]; DNA binding site 265072006156 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 265072006157 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072006158 homodimer interface [polypeptide binding]; other site 265072006159 catalytic residue [active] 265072006160 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 265072006161 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 265072006162 dimer interface [polypeptide binding]; other site 265072006163 active site 265072006164 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 265072006165 active site 1 [active] 265072006166 dimer interface [polypeptide binding]; other site 265072006167 active site 2 [active] 265072006168 MoxR-like ATPases [General function prediction only]; Region: COG0714 265072006169 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 265072006170 Walker A motif; other site 265072006171 ATP binding site [chemical binding]; other site 265072006172 Walker B motif; other site 265072006173 arginine finger; other site 265072006174 Protein of unknown function DUF58; Region: DUF58; pfam01882 265072006175 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 265072006176 metal ion-dependent adhesion site (MIDAS); other site 265072006177 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 265072006178 metal ion-dependent adhesion site (MIDAS); other site 265072006179 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 265072006180 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 265072006181 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 265072006182 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 265072006183 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 265072006184 N-terminal plug; other site 265072006185 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072006186 ligand-binding site [chemical binding]; other site 265072006187 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 265072006188 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072006189 catalytic residues [active] 265072006190 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072006191 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072006192 metal binding site [ion binding]; metal-binding site 265072006193 active site 265072006194 I-site; other site 265072006195 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 265072006196 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 265072006197 enolase; Provisional; Region: eno; PRK00077 265072006198 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 265072006199 dimer interface [polypeptide binding]; other site 265072006200 metal binding site [ion binding]; metal-binding site 265072006201 substrate binding pocket [chemical binding]; other site 265072006202 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 265072006203 CTP synthetase; Validated; Region: pyrG; PRK05380 265072006204 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 265072006205 Catalytic site [active] 265072006206 active site 265072006207 UTP binding site [chemical binding]; other site 265072006208 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 265072006209 active site 265072006210 putative oxyanion hole; other site 265072006211 catalytic triad [active] 265072006212 Uncharacterized conserved protein [Function unknown]; Region: COG0062 265072006213 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 265072006214 putative substrate binding site [chemical binding]; other site 265072006215 putative ATP binding site [chemical binding]; other site 265072006216 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 265072006217 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 265072006218 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 265072006219 active site 265072006220 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 265072006221 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 265072006222 catalytic motif [active] 265072006223 Zn binding site [ion binding]; other site 265072006224 RibD C-terminal domain; Region: RibD_C; cl17279 265072006225 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 265072006226 ATP cone domain; Region: ATP-cone; pfam03477 265072006227 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 265072006228 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 265072006229 dimer interface [polypeptide binding]; other site 265072006230 active site 265072006231 glycine-pyridoxal phosphate binding site [chemical binding]; other site 265072006232 folate binding site [chemical binding]; other site 265072006233 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 265072006234 Fumarase C-terminus; Region: Fumerase_C; pfam05683 265072006235 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 265072006236 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 265072006237 active site 265072006238 FMN binding site [chemical binding]; other site 265072006239 substrate binding site [chemical binding]; other site 265072006240 homotetramer interface [polypeptide binding]; other site 265072006241 catalytic residue [active] 265072006242 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 265072006243 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 265072006244 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 265072006245 active site 265072006246 substrate binding site [chemical binding]; other site 265072006247 metal binding site [ion binding]; metal-binding site 265072006248 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 265072006249 catalytic motif [active] 265072006250 Catalytic residue [active] 265072006251 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 265072006252 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 265072006253 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction; Region: PGM1; cd03085 265072006254 phosphoglucomutase; Region: PLN02307 265072006255 substrate binding site [chemical binding]; other site 265072006256 dimer interface [polypeptide binding]; other site 265072006257 active site 265072006258 metal binding site [ion binding]; metal-binding site 265072006259 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 265072006260 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 265072006261 ligand binding site [chemical binding]; other site 265072006262 flexible hinge region; other site 265072006263 transcriptional regulator EpsA; Region: EpsA; TIGR03020 265072006264 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 265072006265 DNA binding residues [nucleotide binding] 265072006266 dimerization interface [polypeptide binding]; other site 265072006267 chemotaxis regulator CheZ; Provisional; Region: PRK11166 265072006268 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 265072006269 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072006270 active site 265072006271 phosphorylation site [posttranslational modification] 265072006272 intermolecular recognition site; other site 265072006273 dimerization interface [polypeptide binding]; other site 265072006274 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 265072006275 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072006276 active site 265072006277 phosphorylation site [posttranslational modification] 265072006278 intermolecular recognition site; other site 265072006279 dimerization interface [polypeptide binding]; other site 265072006280 CheB methylesterase; Region: CheB_methylest; pfam01339 265072006281 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 265072006282 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 265072006283 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 265072006284 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 265072006285 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072006286 PAS domain; Region: PAS_9; pfam13426 265072006287 putative active site [active] 265072006288 heme pocket [chemical binding]; other site 265072006289 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 265072006290 dimerization interface [polypeptide binding]; other site 265072006291 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072006292 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072006293 dimer interface [polypeptide binding]; other site 265072006294 putative CheW interface [polypeptide binding]; other site 265072006295 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072006296 dimer interface [polypeptide binding]; other site 265072006297 putative CheW interface [polypeptide binding]; other site 265072006298 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 265072006299 putative CheA interaction surface; other site 265072006300 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 265072006301 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 265072006302 putative binding surface; other site 265072006303 active site 265072006304 CheY binding; Region: CheY-binding; pfam09078 265072006305 CheY binding; Region: CheY-binding; pfam09078 265072006306 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 265072006307 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072006308 ATP binding site [chemical binding]; other site 265072006309 Mg2+ binding site [ion binding]; other site 265072006310 G-X-G motif; other site 265072006311 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 265072006312 Response regulator receiver domain; Region: Response_reg; pfam00072 265072006313 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072006314 active site 265072006315 phosphorylation site [posttranslational modification] 265072006316 intermolecular recognition site; other site 265072006317 dimerization interface [polypeptide binding]; other site 265072006318 flagellar motor protein MotB; Validated; Region: motB; PRK09041 265072006319 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 265072006320 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 265072006321 ligand binding site [chemical binding]; other site 265072006322 flagellar motor protein MotA; Validated; Region: PRK09110 265072006323 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 265072006324 Methyltransferase domain; Region: Methyltransf_18; pfam12847 265072006325 transcriptional activator FlhC; Provisional; Region: PRK12722 265072006326 transcriptional activator FlhD; Provisional; Region: PRK02909 265072006327 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 265072006328 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 265072006329 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 265072006330 FHIPEP family; Region: FHIPEP; pfam00771 265072006331 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 265072006332 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072006333 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072006334 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 265072006335 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072006336 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 265072006337 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 265072006338 DNA binding residues [nucleotide binding] 265072006339 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 265072006340 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 265072006341 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 265072006342 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 265072006343 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 265072006344 ligand binding site [chemical binding]; other site 265072006345 FlgN protein; Region: FlgN; pfam05130 265072006346 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 265072006347 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 265072006348 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 265072006349 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 265072006350 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 265072006351 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 265072006352 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 265072006353 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 265072006354 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 265072006355 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 265072006356 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 265072006357 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 265072006358 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 265072006359 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 265072006360 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 265072006361 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 265072006362 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 265072006363 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 265072006364 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 265072006365 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 265072006366 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 265072006367 Flagellar L-ring protein; Region: FlgH; pfam02107 265072006368 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 265072006369 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 265072006370 Rod binding protein; Region: Rod-binding; cl01626 265072006371 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 265072006372 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 265072006373 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 265072006374 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 265072006375 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 265072006376 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 265072006377 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 265072006378 EAL domain; Region: EAL; pfam00563 265072006379 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 265072006380 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 265072006381 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 265072006382 flagellar motor switch protein; Validated; Region: fliN; PRK05698 265072006383 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 265072006384 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 265072006385 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 265072006386 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07021 265072006387 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 265072006388 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 265072006389 Flagellar FliJ protein; Region: FliJ; pfam02050 265072006390 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 265072006391 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 265072006392 Walker A motif/ATP binding site; other site 265072006393 Walker B motif; other site 265072006394 flagellar assembly protein H; Validated; Region: fliH; PRK05687 265072006395 Flagellar assembly protein FliH; Region: FliH; pfam02108 265072006396 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 265072006397 MgtE intracellular N domain; Region: MgtE_N; cl15244 265072006398 FliG C-terminal domain; Region: FliG_C; pfam01706 265072006399 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 265072006400 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 265072006401 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 265072006402 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 265072006403 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 265072006404 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 265072006405 Flagellar protein FliT; Region: FliT; pfam05400 265072006406 Flagellar protein FliS; Region: FliS; cl00654 265072006407 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 265072006408 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 265072006409 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 265072006410 FlaG protein; Region: FlaG; pfam03646 265072006411 flagellin; Provisional; Region: PRK12802 265072006412 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 265072006413 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 265072006414 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 265072006415 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072006416 active site 265072006417 phosphorylation site [posttranslational modification] 265072006418 intermolecular recognition site; other site 265072006419 dimerization interface [polypeptide binding]; other site 265072006420 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 265072006421 DNA binding residues [nucleotide binding] 265072006422 dimerization interface [polypeptide binding]; other site 265072006423 PAS fold; Region: PAS_3; pfam08447 265072006424 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 265072006425 Histidine kinase; Region: HisKA_3; pfam07730 265072006426 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072006427 ATP binding site [chemical binding]; other site 265072006428 Mg2+ binding site [ion binding]; other site 265072006429 G-X-G motif; other site 265072006430 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 265072006431 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 265072006432 N-terminal plug; other site 265072006433 ligand-binding site [chemical binding]; other site 265072006434 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 265072006435 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 265072006436 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 265072006437 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 265072006438 putative transporter; Provisional; Region: PRK11660 265072006439 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 265072006440 Sulfate transporter family; Region: Sulfate_transp; pfam00916 265072006441 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 265072006442 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 265072006443 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 265072006444 N-terminal plug; other site 265072006445 ligand-binding site [chemical binding]; other site 265072006446 Protein of unknown function (DUF779); Region: DUF779; pfam05610 265072006447 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 265072006448 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 265072006449 NAD(P) binding site [chemical binding]; other site 265072006450 catalytic residues [active] 265072006451 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 265072006452 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 265072006453 DNA binding residues [nucleotide binding] 265072006454 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 265072006455 IHF dimer interface [polypeptide binding]; other site 265072006456 IHF - DNA interface [nucleotide binding]; other site 265072006457 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 265072006458 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 265072006459 putative tRNA-binding site [nucleotide binding]; other site 265072006460 B3/4 domain; Region: B3_4; pfam03483 265072006461 tRNA synthetase B5 domain; Region: B5; smart00874 265072006462 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 265072006463 dimer interface [polypeptide binding]; other site 265072006464 motif 1; other site 265072006465 motif 3; other site 265072006466 motif 2; other site 265072006467 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 265072006468 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 265072006469 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 265072006470 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 265072006471 dimer interface [polypeptide binding]; other site 265072006472 motif 1; other site 265072006473 active site 265072006474 motif 2; other site 265072006475 motif 3; other site 265072006476 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 265072006477 23S rRNA binding site [nucleotide binding]; other site 265072006478 L21 binding site [polypeptide