-- dump date 20120504_145556 -- class Genbank::misc_feature -- table misc_feature_note -- id note 557723000001 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 557723000002 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 557723000003 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 557723000004 DNA gyrase subunit A; Validated; Region: PRK05560 557723000005 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 557723000006 CAP-like domain; other site 557723000007 active site 557723000008 primary dimer interface [polypeptide binding]; other site 557723000009 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557723000010 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557723000011 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557723000012 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557723000013 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557723000014 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557723000015 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 557723000016 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723000017 domain; Region: Succ_DH_flav_C; pfam02910 557723000018 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 557723000019 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 557723000020 catalytic loop [active] 557723000021 iron binding site [ion binding]; other site 557723000022 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitC; cd00546 557723000023 D-subunit interface [polypeptide binding]; other site 557723000024 Iron-sulfur protein interface; other site 557723000025 proximal quinone binding site [chemical binding]; other site 557723000026 distal quinone binding site [chemical binding]; other site 557723000027 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitD; cd00547 557723000028 Iron-sulfur protein interface; other site 557723000029 proximal quinone binding site [chemical binding]; other site 557723000030 C-subunit interface; other site 557723000031 distal quinone binding site; other site 557723000032 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 557723000033 cell division protein ZipA; Provisional; Region: PRK01741 557723000034 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 557723000035 FtsZ protein binding site [polypeptide binding]; other site 557723000036 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 557723000037 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 557723000038 nucleotide binding pocket [chemical binding]; other site 557723000039 K-X-D-G motif; other site 557723000040 catalytic site [active] 557723000041 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 557723000042 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 557723000043 Dimer interface [polypeptide binding]; other site 557723000044 BRCT sequence motif; other site 557723000045 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 557723000046 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 557723000047 ATP binding site [chemical binding]; other site 557723000048 putative Mg++ binding site [ion binding]; other site 557723000049 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 557723000050 nucleotide binding region [chemical binding]; other site 557723000051 ATP-binding site [chemical binding]; other site 557723000052 RQC domain; Region: RQC; cl09632 557723000053 HRDC domain; Region: HRDC; cl02578 557723000054 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 557723000055 putative iron binding site [ion binding]; other site 557723000056 LexA repressor; Validated; Region: PRK00215 557723000057 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000058 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 557723000059 Catalytic site [active] 557723000060 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557723000061 Sel1 repeat; Region: Sel1; cl02723 557723000062 Chain length determinant protein; Region: Wzz; cl01623 557723000063 Sel1 repeat; Region: Sel1; cl02723 557723000064 Sel1 repeat; Region: Sel1; cl02723 557723000065 Sel1 repeat; Region: Sel1; cl02723 557723000066 Sel1 repeat; Region: Sel1; cl02723 557723000067 Sel1 repeat; Region: Sel1; cl02723 557723000068 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 557723000069 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 557723000070 putative acyl-acceptor binding pocket; other site 557723000071 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723000072 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 557723000073 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 557723000074 Walker A motif; other site 557723000075 ATP binding site [chemical binding]; other site 557723000076 Walker B motif; other site 557723000077 arginine finger; other site 557723000078 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 557723000079 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 557723000080 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 557723000081 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 557723000082 Walker A/P-loop; other site 557723000083 ATP binding site [chemical binding]; other site 557723000084 Q-loop/lid; other site 557723000085 ABC transporter signature motif; other site 557723000086 Walker B; other site 557723000087 D-loop; other site 557723000088 H-loop/switch region; other site 557723000089 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557723000090 Phd_YefM; Region: PhdYeFM; cl09153 557723000091 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 557723000092 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 557723000093 active site 557723000094 substrate binding site [chemical binding]; other site 557723000095 catalytic site [active] 557723000096 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 557723000097 Uncharacterized conserved protein [Function unknown]; Region: COG1912 557723000098 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 557723000099 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 557723000100 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 557723000101 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 557723000102 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 557723000103 putative valine binding site [chemical binding]; other site 557723000104 dimer interface [polypeptide binding]; other site 557723000105 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 557723000106 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06882 557723000107 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557723000108 PYR/PP interface [polypeptide