binding]; other site 265072006479 L13 binding site [polypeptide binding]; other site 265072006480 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 265072006481 translation initiation factor IF-3; Region: infC; TIGR00168 265072006482 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 265072006483 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 265072006484 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 265072006485 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 265072006486 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 265072006487 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 265072006488 active site 265072006489 dimer interface [polypeptide binding]; other site 265072006490 motif 1; other site 265072006491 motif 2; other site 265072006492 motif 3; other site 265072006493 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 265072006494 anticodon binding site; other site 265072006495 TIGR03790 family protein; Region: TIGR03790 265072006496 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 265072006497 UDP-glucose 4-epimerase; Region: PLN02240 265072006498 NAD binding site [chemical binding]; other site 265072006499 homodimer interface [polypeptide binding]; other site 265072006500 active site 265072006501 substrate binding site [chemical binding]; other site 265072006502 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 265072006503 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 265072006504 NAD binding site [chemical binding]; other site 265072006505 substrate binding site [chemical binding]; other site 265072006506 homodimer interface [polypeptide binding]; other site 265072006507 active site 265072006508 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 265072006509 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 265072006510 substrate binding site; other site 265072006511 tetramer interface; other site 265072006512 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 265072006513 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 265072006514 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 265072006515 NADP binding site [chemical binding]; other site 265072006516 active site 265072006517 putative substrate binding site [chemical binding]; other site 265072006518 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 265072006519 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 265072006520 Substrate binding site; other site 265072006521 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 265072006522 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072006523 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_6; cd04955 265072006524 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 265072006525 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 265072006526 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 265072006527 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 265072006528 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 265072006529 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 265072006530 Probable Catalytic site; other site 265072006531 metal-binding site 265072006532 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 265072006533 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 265072006534 active site 265072006535 O-Antigen ligase; Region: Wzy_C; pfam04932 265072006536 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cd02062 265072006537 FMN binding site [chemical binding]; other site 265072006538 dimer interface [polypeptide binding]; other site 265072006539 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; COG2327 265072006540 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 265072006541 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 265072006542 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 265072006543 EpsI family protein; Region: EpsI_fam; TIGR02914 265072006544 exosortase B; Region: exosortase_2; TIGR03113 265072006545 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 265072006546 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 265072006547 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 265072006548 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 265072006549 chain length determinant protein EpsF; Region: EpsF; TIGR03017 265072006550 Chain length determinant protein; Region: Wzz; cl15801 265072006551 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 265072006552 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 265072006553 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 265072006554 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 265072006555 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 265072006556 Bacterial sugar transferase; Region: Bac_transf; pfam02397 265072006557 exopolysaccharide biosynthesis operon protein EpsL; Region: EpsL; TIGR03014 265072006558 CAAX protease self-immunity; Region: Abi; cl00558 265072006559 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072006560 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 265072006561 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 265072006562 tyrosine decarboxylase; Region: PLN02880 265072006563 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 265072006564 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072006565 catalytic residue [active] 265072006566 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 265072006567 putative hydrophobic ligand binding site [chemical binding]; other site 265072006568 protein interface [polypeptide binding]; other site 265072006569 gate; other site 265072006570 von Willebrand factor type A domain; Region: VWA_2; pfam13519 265072006571 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 265072006572 metal ion-dependent adhesion site (MIDAS); other site 265072006573 Protein of unknown function DUF58; Region: DUF58; pfam01882 265072006574 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 265072006575 MoxR-like ATPases [General function prediction only]; Region: COG0714 265072006576 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 265072006577 Walker A motif; other site 265072006578 ATP binding site [chemical binding]; other site 265072006579 Walker B motif; other site 265072006580 arginine finger; other site 265072006581 Methanol dehydrogenase beta subunit; Region: MDH; pfam02315 265072006582 cytochrome c(L), periplasmic; Region: cytochrome_MoxG; TIGR03872 265072006583 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 265072006584 methanol oxidation system protein MoxJ; Region: ABC_MoxJ; TIGR03870 265072006585 substrate binding pocket [chemical binding]; other site 265072006586 membrane-bound complex binding site; other site 265072006587 hinge residues; other site 265072006588 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 265072006589 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 265072006590 Trp docking motif [polypeptide binding]; other site 265072006591 dimer interface [polypeptide binding]; other site 265072006592 active site 265072006593 small subunit binding site [polypeptide binding]; other site 265072006594 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 265072006595 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 265072006596 putative NAD(P) binding site [chemical binding]; other site 265072006597 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 265072006598 dimer interface [polypeptide binding]; other site 265072006599 ADP-ribose binding site [chemical binding]; other site 265072006600 active site 265072006601 nudix motif; other site 265072006602 metal binding site [ion binding]; metal-binding site 265072006603 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 265072006604 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 265072006605 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 265072006606 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 265072006607 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 265072006608 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 265072006609 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 265072006610 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 265072006611 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 265072006612 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 265072006613 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 265072006614 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 265072006615 4Fe-4S binding domain; Region: Fer4; pfam00037 265072006616 4Fe-4S binding domain; Region: Fer4; pfam00037 265072006617 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 265072006618 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 265072006619 NADH dehydrogenase subunit G; Validated; Region: PRK09129 265072006620 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 265072006621 catalytic loop [active] 265072006622 iron binding site [ion binding]; other site 265072006623 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 265072006624 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 265072006625 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; cd02775 265072006626 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 265072006627 SLBB domain; Region: SLBB; pfam10531 265072006628 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 265072006629 NADH dehydrogenase subunit E; Validated; Region: PRK07539 265072006630 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 265072006631 putative dimer interface [polypeptide binding]; other site 265072006632 [2Fe-2S] cluster binding site [ion binding]; other site 265072006633 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 265072006634 NADH dehydrogenase subunit D; Validated; Region: PRK06075 265072006635 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 265072006636 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 265072006637 NADH dehydrogenase subunit B; Validated; Region: PRK06411 265072006638 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 265072006639 Preprotein translocase SecG subunit; Region: SecG; pfam03840 265072006640 triosephosphate isomerase; Provisional; Region: PRK14567 265072006641 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 265072006642 substrate binding site [chemical binding]; other site 265072006643 dimer interface [polypeptide binding]; other site 265072006644 catalytic triad [active] 265072006645 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 265072006646 DHH family; Region: DHH; pfam01368 265072006647 DHHA1 domain; Region: DHHA1; pfam02272 265072006648 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 265072006649 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 265072006650 catalytic core [active] 265072006651 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 265072006652 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 265072006653 P-loop; other site 265072006654 Magnesium ion binding site [ion binding]; other site 265072006655 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 265072006656 putative active site [active] 265072006657 putative metal binding residues [ion binding]; other site 265072006658 signature motif; other site 265072006659 putative triphosphate binding site [ion binding]; other site 265072006660 The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family; Region: CHAD; smart00880 265072006661 Ion channel; Region: Ion_trans_2; pfam07885 265072006662 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 265072006663 TrkA-N domain; Region: TrkA_N; pfam02254 265072006664 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 265072006665 TrkA-N domain; Region: TrkA_N; pfam02254 265072006666 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 265072006667 hypothetical protein; Provisional; Region: PRK09256 265072006668 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 265072006669 interface (dimer of trimers) [polypeptide binding]; other site 265072006670 Substrate-binding/catalytic site; other site 265072006671 Zn-binding sites [ion binding]; other site 265072006672 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 265072006673 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 265072006674 dimer interface [polypeptide binding]; other site 265072006675 TPP-binding site [chemical binding]; other site 265072006676 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 265072006677 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 265072006678 E3 interaction surface; other site 265072006679 lipoyl attachment site [posttranslational modification]; other site 265072006680 e3 binding domain; Region: E3_binding; pfam02817 265072006681 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 265072006682 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 265072006683 E3 interaction surface; other site 265072006684 lipoyl attachment site [posttranslational modification]; other site 265072006685 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 265072006686 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 265072006687 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072006688 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 265072006689 Sporulation related domain; Region: SPOR; pfam05036 265072006690 Type III pantothenate kinase; Region: Pan_kinase; cl17198 265072006691 Biotin operon repressor [Transcription]; Region: BirA; COG1654 265072006692 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 265072006693 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 265072006694 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 265072006695 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 265072006696 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 265072006697 active site 265072006698 HIGH motif; other site 265072006699 nucleotide binding site [chemical binding]; other site 265072006700 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 265072006701 active site 265072006702 KMSKS motif; other site 265072006703 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 265072006704 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 265072006705 methionine sulfoxide reductase A; Provisional; Region: PRK14054 265072006706 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 265072006707 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 265072006708 P-loop; other site 265072006709 Magnesium ion binding site [ion binding]; other site 265072006710 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 265072006711 Magnesium ion binding site [ion binding]; other site 265072006712 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 265072006713 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 265072006714 Ligand binding site; other site 265072006715 oligomer interface; other site 265072006716 Uncharacterized conserved protein [Function unknown]; Region: COG2835 265072006717 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 265072006718 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 265072006719 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 265072006720 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072006721 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 265072006722 Walker A/P-loop; other site 265072006723 ATP binding site [chemical binding]; other site 265072006724 Q-loop/lid; other site 265072006725 ABC transporter signature motif; other site 265072006726 Walker B; other site 265072006727 D-loop; other site 265072006728 H-loop/switch region; other site 265072006729 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072006730 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 265072006731 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 265072006732 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 265072006733 Competence protein; Region: Competence; pfam03772 265072006734 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 265072006735 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 265072006736 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 265072006737 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 265072006738 Walker A/P-loop; other site 265072006739 ATP binding site [chemical binding]; other site 265072006740 Q-loop/lid; other site 265072006741 ABC transporter signature motif; other site 265072006742 Walker B; other site 265072006743 D-loop; other site 265072006744 H-loop/switch region; other site 265072006745 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 265072006746 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 265072006747 FtsX-like permease family; Region: FtsX; pfam02687 265072006748 PEP-CTERM motif; Region: VPEP; pfam07589 265072006749 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 265072006750 Lumazine binding domain; Region: Lum_binding; pfam00677 265072006751 Lumazine binding domain; Region: Lum_binding; pfam00677 265072006752 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 265072006753 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 265072006754 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 265072006755 dimerization interface [polypeptide binding]; other site 265072006756 active site 265072006757 hypothetical protein; Validated; Region: PRK00228 265072006758 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 265072006759 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072006760 active site 265072006761 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 265072006762 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 265072006763 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 265072006764 dihydroorotase; Provisional; Region: PRK07627 265072006765 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 265072006766 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 265072006767 active site 265072006768 Predicted acetamidase/formamidase [Energy production and conversion]; Region: COG2421 265072006769 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 265072006770 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 265072006771 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 265072006772 Walker A motif; other site 265072006773 ATP binding site [chemical binding]; other site 265072006774 Walker B motif; other site 265072006775 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 265072006776 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 265072006777 Walker A motif; other site 265072006778 ATP binding site [chemical binding]; other site 265072006779 Walker B motif; other site 265072006780 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 265072006781 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 265072006782 catalytic residue [active] 265072006783 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 265072006784 pyrroline-5-carboxylate reductase; Region: proC; TIGR00112 265072006785 YGGT family; Region: YGGT; pfam02325 265072006786 YGGT family; Region: YGGT; pfam02325 265072006787 Predicted dinucleotide-binding enzymes [General function prediction only]; Region: COG2085 265072006788 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 265072006789 ribonuclease G; Provisional; Region: PRK11712 265072006790 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 265072006791 homodimer interface [polypeptide binding]; other site 265072006792 oligonucleotide binding site [chemical binding]; other site 265072006793 Maf-like protein; Region: Maf; pfam02545 265072006794 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 265072006795 active site 265072006796 dimer interface [polypeptide binding]; other site 265072006797 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 265072006798 nudix motif; other site 265072006799 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 265072006800 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 265072006801 Ligand Binding Site [chemical binding]; other site 265072006802 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 265072006803 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 265072006804 putative C-terminal domain interface [polypeptide binding]; other site 265072006805 putative GSH binding site (G-site) [chemical binding]; other site 265072006806 putative dimer interface [polypeptide binding]; other site 265072006807 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 265072006808 dimer interface [polypeptide binding]; other site 265072006809 N-terminal domain interface [polypeptide binding]; other site 265072006810 putative substrate binding pocket (H-site) [chemical binding]; other site 265072006811 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 265072006812 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 265072006813 dimerization interface [polypeptide binding]; other site 265072006814 active site 265072006815 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 265072006816 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 265072006817 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 265072006818 Walker A motif; other site 265072006819 ATP binding site [chemical binding]; other site 265072006820 Walker B motif; other site 265072006821 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 265072006822 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 265072006823 PYR/PP interface [polypeptide binding]; other site 265072006824 dimer interface [polypeptide binding]; other site 265072006825 TPP binding site [chemical binding]; other site 265072006826 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 265072006827 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 265072006828 TPP-binding site [chemical binding]; other site 265072006829 dimer interface [polypeptide binding]; other site 265072006830 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 265072006831 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 265072006832 putative valine binding site [chemical binding]; other site 265072006833 dimer interface [polypeptide binding]; other site 265072006834 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 265072006835 ketol-acid reductoisomerase; Provisional; Region: PRK05479 265072006836 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 265072006837 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 265072006838 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 265072006839 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 265072006840 putative active site [active] 265072006841 Ap4A binding site [chemical binding]; other site 265072006842 nudix motif; other site 265072006843 putative metal binding site [ion binding]; other site 265072006844 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 265072006845 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006846 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006847 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006848 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006849 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006850 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006851 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072006852 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 265072006853 putative hydrophobic ligand binding site [chemical binding]; other site 265072006854 protein interface [polypeptide binding]; other site 265072006855 gate; other site 265072006856 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 265072006857 Pilin (bacterial filament); Region: Pilin; pfam00114 265072006858 cAMP phosphodiesterases class-II; Region: PDEase_II; cl17776 265072006859 CHASE2 domain; Region: CHASE2; pfam05226 265072006860 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 265072006861 cyclase homology domain; Region: CHD; cd07302 265072006862 nucleotidyl binding site; other site 265072006863 metal binding site [ion binding]; metal-binding site 265072006864 dimer interface [polypeptide binding]; other site 265072006865 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 265072006866 putative hydrolase; Provisional; Region: PRK11460 265072006867 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 265072006868 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 265072006869 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 265072006870 substrate binding pocket [chemical binding]; other site 265072006871 chain length determination region; other site 265072006872 substrate-Mg2+ binding site; other site 265072006873 catalytic residues [active] 265072006874 aspartate-rich region 1; other site 265072006875 active site lid residues [active] 265072006876 aspartate-rich region 2; other site 265072006877 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 265072006878 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 265072006879 TPP-binding site; other site 265072006880 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 265072006881 PYR/PP interface [polypeptide binding]; other site 265072006882 dimer interface [polypeptide binding]; other site 265072006883 TPP binding site [chemical binding]; other site 265072006884 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 265072006885 putative GTP cyclohydrolase; Provisional; Region: PRK13674 265072006886 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 265072006887 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 265072006888 catalytic motif [active] 265072006889 Catalytic residue [active] 265072006890 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 265072006891 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 265072006892 putative substrate translocation pore; other site 265072006893 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 265072006894 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 265072006895 Tetramer interface [polypeptide binding]; other site 265072006896 active site 265072006897 FMN-binding site [chemical binding]; other site 265072006898 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 265072006899 pseudouridine synthase; Region: TIGR00093 265072006900 probable active site [active] 265072006901 isocitrate dehydrogenase; Validated; Region: PRK07362 265072006902 isocitrate dehydrogenase; Reviewed; Region: PRK07006 265072006903 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 265072006904 DNA-binding site [nucleotide binding]; DNA binding site 265072006905 RNA-binding motif; other site 265072006906 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 265072006907 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 265072006908 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 265072006909 Walker A motif; other site 265072006910 ATP binding site [chemical binding]; other site 265072006911 Walker B motif; other site 265072006912 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 265072006913 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072006914 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072006915 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 265072006916 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 265072006917 dimerization domain [polypeptide binding]; other site 265072006918 dimer interface [polypeptide binding]; other site 265072006919 catalytic residues [active] 265072006920 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 265072006921 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 265072006922 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 265072006923 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 265072006924 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 265072006925 proline aminopeptidase P II; Provisional; Region: PRK10879 265072006926 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 265072006927 active site 265072006928 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 265072006929 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 265072006930 Substrate binding site; other site 265072006931 metal-binding site 265072006932 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 265072006933 Phosphotransferase enzyme family; Region: APH; pfam01636 265072006934 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 265072006935 OstA-like protein; Region: OstA; cl00844 265072006936 Organic solvent tolerance protein; Region: OstA_C; pfam04453 265072006937 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 265072006938 SurA N-terminal domain; Region: SurA_N; pfam09312 265072006939 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 265072006940 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 265072006941 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 265072006942 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 265072006943 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 265072006944 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 265072006945 adenylate kinase; Reviewed; Region: adk; PRK00279 265072006946 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 265072006947 AMP-binding site [chemical binding]; other site 265072006948 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 265072006949 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 265072006950 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 265072006951 dimerization interface [polypeptide binding]; other site 265072006952 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 265072006953 dimer interface [polypeptide binding]; other site 265072006954 putative CheW interface [polypeptide binding]; other site 265072006955 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 265072006956 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 265072006957 HIGH motif; other site 265072006958 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 265072006959 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 265072006960 active site 265072006961 KMSKS motif; other site 265072006962 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 265072006963 tRNA binding surface [nucleotide binding]; other site 265072006964 Lipopolysaccharide-assembly; Region: LptE; cl01125 265072006965 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 265072006966 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 265072006967 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 265072006968 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 265072006969 putative catalytic cysteine [active] 265072006970 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 265072006971 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 265072006972 active site 265072006973 (T/H)XGH motif; other site 265072006974 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 265072006975 AAA domain; Region: AAA_26; pfam13500 265072006976 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 265072006977 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 265072006978 S-adenosylmethionine binding site [chemical binding]; other site 265072006979 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 265072006980 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 265072006981 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 265072006982 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072006983 catalytic residue [active] 265072006984 biotin synthase; Region: bioB; TIGR00433 265072006985 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 265072006986 FeS/SAM binding site; other site 265072006987 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 265072006988 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 265072006989 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 265072006990 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 265072006991 cyanate hydratase; Validated; Region: PRK02866 265072006992 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 265072006993 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 265072006994 oligomer interface [polypeptide binding]; other site 265072006995 active site 265072006996 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 265072006997 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 265072006998 Walker A/P-loop; other site 265072006999 ATP binding site [chemical binding]; other site 265072007000 Q-loop/lid; other site 265072007001 ABC transporter signature motif; other site 265072007002 Walker B; other site 265072007003 D-loop; other site 265072007004 H-loop/switch region; other site 265072007005 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 265072007006 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 265072007007 dimer interface [polypeptide binding]; other site 265072007008 conserved gate region; other site 265072007009 putative PBP binding loops; other site 265072007010 ABC-ATPase subunit interface; other site 265072007011 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 265072007012 NMT1-like family; Region: NMT1_2; pfam13379 265072007013 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 265072007014 Rubredoxin; Region: Rubredoxin; pfam00301 265072007015 iron binding site [ion binding]; other site 265072007016 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 265072007017 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072007018 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 265072007019 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 265072007020 active site 265072007021 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 265072007022 OsmC-like protein; Region: OsmC; pfam02566 265072007023 Nif-specific regulatory protein; Region: nifA; TIGR01817 265072007024 GAF domain; Region: GAF; pfam01590 265072007025 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 265072007026 Walker B motif; other site 265072007027 arginine finger; other site 265072007028 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072007029 Integrase core domain; Region: rve; pfam00665 265072007030 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 265072007031 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072007032 active site 265072007033 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 265072007034 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 265072007035 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 265072007036 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 265072007037 Bacterial SH3 domain; Region: SH3_4; pfam06347 265072007038 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 265072007039 preprotein translocase subunit SecB; Validated; Region: PRK05751 265072007040 SecA binding site; other site 265072007041 Preprotein binding site; other site 265072007042 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 265072007043 GSH binding site [chemical binding]; other site 265072007044 catalytic residues [active] 265072007045 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 265072007046 active site residue [active] 265072007047 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 265072007048 phosphoglyceromutase; Provisional; Region: PRK05434 265072007049 AmiB activator; Provisional; Region: PRK11637 265072007050 Peptidase family M23; Region: Peptidase_M23; pfam01551 265072007051 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 265072007052 Protein of unknown function (DUF461); Region: DUF461; pfam04314 265072007053 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 265072007054 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 265072007055 N-terminal plug; other site 265072007056 ligand-binding site [chemical binding]; other site 265072007057 PEP-CTERM motif; Region: VPEP; pfam07589 265072007058 Cytochrome c; Region: Cytochrom_C; cl11414 265072007059 lipoprotein LpqB; Provisional; Region: PRK13616 265072007060 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 265072007061 Clp amino terminal domain; Region: Clp_N; pfam02861 265072007062 Clp amino terminal domain; Region: Clp_N; pfam02861 265072007063 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 265072007064 Walker A motif; other site 265072007065 ATP binding site [chemical binding]; other site 265072007066 Walker B motif; other site 265072007067 arginine finger; other site 265072007068 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 265072007069 Walker A motif; other site 265072007070 ATP binding site [chemical binding]; other site 265072007071 Walker B motif; other site 265072007072 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 265072007073 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072007074 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072007075 ATP binding site [chemical binding]; other site 265072007076 Mg2+ binding site [ion binding]; other site 265072007077 G-X-G motif; other site 265072007078 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 265072007079 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072007080 active site 265072007081 phosphorylation site [posttranslational modification] 265072007082 intermolecular recognition site; other site 265072007083 dimerization interface [polypeptide binding]; other site 265072007084 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072007085 phosphoenolpyruvate synthase; Validated; Region: PRK06464 265072007086 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 265072007087 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 265072007088 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 265072007089 PEP synthetase regulatory protein; Provisional; Region: PRK05339 265072007090 Predicted membrane protein [Function unknown]; Region: COG2259 265072007091 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 265072007092 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 265072007093 putative NAD(P) binding site [chemical binding]; other site 265072007094 putative substrate binding site [chemical binding]; other site 265072007095 catalytic Zn binding site [ion binding]; other site 265072007096 structural Zn binding site [ion binding]; other site 265072007097 dimer interface [polypeptide binding]; other site 265072007098 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 265072007099 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 265072007100 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 265072007101 active site 265072007102 HIGH motif; other site 265072007103 nucleotide binding site [chemical binding]; other site 265072007104 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 265072007105 active site 265072007106 KMSKS motif; other site 265072007107 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 265072007108 tRNA binding surface [nucleotide binding]; other site 265072007109 anticodon binding site; other site 265072007110 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 265072007111 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 265072007112 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 265072007113 active site 265072007114 Riboflavin kinase; Region: Flavokinase; smart00904 265072007115 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 265072007116 MviN-like protein; Region: MVIN; pfam03023 265072007117 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 265072007118 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 265072007119 ATP-grasp domain; Region: ATP-grasp; pfam02222 265072007120 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 265072007121 gamma-glutamyl kinase; Provisional; Region: PRK05429 265072007122 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 265072007123 nucleotide binding site [chemical binding]; other site 265072007124 homotetrameric interface [polypeptide binding]; other site 265072007125 putative phosphate binding site [ion binding]; other site 265072007126 putative allosteric binding site; other site 265072007127 PUA domain; Region: PUA; pfam01472 265072007128 GTPase CgtA; Reviewed; Region: obgE; PRK12299 265072007129 GTP1/OBG; Region: GTP1_OBG; pfam01018 265072007130 Obg GTPase; Region: Obg; cd01898 265072007131 G1 box; other site 265072007132 GTP/Mg2+ binding site [chemical binding]; other site 265072007133 Switch I region; other site 265072007134 G2 box; other site 265072007135 G3 box; other site 265072007136 Switch II region; other site 265072007137 G4 box; other site 265072007138 G5 box; other site 265072007139 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 265072007140 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 265072007141 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 265072007142 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 265072007143 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 265072007144 substrate binding pocket [chemical binding]; other site 265072007145 chain length determination region; other site 265072007146 substrate-Mg2+ binding site; other site 265072007147 catalytic residues [active] 265072007148 aspartate-rich region 1; other site 265072007149 active site lid residues [active] 265072007150 aspartate-rich region 2; other site 265072007151 Outer membrane efflux protein; Region: OEP; pfam02321 265072007152 Outer membrane efflux protein; Region: OEP; pfam02321 265072007153 HlyD family secretion protein; Region: HlyD; pfam00529 265072007154 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072007155 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072007156 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072007157 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072007158 Walker A/P-loop; other site 265072007159 ATP binding site [chemical binding]; other site 265072007160 Q-loop/lid; other site 265072007161 ABC transporter signature motif; other site 265072007162 Walker B; other site 265072007163 D-loop; other site 265072007164 H-loop/switch region; other site 265072007165 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 265072007166 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 265072007167 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 265072007168 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 265072007169 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 265072007170 CoA-binding site [chemical binding]; other site 265072007171 ATP-binding [chemical binding]; other site 265072007172 hypothetical protein; Provisional; Region: PRK05287 265072007173 Domain of unknown function (DUF329); Region: DUF329; pfam03884 265072007174 hypothetical protein; Provisional; Region: PRK08999 265072007175 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 265072007176 active site 265072007177 8-oxo-dGMP binding site [chemical binding]; other site 265072007178 nudix motif; other site 265072007179 metal binding site [ion binding]; metal-binding site 265072007180 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 265072007181 thiamine phosphate binding site [chemical binding]; other site 265072007182 active site 265072007183 pyrophosphate binding site [ion binding]; other site 265072007184 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 265072007185 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 265072007186 Walker A motif; other site 265072007187 ATP binding site [chemical binding]; other site 265072007188 Walker B motif; other site 265072007189 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 265072007190 heterotetramer interface [polypeptide binding]; other site 265072007191 active site pocket [active] 265072007192 cleavage site 265072007193 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 265072007194 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 265072007195 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 265072007196 SEC-C motif; Region: SEC-C; pfam02810 265072007197 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 265072007198 Peptidase family M23; Region: Peptidase_M23; pfam01551 265072007199 Protein of unknown function (DUF721); Region: DUF721; pfam05258 265072007200 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 265072007201 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 265072007202 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 265072007203 Walker A/P-loop; other site 265072007204 ATP binding site [chemical binding]; other site 265072007205 Q-loop/lid; other site 265072007206 ABC transporter signature motif; other site 265072007207 Walker B; other site 265072007208 D-loop; other site 265072007209 H-loop/switch region; other site 265072007210 ABC-2 type transporter; Region: ABC2_membrane; cl17235 265072007211 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 265072007212 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 265072007213 dimer interface [polypeptide binding]; other site 265072007214 substrate binding site [chemical binding]; other site 265072007215 metal binding sites [ion binding]; metal-binding site 265072007216 Uncharacterized conserved protein [Function unknown]; Region: COG3339 265072007217 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 265072007218 ATP binding site [chemical binding]; other site 265072007219 active site 265072007220 substrate binding site [chemical binding]; other site 265072007221 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 265072007222 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 265072007223 intersubunit interface [polypeptide binding]; other site 265072007224 active site 265072007225 zinc binding site [ion binding]; other site 265072007226 Na+ binding site [ion binding]; other site 265072007227 pyruvate kinase; Provisional; Region: PRK05826 265072007228 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 265072007229 domain interfaces; other site 265072007230 active site 265072007231 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 265072007232 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 265072007233 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 265072007234 Phosphoglycerate kinase; Region: PGK; pfam00162 265072007235 substrate binding site [chemical binding]; other site 265072007236 hinge regions; other site 265072007237 ADP binding site [chemical binding]; other site 265072007238 catalytic site [active] 265072007239 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 265072007240 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 265072007241 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 265072007242 transketolase; Reviewed; Region: PRK12753 265072007243 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 265072007244 TPP-binding site [chemical binding]; other site 265072007245 dimer interface [polypeptide binding]; other site 265072007246 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 265072007247 PYR/PP interface [polypeptide binding]; other site 265072007248 dimer interface [polypeptide binding]; other site 265072007249 TPP binding site [chemical binding]; other site 265072007250 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 265072007251 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 265072007252 putative catalytic residue [active] 265072007253 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 265072007254 RNA methyltransferase, RsmE family; Region: TIGR00046 265072007255 N-acetylglutamate synthase; Validated; Region: PRK05279 265072007256 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 265072007257 putative feedback inhibition sensing region; other site 265072007258 putative nucleotide binding site [chemical binding]; other site 265072007259 putative substrate binding site [chemical binding]; other site 265072007260 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 265072007261 Coenzyme A binding pocket [chemical binding]; other site 265072007262 PEP-CTERM motif; Region: VPEP; pfam07589 265072007263 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 265072007264 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 265072007265 Potassium binding sites [ion binding]; other site 265072007266 Cesium cation binding sites [ion binding]; other site 265072007267 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 265072007268 homohexameric interface [polypeptide binding]; other site 265072007269 nucleotide binding site [chemical binding]; other site 265072007270 N-acetyl-L-glutamate binding site [chemical binding]; other site 265072007271 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 265072007272 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 265072007273 motif II; other site 265072007274 division inhibitor protein; Provisional; Region: slmA; PRK09480 265072007275 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072007276 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 265072007277 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 265072007278 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 265072007279 active site 265072007280 NTP binding site [chemical binding]; other site 265072007281 metal binding triad [ion binding]; metal-binding site 265072007282 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 265072007283 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 265072007284 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 265072007285 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 265072007286 putative NAD(P) binding site [chemical binding]; other site 265072007287 active site 265072007288 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 265072007289 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 265072007290 N-acetyl-D-glucosamine binding site [chemical binding]; other site 265072007291 catalytic residue [active] 265072007292 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 265072007293 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 265072007294 cell division protein FtsZ; Validated; Region: PRK09330 265072007295 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 265072007296 nucleotide binding site [chemical binding]; other site 265072007297 SulA interaction site; other site 265072007298 cell division protein FtsA; Region: ftsA; TIGR01174 265072007299 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 265072007300 nucleotide binding site [chemical binding]; other site 265072007301 Cell division protein FtsA; Region: FtsA; pfam14450 265072007302 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 265072007303 Cell division protein FtsQ; Region: FtsQ; pfam03799 265072007304 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 265072007305 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 265072007306 ATP-grasp domain; Region: ATP-grasp_4; cl17255 265072007307 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 265072007308 FAD binding domain; Region: FAD_binding_4; pfam01565 265072007309 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 265072007310 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 265072007311 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 265072007312 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 265072007313 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 265072007314 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 265072007315 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 265072007316 active site 265072007317 homodimer interface [polypeptide binding]; other site 265072007318 cell division protein FtsW; Region: ftsW; TIGR02614 265072007319 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 265072007320 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 265072007321 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 265072007322 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 265072007323 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 265072007324 Mg++ binding site [ion binding]; other site 265072007325 putative catalytic motif [active] 265072007326 putative substrate binding site [chemical binding]; other site 265072007327 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 265072007328 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 265072007329 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 265072007330 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 265072007331 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 265072007332 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 265072007333 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 265072007334 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 265072007335 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 265072007336 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 265072007337 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 265072007338 Cell division protein FtsL; Region: FtsL; pfam04999 265072007339 MraW methylase family; Region: Methyltransf_5; cl17771 265072007340 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 265072007341 cell division protein MraZ; Reviewed; Region: PRK00326 265072007342 MraZ protein; Region: MraZ; pfam02381 265072007343 MraZ protein; Region: MraZ; pfam02381 265072007344 PEP-CTERM motif; Region: VPEP; pfam07589 265072007345 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 265072007346 active site 265072007347 substrate binding pocket [chemical binding]; other site 265072007348 dimer interface [polypeptide binding]; other site 265072007349 Predicted methyltransferases [General function prediction only]; Region: COG0313 265072007350 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 265072007351 putative SAM binding site [chemical binding]; other site 265072007352 putative homodimer interface [polypeptide binding]; other site 265072007353 LppC putative lipoprotein; Region: LppC; pfam04348 265072007354 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 265072007355 putative ligand binding site [chemical binding]; other site 265072007356 hypothetical protein; Reviewed; Region: PRK12497 265072007357 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 265072007358 dimer interface [polypeptide binding]; other site 265072007359 active site 265072007360 BON domain; Region: BON; cl02771 265072007361 bacterial OsmY and nodulation domain; Region: BON; smart00749 265072007362 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 265072007363 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 265072007364 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 265072007365 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072007366 catalytic residues [active] 265072007367 transcription termination factor Rho; Provisional; Region: rho; PRK09376 265072007368 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 265072007369 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 265072007370 RNA binding site [nucleotide binding]; other site 265072007371 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 265072007372 multimer interface [polypeptide binding]; other site 265072007373 Walker A motif; other site 265072007374 ATP binding site [chemical binding]; other site 265072007375 Walker B motif; other site 265072007376 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 265072007377 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 265072007378 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 265072007379 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 265072007380 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 265072007381 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 265072007382 FeS/SAM binding site; other site 265072007383 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 265072007384 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 265072007385 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 265072007386 GTP binding site; other site 265072007387 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 265072007388 Walker A motif; other site 265072007389 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 265072007390 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 265072007391 dimer interface [polypeptide binding]; other site 265072007392 putative functional site; other site 265072007393 putative MPT binding site; other site 265072007394 LGFP repeat; Region: LGFP; pfam08310 265072007395 LGFP repeat; Region: LGFP; pfam08310 265072007396 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 265072007397 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 265072007398 DNA-binding site [nucleotide binding]; DNA binding site 265072007399 UTRA domain; Region: UTRA; pfam07702 265072007400 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 265072007401 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 265072007402 substrate binding site [chemical binding]; other site 265072007403 ATP binding site [chemical binding]; other site 265072007404 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 265072007405 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 265072007406 N-terminal plug; other site 265072007407 ligand-binding site [chemical binding]; other site 265072007408 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 265072007409 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 265072007410 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072007411 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072007412 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072007413 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072007414 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 265072007415 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 265072007416 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 265072007417 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 265072007418 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 265072007419 dimerization interface [polypeptide binding]; other site 265072007420 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 265072007421 dimer interface [polypeptide binding]; other site 265072007422 phosphorylation site [posttranslational modification] 265072007423 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072007424 ATP binding site [chemical binding]; other site 265072007425 G-X-G motif; other site 265072007426 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 265072007427 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 265072007428 catalytic triad [active] 265072007429 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 265072007430 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 265072007431 putative active site [active] 265072007432 PhoH-like protein; Region: PhoH; pfam02562 265072007433 lysophospholipid transporter LplT; Provisional; Region: PRK11195 265072007434 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 265072007435 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 265072007436 Cytochrome c; Region: Cytochrom_C; cl11414 265072007437 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein; Region: ABC_peri_MoxJ_2; TIGR03871 265072007438 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 265072007439 substrate binding pocket [chemical binding]; other site 265072007440 membrane-bound complex binding site; other site 265072007441 hinge residues; other site 265072007442 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 265072007443 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 265072007444 Trp docking motif [polypeptide binding]; other site 265072007445 dimer interface [polypeptide binding]; other site 265072007446 active site 265072007447 small subunit binding site [polypeptide binding]; other site 265072007448 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 265072007449 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 265072007450 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 265072007451 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 265072007452 ligand binding site [chemical binding]; other site 265072007453 flexible hinge region; other site 265072007454 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 265072007455 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 265072007456 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 265072007457 N-terminal plug; other site 265072007458 ligand-binding site [chemical binding]; other site 265072007459 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 265072007460 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 265072007461 active site residue [active] 265072007462 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 265072007463 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072007464 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 265072007465 putative dimerization interface [polypeptide binding]; other site 265072007466 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 265072007467 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 265072007468 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 265072007469 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 265072007470 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072007471 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 265072007472 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 265072007473 DNA binding residues [nucleotide binding] 265072007474 DNA primase; Validated; Region: dnaG; PRK05667 265072007475 CHC2 zinc finger; Region: zf-CHC2; pfam01807 265072007476 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 265072007477 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 265072007478 active site 265072007479 metal binding site [ion binding]; metal-binding site 265072007480 interdomain interaction site; other site 265072007481 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 265072007482 Yqey-like protein; Region: YqeY; pfam09424 265072007483 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 265072007484 UGMP family protein; Validated; Region: PRK09604 265072007485 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 265072007486 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 265072007487 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 265072007488 homooctamer interface [polypeptide binding]; other site 265072007489 active site 265072007490 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 265072007491 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 265072007492 active site 265072007493 Int/Topo IB signature motif; other site 265072007494 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 265072007495 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 265072007496 DNA binding site [nucleotide binding] 265072007497 active site 265072007498 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 265072007499 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 265072007500 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 265072007501 RimM N-terminal domain; Region: RimM; pfam01782 265072007502 PRC-barrel domain; Region: PRC; pfam05239 265072007503 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 265072007504 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 265072007505 Ligand Binding Site [chemical binding]; other site 265072007506 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 265072007507 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 265072007508 FeS/SAM binding site; other site 265072007509 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 265072007510 TPR motif; other site 265072007511 binding surface 265072007512 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 265072007513 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 265072007514 ligand binding site [chemical binding]; other site 265072007515 translocation protein TolB; Provisional; Region: tolB; PRK02889 265072007516 TolB amino-terminal domain; Region: TolB_N; pfam04052 265072007517 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 265072007518 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 265072007519 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 265072007520 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 265072007521 TolA protein; Region: tolA_full; TIGR02794 265072007522 TonB C terminal; Region: TonB_2; pfam13103 265072007523 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072007524 TolR protein; Region: tolR; TIGR02801 265072007525 TolQ protein; Region: tolQ; TIGR02796 265072007526 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 265072007527 active site 265072007528 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 265072007529 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 265072007530 Walker A motif; other site 265072007531 ATP binding site [chemical binding]; other site 265072007532 Walker B motif; other site 265072007533 arginine finger; other site 265072007534 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 265072007535 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 265072007536 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 265072007537 active site 265072007538 catalytic tetrad [active] 265072007539 Transcriptional regulators [Transcription]; Region: PurR; COG1609 265072007540 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 265072007541 DNA binding site [nucleotide binding] 265072007542 domain linker motif; other site 265072007543 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 265072007544 putative dimerization interface [polypeptide binding]; other site 265072007545 putative ligand binding site [chemical binding]; other site 265072007546 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 265072007547 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 265072007548 Walker A/P-loop; other site 265072007549 ATP binding site [chemical binding]; other site 265072007550 Q-loop/lid; other site 265072007551 ABC transporter signature motif; other site 265072007552 Walker B; other site 265072007553 D-loop; other site 265072007554 H-loop/switch region; other site 265072007555 TOBE domain; Region: TOBE_2; pfam08402 265072007556 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 265072007557 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 265072007558 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 265072007559 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 265072007560 putative PBP binding loops; other site 265072007561 dimer interface [polypeptide binding]; other site 265072007562 ABC-ATPase subunit interface; other site 265072007563 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 265072007564 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 265072007565 dimer interface [polypeptide binding]; other site 265072007566 conserved gate region; other site 265072007567 putative PBP binding loops; other site 265072007568 ABC-ATPase subunit interface; other site 265072007569 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 265072007570 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 265072007571 N-terminal plug; other site 265072007572 ligand-binding site [chemical binding]; other site 265072007573 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 265072007574 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 265072007575 active site 265072007576 non-prolyl cis peptide bond; other site 265072007577 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 265072007578 RuvA N terminal domain; Region: RuvA_N; pfam01330 265072007579 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 265072007580 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 265072007581 active site 265072007582 putative DNA-binding cleft [nucleotide binding]; other site 265072007583 dimer interface [polypeptide binding]; other site 265072007584 hypothetical protein; Validated; Region: PRK00110 265072007585 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 265072007586 EamA-like transporter family; Region: EamA; pfam00892 265072007587 EamA-like transporter family; Region: EamA; pfam00892 265072007588 SnoaL-like domain; Region: SnoaL_3; pfam13474 265072007589 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; cd00531 265072007590 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 265072007591 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 265072007592 MarR family; Region: MarR_2; cl17246 265072007593 FOG: CBS domain [General function prediction only]; Region: COG0517 265072007594 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 265072007595 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 265072007596 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 265072007597 TrkA-N domain; Region: TrkA_N; pfam02254 265072007598 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 265072007599 Uncharacterized conserved protein [Function unknown]; Region: COG0432 265072007600 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 265072007601 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 265072007602 Permease; Region: Permease; pfam02405 265072007603 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 265072007604 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072007605 Walker A/P-loop; other site 265072007606 ATP binding site [chemical binding]; other site 265072007607 Q-loop/lid; other site 265072007608 ABC transporter signature motif; other site 265072007609 Walker B; other site 265072007610 D-loop; other site 265072007611 H-loop/switch region; other site 265072007612 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 265072007613 mce related protein; Region: MCE; pfam02470 265072007614 Protein of unknown function (DUF330); Region: DUF330; cl01135 265072007615 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 265072007616 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 265072007617 Helix-turn-helix domain; Region: HTH_18; pfam12833 265072007618 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072007619 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072007620 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 265072007621 E3 interaction surface; other site 265072007622 lipoyl attachment site [posttranslational modification]; other site 265072007623 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072007624 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 265072007625 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 265072007626 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 265072007627 hydroperoxidase II; Provisional; Region: katE; PRK11249 265072007628 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 265072007629 tetramer interface [polypeptide binding]; other site 265072007630 heme binding pocket [chemical binding]; other site 265072007631 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 265072007632 domain interactions; other site 265072007633 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 265072007634 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 265072007635 PLD-like domain; Region: PLDc_2; pfam13091 265072007636 putative active site [active] 265072007637 catalytic site [active] 265072007638 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 265072007639 PLD-like domain; Region: PLDc_2; pfam13091 265072007640 putative active site [active] 265072007641 catalytic site [active] 265072007642 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 265072007643 putative catalytic site [active] 265072007644 putative metal binding site [ion binding]; other site 265072007645 putative phosphate binding site [ion binding]; other site 265072007646 quinolinate synthetase; Provisional; Region: PRK09375 265072007647 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 265072007648 nudix motif; other site 265072007649 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072007650 active site 265072007651 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 265072007652 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 265072007653 dimer interface [polypeptide binding]; other site 265072007654 anticodon binding site; other site 265072007655 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 265072007656 homodimer interface [polypeptide binding]; other site 265072007657 motif 1; other site 265072007658 active site 265072007659 motif 2; other site 265072007660 GAD domain; Region: GAD; pfam02938 265072007661 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 265072007662 motif 3; other site 265072007663 Uncharacterized conserved protein [Function unknown]; Region: COG2928 265072007664 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 265072007665 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 265072007666 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 265072007667 N-terminal plug; other site 265072007668 ligand-binding site [chemical binding]; other site 265072007669 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 265072007670 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_3; cd08490 265072007671 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 265072007672 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 265072007673 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 265072007674 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 265072007675 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072007676 Walker A/P-loop; other site 265072007677 ATP binding site [chemical binding]; other site 265072007678 Q-loop/lid; other site 265072007679 ABC transporter signature motif; other site 265072007680 Walker B; other site 265072007681 D-loop; other site 265072007682 H-loop/switch region; other site 265072007683 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 265072007684 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 265072007685 Walker A/P-loop; other site 265072007686 ATP binding site [chemical binding]; other site 265072007687 Q-loop/lid; other site 265072007688 ABC transporter signature motif; other site 265072007689 Walker B; other site 265072007690 D-loop; other site 265072007691 H-loop/switch region; other site 265072007692 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 265072007693 ligand binding site [chemical binding]; other site 265072007694 Domain of unknown function DUF11; Region: DUF11; pfam01345 265072007695 Domain of unknown function DUF11; Region: DUF11; pfam01345 265072007696 Cna protein B-type domain; Region: Cna_B; pfam05738 265072007697 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 265072007698 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 265072007699 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072007700 active site 265072007701 phosphorylation site [posttranslational modification] 265072007702 intermolecular recognition site; other site 265072007703 dimerization interface [polypeptide binding]; other site 265072007704 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 265072007705 DNA binding site [nucleotide binding] 265072007706 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 265072007707 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 265072007708 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072007709 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 265072007710 dimer interface [polypeptide binding]; other site 265072007711 phosphorylation site [posttranslational modification] 265072007712 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072007713 ATP binding site [chemical binding]; other site 265072007714 Mg2+ binding site [ion binding]; other site 265072007715 G-X-G motif; other site 265072007716 PEP-CTERM motif; Region: VPEP; pfam07589 265072007717 PEP-CTERM motif; Region: VPEP; pfam07589 265072007718 PEP-CTERM motif; Region: VPEP; pfam07589 265072007719 TonB C terminal; Region: TonB_2; pfam13103 265072007720 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 265072007721 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072007722 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 265072007723 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 265072007724 Domain of unknown function (DUF2341); Region: DUF2341; pfam10102 265072007725 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 265072007726 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 265072007727 haemagglutination activity domain; Region: Haemagg_act; smart00912 265072007728 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 265072007729 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 265072007730 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 265072007731 Surface antigen; Region: Bac_surface_Ag; pfam01103 265072007732 transcriptional regulator EpsA; Region: EpsA; TIGR03020 265072007733 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 265072007734 DNA binding residues [nucleotide binding] 265072007735 dimerization interface [polypeptide binding]; other site 265072007736 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 265072007737 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 265072007738 N-acetyl-D-glucosamine binding site [chemical binding]; other site 265072007739 catalytic residue [active] 265072007740 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 265072007741 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 265072007742 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 265072007743 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 265072007744 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 265072007745 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 265072007746 Secretin and TonB N terminus short domain; Region: STN; smart00965 265072007747 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 265072007748 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072007749 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 265072007750 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 265072007751 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 265072007752 Walker A motif; other site 265072007753 ATP binding site [chemical binding]; other site 265072007754 Walker B motif; other site 265072007755 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 265072007756 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072007757 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 265072007758 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 265072007759 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 265072007760 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 265072007761 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072007762 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072007763 metal binding site [ion binding]; metal-binding site 265072007764 active site 265072007765 I-site; other site 265072007766 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 265072007767 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 265072007768 active site 265072007769 PEP-CTERM motif; Region: VPEP; pfam07589 265072007770 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 265072007771 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 265072007772 dimer interface [polypeptide binding]; other site 265072007773 ssDNA binding site [nucleotide binding]; other site 265072007774 tetramer (dimer of dimers) interface [polypeptide binding]; other site 265072007775 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 265072007776 Major Facilitator Superfamily; Region: MFS_1; pfam07690 265072007777 putative substrate translocation pore; other site 265072007778 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 265072007779 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 265072007780 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 265072007781 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 265072007782 Lamin Tail Domain; Region: LTD; pfam00932 265072007783 PEP-CTERM motif; Region: VPEP; pfam07589 265072007784 SdiA-regulated; Region: SdiA-regulated; pfam06977 265072007785 SdiA-regulated; Region: SdiA-regulated; cd09971 265072007786 putative active site [active] 265072007787 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 265072007788 Coenzyme A binding pocket [chemical binding]; other site 265072007789 DoxX; Region: DoxX; cl17842 265072007790 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 265072007791 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 265072007792 CobD/Cbib protein; Region: CobD_Cbib; cl00561 265072007793 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 265072007794 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 265072007795 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 265072007796 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 265072007797 putative active site [active] 265072007798 putative substrate binding site [chemical binding]; other site 265072007799 putative cosubstrate binding site; other site 265072007800 catalytic site [active] 265072007801 Outer membrane efflux protein; Region: OEP; pfam02321 265072007802 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 265072007803 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 265072007804 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072007805 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072007806 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 265072007807 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 265072007808 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 265072007809 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 265072007810 Walker A/P-loop; other site 265072007811 ATP binding site [chemical binding]; other site 265072007812 Q-loop/lid; other site 265072007813 ABC transporter signature motif; other site 265072007814 Walker B; other site 265072007815 D-loop; other site 265072007816 H-loop/switch region; other site 265072007817 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 265072007818 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 265072007819 Chromate transporter; Region: Chromate_transp; pfam02417 265072007820 diaminopimelate decarboxylase; Region: lysA; TIGR01048 265072007821 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 265072007822 active site 265072007823 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 265072007824 substrate binding site [chemical binding]; other site 265072007825 catalytic residues [active] 265072007826 dimer interface [polypeptide binding]; other site 265072007827 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 265072007828 Transglycosylase; Region: Transgly; cl17702 265072007829 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 265072007830 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 265072007831 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 265072007832 NAD(P) binding site [chemical binding]; other site 265072007833 shikimate binding site; other site 265072007834 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 265072007835 active site residue [active] 265072007836 glutamine synthetase; Provisional; Region: glnA; PRK09469 265072007837 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 265072007838 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 265072007839 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 265072007840 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 265072007841 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072007842 putative active site [active] 265072007843 heme pocket [chemical binding]; other site 265072007844 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 265072007845 dimer interface [polypeptide binding]; other site 265072007846 phosphorylation site [posttranslational modification] 265072007847 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072007848 ATP binding site [chemical binding]; other site 265072007849 Mg2+ binding site [ion binding]; other site 265072007850 G-X-G motif; other site 265072007851 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 265072007852 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072007853 active site 265072007854 phosphorylation site [posttranslational modification] 265072007855 intermolecular recognition site; other site 265072007856 dimerization interface [polypeptide binding]; other site 265072007857 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 265072007858 Walker A motif; other site 265072007859 ATP binding site [chemical binding]; other site 265072007860 Walker B motif; other site 265072007861 arginine finger; other site 265072007862 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 265072007863 Uncharacterized conserved protein [Function unknown]; Region: COG2361 265072007864 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 265072007865 Gram-negative porin; Region: Porin_4; pfam13609 265072007866 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 265072007867 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072007868 Zn2+ binding site [ion binding]; other site 265072007869 Mg2+ binding site [ion binding]; other site 265072007870 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 265072007871 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 265072007872 active site 265072007873 dimer interface [polypeptide binding]; other site 265072007874 metal binding site [ion binding]; metal-binding site 265072007875 shikimate kinase; Reviewed; Region: aroK; PRK00131 265072007876 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 265072007877 ADP binding site [chemical binding]; other site 265072007878 magnesium binding site [ion binding]; other site 265072007879 putative shikimate binding site; other site 265072007880 AMIN domain; Region: AMIN; pfam11741 265072007881 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 265072007882 Secretin and TonB N terminus short domain; Region: STN; smart00965 265072007883 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 265072007884 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 265072007885 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 265072007886 Pilus assembly protein, PilP; Region: PilP; pfam04351 265072007887 Pilus assembly protein, PilO; Region: PilO; pfam04350 265072007888 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 265072007889 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 265072007890 Competence protein A; Region: Competence_A; pfam11104 265072007891 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 265072007892 nucleotide binding site [chemical binding]; other site 265072007893 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 265072007894 Transglycosylase; Region: Transgly; pfam00912 265072007895 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 265072007896 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 265072007897 dimer interface [polypeptide binding]; other site 265072007898 active site 265072007899 aspartate-rich active site metal binding site; other site 265072007900 allosteric magnesium binding site [ion binding]; other site 265072007901 Schiff base residues; other site 265072007902 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 265072007903 active site 265072007904 ribulose/triose binding site [chemical binding]; other site 265072007905 phosphate binding site [ion binding]; other site 265072007906 substrate (anthranilate) binding pocket [chemical binding]; other site 265072007907 product (indole) binding pocket [chemical binding]; other site 265072007908 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 265072007909 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 265072007910 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 265072007911 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 265072007912 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 265072007913 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 265072007914 glutamine binding [chemical binding]; other site 265072007915 catalytic triad [active] 265072007916 PAS domain S-box; Region: sensory_box; TIGR00229 265072007917 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072007918 putative active site [active] 265072007919 heme pocket [chemical binding]; other site 265072007920 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072007921 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072007922 metal binding site [ion binding]; metal-binding site 265072007923 active site 265072007924 I-site; other site 265072007925 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 265072007926 anthranilate synthase component I; Provisional; Region: PRK13565 265072007927 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 265072007928 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 265072007929 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 265072007930 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 265072007931 substrate binding site [chemical binding]; other site 265072007932 hexamer interface [polypeptide binding]; other site 265072007933 metal binding site [ion binding]; metal-binding site 265072007934 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 265072007935 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 265072007936 tRNA; other site 265072007937 putative tRNA binding site [nucleotide binding]; other site 265072007938 putative NADP binding site [chemical binding]; other site 265072007939 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 265072007940 peptide chain release factor 1; Validated; Region: prfA; PRK00591 265072007941 This domain is found in peptide chain release factors; Region: PCRF; smart00937 265072007942 RF-1 domain; Region: RF-1; pfam00472 265072007943 Predicted membrane protein (DUF2127); Region: DUF2127; pfam09900 265072007944 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 265072007945 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 265072007946 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 265072007947 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 265072007948 EamA-like transporter family; Region: EamA; pfam00892 265072007949 EamA-like transporter family; Region: EamA; pfam00892 265072007950 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 265072007951 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 265072007952 trimer interface [polypeptide binding]; other site 265072007953 putative metal binding site [ion binding]; other site 265072007954 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 265072007955 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 265072007956 Methyltransferase domain; Region: Methyltransf_23; pfam13489 265072007957 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 265072007958 S-adenosylmethionine binding site [chemical binding]; other site 265072007959 Uncharacterized conserved protein [Function unknown]; Region: COG2836 265072007960 muropeptide transporter; Reviewed; Region: ampG; PRK11902 265072007961 muropeptide transporter; Validated; Region: ampG; cl17669 265072007962 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 265072007963 putative active site [active] 265072007964 putative catalytic site [active] 265072007965 putative DNA binding site [nucleotide binding]; other site 265072007966 putative phosphate binding site [ion binding]; other site 265072007967 metal binding site A [ion binding]; metal-binding site 265072007968 putative AP binding site [nucleotide binding]; other site 265072007969 putative metal binding site B [ion binding]; other site 265072007970 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 265072007971 active site 265072007972 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 265072007973 putative active site [active] 265072007974 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 265072007975 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 265072007976 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 265072007977 GatB domain; Region: GatB_Yqey; smart00845 265072007978 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 265072007979 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 265072007980 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 265072007981 rod shape-determining protein MreB; Provisional; Region: PRK13927 265072007982 MreB and similar proteins; Region: MreB_like; cd10225 265072007983 nucleotide binding site [chemical binding]; other site 265072007984 Mg binding site [ion binding]; other site 265072007985 putative protofilament interaction site [polypeptide binding]; other site 265072007986 RodZ interaction site [polypeptide binding]; other site 265072007987 rod shape-determining protein MreC; Provisional; Region: PRK13922 265072007988 rod shape-determining protein MreC; Region: MreC; pfam04085 265072007989 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 265072007990 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 265072007991 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 265072007992 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 265072007993 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 265072007994 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 265072007995 rare lipoprotein A; Region: rlpA; TIGR00413 265072007996 Sporulation related domain; Region: SPOR; pfam05036 265072007997 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 265072007998 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 265072007999 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 265072008000 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 265072008001 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 265072008002 homodimer interface [polypeptide binding]; other site 265072008003 substrate-cofactor binding pocket; other site 265072008004 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072008005 catalytic residue [active] 265072008006 Protein of unknown function (DUF493); Region: DUF493; pfam04359 265072008007 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 265072008008 lipoyl synthase; Provisional; Region: PRK05481 265072008009 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 265072008010 FeS/SAM binding site; other site 265072008011 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 265072008012 Domain of unknown function DUF21; Region: DUF21; pfam01595 265072008013 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 265072008014 Transporter associated domain; Region: CorC_HlyC; smart01091 265072008015 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 265072008016 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 265072008017 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 265072008018 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 265072008019 Predicted flavoprotein [General function prediction only]; Region: COG0431 265072008020 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 265072008021 nucleotide binding site/active site [active] 265072008022 HIT family signature motif; other site 265072008023 catalytic residue [active] 265072008024 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 265072008025 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 265072008026 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 265072008027 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 265072008028 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 265072008029 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 265072008030 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 265072008031 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 265072008032 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 265072008033 substrate binding pocket [chemical binding]; other site 265072008034 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 265072008035 B12 binding site [chemical binding]; other site 265072008036 cobalt ligand [ion binding]; other site 265072008037 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 265072008038 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 265072008039 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 265072008040 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 265072008041 Walker A motif; other site 265072008042 ATP binding site [chemical binding]; other site 265072008043 Walker B motif; other site 265072008044 arginine finger; other site 265072008045 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 265072008046 Membrane fusogenic activity; Region: BMFP; pfam04380 265072008047 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; pfam09694 265072008048 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 265072008049 Nitrogen regulatory protein P-II; Region: P-II; smart00938 265072008050 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 265072008051 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 265072008052 Glutamate-cysteine ligase; Region: GshA; pfam08886 265072008053 glutathione synthetase; Provisional; Region: PRK05246 265072008054 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 265072008055 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 265072008056 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 265072008057 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 265072008058 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 265072008059 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 265072008060 Type II transport protein GspH; Region: GspH; pfam12019 265072008061 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 265072008062 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 265072008063 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 265072008064 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 265072008065 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 265072008066 minor groove reading motif; other site 265072008067 helix-hairpin-helix signature motif; other site 265072008068 substrate binding pocket [chemical binding]; other site 265072008069 active site 265072008070 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 265072008071 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 265072008072 DNA binding and oxoG recognition site [nucleotide binding] 265072008073 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 265072008074 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 265072008075 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 265072008076 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 265072008077 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 265072008078 RNA binding surface [nucleotide binding]; other site 265072008079 Pseudouridine synthase, a subgroup of the RsuA family; Region: PSSA_1; cd02555 265072008080 active site 265072008081 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 265072008082 ThiC-associated domain; Region: ThiC-associated; pfam13667 265072008083 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 265072008084 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 265072008085 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 265072008086 S-adenosylmethionine binding site [chemical binding]; other site 265072008087 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 265072008088 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072008089 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072008090 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 265072008091 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 265072008092 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 265072008093 Isochorismatase family; Region: Isochorismatase; pfam00857 265072008094 catalytic triad [active] 265072008095 dimer interface [polypeptide binding]; other site 265072008096 conserved cis-peptide bond; other site 265072008097 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 265072008098 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 265072008099 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 265072008100 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 265072008101 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072008102 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 265072008103 dimer interface [polypeptide binding]; other site 265072008104 phosphorylation site [posttranslational modification] 265072008105 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 265072008106 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008107 active site 265072008108 phosphorylation site [posttranslational modification] 265072008109 intermolecular recognition site; other site 265072008110 dimerization interface [polypeptide binding]; other site 265072008111 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 265072008112 DNA binding site [nucleotide binding] 265072008113 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 265072008114 Autotransporter beta-domain; Region: Autotransporter; smart00869 265072008115 Isochorismatase family; Region: Isochorismatase; pfam00857 265072008116 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 265072008117 catalytic triad [active] 265072008118 conserved cis-peptide bond; other site 265072008119 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 265072008120 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 265072008121 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 265072008122 active site 265072008123 dimer interface [polypeptide binding]; other site 265072008124 effector binding site; other site 265072008125 TSCPD domain; Region: TSCPD; pfam12637 265072008126 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 265072008127 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072008128 Protein export membrane protein; Region: SecD_SecF; cl14618 265072008129 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 265072008130 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 265072008131 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 265072008132 Walker A motif; other site 265072008133 ATP binding site [chemical binding]; other site 265072008134 Walker B motif; other site 265072008135 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 265072008136 Integrase core domain; Region: rve; pfam00665 265072008137 Heavy-metal-associated domain; Region: HMA; pfam00403 265072008138 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 265072008139 metal-binding site [ion binding] 265072008140 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 265072008141 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 265072008142 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 265072008143 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 265072008144 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072008145 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 265072008146 hypothetical protein; Provisional; Region: PRK02237 265072008147 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 265072008148 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 265072008149 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072008150 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072008151 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 265072008152 Transcriptional regulator [Transcription]; Region: IclR; COG1414 265072008153 Bacterial transcriptional regulator; Region: IclR; pfam01614 265072008154 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 265072008155 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 265072008156 dimer interface [polypeptide binding]; other site 265072008157 conserved gate region; other site 265072008158 putative PBP binding loops; other site 265072008159 ABC-ATPase subunit interface; other site 265072008160 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 265072008161 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 265072008162 Walker A/P-loop; other site 265072008163 ATP binding site [chemical binding]; other site 265072008164 Q-loop/lid; other site 265072008165 ABC transporter signature motif; other site 265072008166 Walker B; other site 265072008167 D-loop; other site 265072008168 H-loop/switch region; other site 265072008169 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 265072008170 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 265072008171 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 265072008172 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 265072008173 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 265072008174 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 265072008175 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 265072008176 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072008177 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072008178 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 265072008179 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 265072008180 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072008181 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 265072008182 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072008183 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 265072008184 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 265072008185 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072008186 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 265072008187 putative dimerization interface [polypeptide binding]; other site 265072008188 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 265072008189 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 265072008190 THF binding site; other site 265072008191 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 265072008192 substrate binding site [chemical binding]; other site 265072008193 THF binding site; other site 265072008194 zinc-binding site [ion binding]; other site 265072008195 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 265072008196 putative heme binding pocket [chemical binding]; other site 265072008197 Isochorismatase family; Region: Isochorismatase; pfam00857 265072008198 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 265072008199 catalytic triad [active] 265072008200 dimer interface [polypeptide binding]; other site 265072008201 conserved cis-peptide bond; other site 265072008202 Pirin-related protein [General function prediction only]; Region: COG1741 265072008203 Pirin; Region: Pirin; pfam02678 265072008204 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 265072008205 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072008206 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072008207 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 265072008208 putative effector binding pocket; other site 265072008209 dimerization interface [polypeptide binding]; other site 265072008210 EamA-like transporter family; Region: EamA; pfam00892 265072008211 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 265072008212 EamA-like transporter family; Region: EamA; pfam00892 265072008213 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 265072008214 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 265072008215 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 265072008216 Cytochrome c; Region: Cytochrom_C; cl11414 265072008217 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 265072008218 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 265072008219 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 265072008220 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 265072008221 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 265072008222 MarR family; Region: MarR_2; cl17246 265072008223 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 265072008224 Fusaric acid resistance protein family; Region: FUSC; pfam04632 265072008225 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 265072008226 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 265072008227 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 265072008228 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 265072008229 HlyD family secretion protein; Region: HlyD_3; pfam13437 265072008230 Protein of unknwon function (DUF3008); Region: DUF3008; pfam11450 265072008231 CHASE3 domain; Region: CHASE3; pfam05227 265072008232 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 265072008233 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 265072008234 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 265072008235 dimer interface [polypeptide binding]; other site 265072008236 phosphorylation site [posttranslational modification] 265072008237 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072008238 ATP binding site [chemical binding]; other site 265072008239 Mg2+ binding site [ion binding]; other site 265072008240 G-X-G motif; other site 265072008241 Response regulator receiver domain; Region: Response_reg; pfam00072 265072008242 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008243 active site 265072008244 phosphorylation site [posttranslational modification] 265072008245 intermolecular recognition site; other site 265072008246 dimerization interface [polypeptide binding]; other site 265072008247 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 265072008248 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008249 active site 265072008250 phosphorylation site [posttranslational modification] 265072008251 intermolecular recognition site; other site 265072008252 Response regulator receiver domain; Region: Response_reg; pfam00072 265072008253 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008254 active site 265072008255 phosphorylation site [posttranslational modification] 265072008256 intermolecular recognition site; other site 265072008257 dimerization interface [polypeptide binding]; other site 265072008258 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 265072008259 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 265072008260 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 265072008261 CheB methylesterase; Region: CheB_methylest; pfam01339 265072008262 Response regulator receiver domain; Region: Response_reg; pfam00072 265072008263 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008264 active site 265072008265 phosphorylation site [posttranslational modification] 265072008266 intermolecular recognition site; other site 265072008267 dimerization interface [polypeptide binding]; other site 265072008268 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072008269 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 265072008270 dimer interface [polypeptide binding]; other site 265072008271 phosphorylation site [posttranslational modification] 265072008272 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072008273 ATP binding site [chemical binding]; other site 265072008274 Mg2+ binding site [ion binding]; other site 265072008275 G-X-G motif; other site 265072008276 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 265072008277 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072008278 NAD(P) binding site [chemical binding]; other site 265072008279 active site 265072008280 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072008281 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072008282 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 265072008283 putative effector binding pocket; other site 265072008284 putative dimerization interface [polypeptide binding]; other site 265072008285 hypothetical protein; Provisional; Region: PRK11505 265072008286 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 265072008287 ligand binding site [chemical binding]; other site 265072008288 active site 265072008289 UGI interface [polypeptide binding]; other site 265072008290 catalytic site [active] 265072008291 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 265072008292 MerC mercury resistance protein; Region: MerC; pfam03203 265072008293 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 265072008294 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 265072008295 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 265072008296 psiF repeat; Region: PsiF_repeat; pfam07769 265072008297 psiF repeat; Region: PsiF_repeat; pfam07769 265072008298 psiF repeat; Region: PsiF_repeat; pfam07769 265072008299 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 265072008300 Uncharacterized conserved protein [Function unknown]; Region: COG4127 265072008301 Restriction endonuclease; Region: Mrr_cat; pfam04471 265072008302 HsdM N-terminal domain; Region: HsdM_N; pfam12161 265072008303 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 265072008304 Methyltransferase domain; Region: Methyltransf_26; pfam13659 265072008305 Virulence protein [General function prediction only]; Region: COG3943 265072008306 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 265072008307 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 265072008308 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 265072008309 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 265072008310 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 265072008311 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 265072008312 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 265072008313 ATP binding site [chemical binding]; other site 265072008314 putative Mg++ binding site [ion binding]; other site 265072008315 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 265072008316 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 265072008317 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 265072008318 putative substrate binding site [chemical binding]; other site 265072008319 putative ATP binding site [chemical binding]; other site 265072008320 sucrose-phosphate synthase, putative, glycosyltransferase domain; Region: sucr_P_syn_N; TIGR02472 265072008321 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 265072008322 putative ADP-binding pocket [chemical binding]; other site 265072008323 sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial; Region: sucr_syn_bact_C; TIGR02471 265072008324 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 265072008325 active site 265072008326 motif I; other site 265072008327 motif II; other site 265072008328 Alpha amylase catalytic domain found in Amylosucrase; Region: AmyAc_Amylosucrase; cd11324 265072008329 trehalose synthase; Region: treS_nterm; TIGR02456 265072008330 active site 265072008331 catalytic site [active] 265072008332 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 265072008333 Mechanosensitive ion channel; Region: MS_channel; pfam00924 265072008334 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 265072008335 putative DNA binding site [nucleotide binding]; other site 265072008336 dimerization interface [polypeptide binding]; other site 265072008337 putative Zn2+ binding site [ion binding]; other site 265072008338 putative RNA binding sites [nucleotide binding]; other site 265072008339 ProQ/FINO family; Region: ProQ; pfam04352 265072008340 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_15; cd04673 265072008341 nudix motif; other site 265072008342 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 265072008343 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 265072008344 Ligand binding site; other site 265072008345 metal-binding site 265072008346 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 265072008347 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 265072008348 XdhC Rossmann domain; Region: XdhC_C; pfam13478 265072008349 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 265072008350 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 265072008351 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 265072008352 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 265072008353 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 265072008354 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 265072008355 catalytic loop [active] 265072008356 iron binding site [ion binding]; other site 265072008357 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 265072008358 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072008359 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072008360 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 265072008361 putative effector binding pocket; other site 265072008362 dimerization interface [polypeptide binding]; other site 265072008363 H+ Antiporter protein; Region: 2A0121; TIGR00900 265072008364 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 265072008365 putative substrate translocation pore; other site 265072008366 AAA ATPase domain; Region: AAA_15; pfam13175 265072008367 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072008368 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072008369 metal binding site [ion binding]; metal-binding site 265072008370 active site 265072008371 I-site; other site 265072008372 NMT1/THI5 like; Region: NMT1; pfam09084 265072008373 PAS domain S-box; Region: sensory_box; TIGR00229 265072008374 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072008375 putative active site [active] 265072008376 heme pocket [chemical binding]; other site 265072008377 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 265072008378 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 265072008379 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072008380 PAS domain; Region: PAS_9; pfam13426 265072008381 putative active site [active] 265072008382 heme pocket [chemical binding]; other site 265072008383 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 265072008384 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072008385 metal binding site [ion binding]; metal-binding site 265072008386 active site 265072008387 I-site; other site 265072008388 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 265072008389 Biofilm formation and stress response factor; Region: BsmA; pfam10014 265072008390 lysophospholipid transporter LplT; Provisional; Region: PRK11195 265072008391 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 265072008392 Predicted small secreted protein [Function unknown]; Region: COG5510 265072008393 Transcriptional regulator [Transcription]; Region: LysR; COG0583 265072008394 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 265072008395 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 265072008396 putative effector binding pocket; other site 265072008397 dimerization interface [polypeptide binding]; other site 265072008398 Predicted membrane protein [Function unknown]; Region: COG2259 265072008399 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 265072008400 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 265072008401 putative active site [active] 265072008402 metal binding site [ion binding]; metal-binding site 265072008403 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 265072008404 MltA specific insert domain; Region: MltA; smart00925 265072008405 3D domain; Region: 3D; pfam06725 265072008406 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 265072008407 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 265072008408 ThiS interaction site; other site 265072008409 putative active site [active] 265072008410 tetramer interface [polypeptide binding]; other site 265072008411 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 265072008412 thiS-thiF/thiG interaction site; other site 265072008413 TPR repeat; Region: TPR_11; pfam13414 265072008414 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 265072008415 binding surface 265072008416 TPR motif; other site 265072008417 TPR repeat; Region: TPR_11; pfam13414 265072008418 Glycosyl transferase family 41; Region: Glyco_transf_41; pfam13844 265072008419 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 265072008420 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 265072008421 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 265072008422 catalytic residue [active] 265072008423 Phosphopantetheine attachment site; Region: PP-binding; cl09936 265072008424 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 265072008425 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 265072008426 dimer interface [polypeptide binding]; other site 265072008427 active site 265072008428 CoA binding pocket [chemical binding]; other site 265072008429 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 265072008430 classical (c) SDRs; Region: SDR_c; cd05233 265072008431 NAD(P) binding site [chemical binding]; other site 265072008432 active site 265072008433 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 265072008434 classical (c) SDRs; Region: SDR_c; cd05233 265072008435 NAD(P) binding site [chemical binding]; other site 265072008436 active site 265072008437 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 265072008438 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 265072008439 putative trimer interface [polypeptide binding]; other site 265072008440 putative CoA binding site [chemical binding]; other site 265072008441 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 265072008442 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 265072008443 [2Fe-2S] cluster binding site [ion binding]; other site 265072008444 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 265072008445 alpha subunit interface [polypeptide binding]; other site 265072008446 active site 265072008447 substrate binding site [chemical binding]; other site 265072008448 Fe binding site [ion binding]; other site 265072008449 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 265072008450 putative trimer interface [polypeptide binding]; other site 265072008451 putative CoA binding site [chemical binding]; other site 265072008452 Methyltransferase FkbM domain; Region: Methyltransf_21; cl17387 265072008453 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 265072008454 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 265072008455 active site 265072008456 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 265072008457 active site 265072008458 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 265072008459 CsbD-like; Region: CsbD; cl17424 265072008460 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 265072008461 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 265072008462 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072008463 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 265072008464 putative substrate translocation pore; other site 265072008465 Major Facilitator Superfamily; Region: MFS_1; pfam07690 265072008466 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 265072008467 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008468 active site 265072008469 phosphorylation site [posttranslational modification] 265072008470 intermolecular recognition site; other site 265072008471 dimerization interface [polypeptide binding]; other site 265072008472 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 265072008473 Zn2+ binding site [ion binding]; other site 265072008474 Mg2+ binding site [ion binding]; other site 265072008475 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 265072008476 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 265072008477 dimer interface [polypeptide binding]; other site 265072008478 phosphorylation site [posttranslational modification] 265072008479 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072008480 ATP binding site [chemical binding]; other site 265072008481 Mg2+ binding site [ion binding]; other site 265072008482 G-X-G motif; other site 265072008483 Response regulator receiver domain; Region: Response_reg; pfam00072 265072008484 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008485 active site 265072008486 phosphorylation site [posttranslational modification] 265072008487 intermolecular recognition site; other site 265072008488 dimerization interface [polypeptide binding]; other site 265072008489 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 265072008490 enoyl-CoA hydratase; Validated; Region: PRK08788 265072008491 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 265072008492 substrate binding site [chemical binding]; other site 265072008493 oxyanion hole (OAH) forming residues; other site 265072008494 trimer interface [polypeptide binding]; other site 265072008495 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 265072008496 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; pfam09939 265072008497 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 265072008498 Ligand Binding Site [chemical binding]; other site 265072008499 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 265072008500 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 265072008501 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 265072008502 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 265072008503 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 265072008504 motif II; other site 265072008505 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 265072008506 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 265072008507 substrate binding site [chemical binding]; other site 265072008508 dimer interface [polypeptide binding]; other site 265072008509 ATP binding site [chemical binding]; other site 265072008510 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 265072008511 thiamine phosphate binding site [chemical binding]; other site 265072008512 active site 265072008513 pyrophosphate binding site [ion binding]; other site 265072008514 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 265072008515 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 265072008516 inhibitor-cofactor binding pocket; inhibition site 265072008517 pyridoxal 5'-phosphate binding site [chemical binding]; other site 265072008518 catalytic residue [active] 265072008519 hypothetical protein; Validated; Region: PRK06217 265072008520 Adenylate kinase and related kinases [Nucleotide transport and metabolism]; Region: Adk; COG0563 265072008521 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 265072008522 substrate binding site [chemical binding]; other site 265072008523 active site 265072008524 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 265072008525 BON domain; Region: BON; pfam04972 265072008526 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 265072008527 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 265072008528 classical (c) SDRs; Region: SDR_c; cd05233 265072008529 NAD(P) binding site [chemical binding]; other site 265072008530 active site 265072008531 primosome assembly protein PriA; Validated; Region: PRK05580 265072008532 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 265072008533 ATP binding site [chemical binding]; other site 265072008534 putative Mg++ binding site [ion binding]; other site 265072008535 helicase superfamily c-terminal domain; Region: HELICc; smart00490 265072008536 ATP-binding site [chemical binding]; other site 265072008537 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 265072008538 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 265072008539 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 265072008540 active site 265072008541 HIGH motif; other site 265072008542 KMSK motif region; other site 265072008543 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 265072008544 tRNA binding surface [nucleotide binding]; other site 265072008545 anticodon binding site; other site 265072008546 Sporulation related domain; Region: SPOR; pfam05036 265072008547 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 265072008548 catalytic residues [active] 265072008549 hinge region; other site 265072008550 alpha helical domain; other site 265072008551 short chain dehydrogenase; Provisional; Region: PRK07024 265072008552 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 265072008553 NAD(P) binding site [chemical binding]; other site 265072008554 active site 265072008555 TPR repeat; Region: TPR_11; pfam13414 265072008556 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 265072008557 binding surface 265072008558 TPR motif; other site 265072008559 Protein of unknown function (DUF560); Region: DUF560; pfam04575 265072008560 Secretin and TonB N terminus short domain; Region: STN; smart00965 265072008561 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 265072008562 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072008563 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 265072008564 fec operon regulator FecR; Reviewed; Region: PRK09774 265072008565 FecR protein; Region: FecR; pfam04773 265072008566 RNA polymerase sigma factor; Provisional; Region: PRK12528 265072008567 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 265072008568 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 265072008569 DNA binding residues [nucleotide binding] 265072008570 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 265072008571 Putative phage tail protein; Region: Phage-tail_3; pfam13550 265072008572 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 265072008573 tape measure domain; Region: tape_meas_nterm; TIGR02675 265072008574 Phage-related minor tail protein [Function unknown]; Region: COG5281 265072008575 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 265072008576 Phage related hypothetical protein (DUF1799); Region: DUF1799; pfam08809 265072008577 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 265072008578 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 265072008579 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 265072008580 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 265072008581 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 265072008582 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 265072008583 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 265072008584 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 265072008585 substrate binding site [chemical binding]; other site 265072008586 amidase catalytic site [active] 265072008587 Zn binding residues [ion binding]; other site 265072008588 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 265072008589 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 265072008590 non-specific DNA binding site [nucleotide binding]; other site 265072008591 salt bridge; other site 265072008592 sequence-specific DNA binding site [nucleotide binding]; other site 265072008593 phage-associated protein, BcepMu gp16 family; Region: BcepMu_gp16; TIGR04111 265072008594 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 265072008595 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]; Region: HEC1; COG5185 265072008596 Integrase core domain; Region: rve; pfam00665 265072008597 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 265072008598 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 265072008599 Phage protein (N4 Gp49/phage Sf6 gene 66) family; Region: Phage_gp49_66; pfam13876 265072008600 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 265072008601 IHF dimer interface [polypeptide binding]; other site 265072008602 IHF - DNA interface [nucleotide binding]; other site 265072008603 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 265072008604 Mor transcription activator family; Region: Mor; cl02360 265072008605 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 265072008606 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 265072008607 Sel1-like repeats; Region: SEL1; smart00671 265072008608 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 265072008609 Flavodoxin; Region: Flavodoxin_1; pfam00258 265072008610 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 265072008611 FAD binding pocket [chemical binding]; other site 265072008612 FAD binding motif [chemical binding]; other site 265072008613 catalytic residues [active] 265072008614 NAD binding pocket [chemical binding]; other site 265072008615 phosphate binding motif [ion binding]; other site 265072008616 beta-alpha-beta structure motif; other site 265072008617 Glutamate synthase domain 1 [Amino acid transport and metabolism]; Region: GltB; COG0067 265072008618 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 265072008619 active site 265072008620 dimer interface [polypeptide binding]; other site 265072008621 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 265072008622 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 265072008623 active site 265072008624 FMN binding site [chemical binding]; other site 265072008625 substrate binding site [chemical binding]; other site 265072008626 3Fe-4S cluster binding site [ion binding]; other site 265072008627 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 265072008628 domain_subunit interface; other site 265072008629 fec operon regulator FecR; Reviewed; Region: PRK09774 265072008630 FecR protein; Region: FecR; pfam04773 265072008631 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072008632 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 265072008633 putative active site [active] 265072008634 heme pocket [chemical binding]; other site 265072008635 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072008636 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 265072008637 putative active site [active] 265072008638 heme pocket [chemical binding]; other site 265072008639 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 265072008640 putative active site [active] 265072008641 heme pocket [chemical binding]; other site 265072008642 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 265072008643 metal binding site [ion binding]; metal-binding site 265072008644 active site 265072008645 I-site; other site 265072008646 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 265072008647 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 265072008648 dimerization interface [polypeptide binding]; other site 265072008649 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 265072008650 dimer interface [polypeptide binding]; other site 265072008651 phosphorylation site [posttranslational modification] 265072008652 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 265072008653 ATP binding site [chemical binding]; other site 265072008654 G-X-G motif; other site 265072008655 osmolarity response regulator; Provisional; Region: ompR; PRK09468 265072008656 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 265072008657 active site 265072008658 phosphorylation site [posttranslational modification] 265072008659 intermolecular recognition site; other site 265072008660 dimerization interface [polypeptide binding]; other site 265072008661 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 265072008662 DNA binding site [nucleotide binding] 265072008663 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 265072008664 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 265072008665 glutaminase active site [active] 265072008666 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 265072008667 dimer interface [polypeptide binding]; other site 265072008668 active site 265072008669 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 265072008670 dimer interface [polypeptide binding]; other site 265072008671 active site 265072008672 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 265072008673 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 265072008674 Substrate binding site; other site 265072008675 Mg++ binding site; other site 265072008676 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 265072008677 active site 265072008678 substrate binding site [chemical binding]; other site 265072008679 CoA binding site [chemical binding]; other site 265072008680 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 265072008681 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 265072008682 gamma subunit interface [polypeptide binding]; other site 265072008683 epsilon subunit interface [polypeptide binding]; other site 265072008684 LBP interface [polypeptide binding]; other site 265072008685 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 265072008686 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 265072008687 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 265072008688 alpha subunit interaction interface [polypeptide binding]; other site 265072008689 Walker A motif; other site 265072008690 ATP binding site [chemical binding]; other site 265072008691 Walker B motif; other site 265072008692 inhibitor binding site; inhibition site 265072008693 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 265072008694 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 265072008695 core domain interface [polypeptide binding]; other site 265072008696 delta subunit interface [polypeptide binding]; other site 265072008697 epsilon subunit interface [polypeptide binding]; other site 265072008698 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 265072008699 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 265072008700 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 265072008701 beta subunit interaction interface [polypeptide binding]; other site 265072008702 Walker A motif; other site 265072008703 ATP binding site [chemical binding]; other site 265072008704 Walker B motif; other site 265072008705 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 265072008706 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 265072008707 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 265072008708 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 265072008709 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 265072008710 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 265072008711 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 265072008712 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 265072008713 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 265072008714 ParB-like nuclease domain; Region: ParBc; pfam02195 265072008715 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 265072008716 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 265072008717 P-loop; other site 265072008718 Magnesium ion binding site [ion binding]; other site 265072008719 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 265072008720 Magnesium ion binding site [ion binding]; other site 265072008721 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 265072008722 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 265072008723 S-adenosylmethionine binding site [chemical binding]; other site 265072008724 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 265072008725 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 265072008726 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 265072008727 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 265072008728 choice-of-anchor A domain; Region: choice_anch_A; TIGR04215 265072008729 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 265072008730 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 265072008731 trmE is a tRNA modification GTPase; Region: trmE; cd04164 265072008732 G1 box; other site 265072008733 GTP/Mg2+ binding site [chemical binding]; other site 265072008734 Switch I region; other site 265072008735 G2 box; other site 265072008736 Switch II region; other site 265072008737 G3 box; other site 265072008738 G4 box; other site 265072008739 G5 box; other site 265072008740 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 265072008741 membrane protein insertase; Provisional; Region: PRK01318 265072008742 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 265072008743 Haemolytic domain; Region: Haemolytic; pfam01809 265072008744 ribonuclease P; Reviewed; Region: rnpA; PRK04390 265072008745 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399