binding]; other site 557723000109 dimer interface [polypeptide binding]; other site 557723000110 TPP binding site [chemical binding]; other site 557723000111 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557723000112 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 557723000113 TPP-binding site [chemical binding]; other site 557723000114 dimer interface [polypeptide binding]; other site 557723000115 tartrate dehydrogenase; Provisional; Region: PRK08194 557723000116 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 557723000117 multidrug efflux protein; Reviewed; Region: PRK09579 557723000118 Protein export membrane protein; Region: SecD_SecF; cl14618 557723000119 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557723000120 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557723000121 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557723000122 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000123 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 557723000124 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 557723000125 purine monophosphate binding site [chemical binding]; other site 557723000126 dimer interface [polypeptide binding]; other site 557723000127 putative catalytic residues [active] 557723000128 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 557723000129 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 557723000130 cystathionine beta-lyase; Provisional; Region: PRK08114 557723000131 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 557723000132 homodimer interface [polypeptide binding]; other site 557723000133 substrate-cofactor binding pocket; other site 557723000134 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723000135 catalytic residue [active] 557723000136 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 557723000137 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 557723000138 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 557723000139 DNA binding site [nucleotide binding] 557723000140 active site 557723000141 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 557723000142 Protein of unknown function (DUF406); Region: DUF406; cl11449 557723000143 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 557723000144 putative active site [active] 557723000145 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 557723000146 ligand binding site; other site 557723000147 tetramer interface; other site 557723000148 MatE; Region: MatE; cl10513 557723000149 Glycosyltransferase family 52; Region: Glyco_transf_52; pfam07922 557723000150 Protein of unknown function (DUF3184); Region: DUF3184; pfam11380 557723000151 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 557723000152 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 557723000153 active site 557723000154 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 557723000155 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 557723000156 inhibitor-cofactor binding pocket; inhibition site 557723000157 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723000158 catalytic residue [active] 557723000159 Bacterial sugar transferase; Region: Bac_transf; cl00939 557723000160 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 557723000161 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 557723000162 NAD(P) binding site [chemical binding]; other site 557723000163 homodimer interface [polypeptide binding]; other site 557723000164 substrate binding site [chemical binding]; other site 557723000165 active site 557723000166 polysaccharide export protein Wza; Provisional; Region: PRK15078 557723000167 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 557723000168 SLBB domain; Region: SLBB; pfam10531 557723000169 Low molecular weight phosphatase family; Region: LMWPc; cd00115 557723000170 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 557723000171 active site 557723000172 tyrosine kinase; Provisional; Region: PRK11519 557723000173 Chain length determinant protein; Region: Wzz; cl01623 557723000174 Chain length determinant protein; Region: Wzz; cl01623 557723000175 Chain length determinant protein; Region: Wzz; cl01623 557723000176 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000177 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 557723000178 P loop; other site 557723000179 Nucleotide binding site [chemical binding]; other site 557723000180 DTAP/Switch II; other site 557723000181 Switch I; other site 557723000182 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000183 Rrf2 family protein; Region: rrf2_super; TIGR00738 557723000184 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 557723000185 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 557723000186 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557723000187 catalytic residue [active] 557723000188 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 557723000189 trimerization site [polypeptide binding]; other site 557723000190 active site 557723000191 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557723000192 co-chaperone HscB; Provisional; Region: hscB; PRK01773 557723000193 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cl02542 557723000194 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 557723000195 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723000196 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723000197 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723000198 Protein of unknown function DUF2625; Region: DUF2625; cl08177 557723000199 chaperone protein HscA; Provisional; Region: hscA; PRK05183 557723000200 lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) biosynthetic pathway; Region: Lumazine_synthase-like; cl00317 557723000201 active site 557723000202 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 557723000203 catalytic loop [active] 557723000204 iron binding site [ion binding]; other site 557723000205 Protein of unknown function (DUF528); Region: DUF528; cl01123 557723000206 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 557723000207 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 557723000208 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 557723000209 G1 box; other site 557723000210 putative GEF interaction site [polypeptide binding]; other site 557723000211 GTP/Mg2+ binding site [chemical binding]; other site 557723000212 Switch I region; other site 557723000213 G2 box; other site 557723000214 G3 box; other site 557723000215 Switch II region; other site 557723000216 G4 box; other site 557723000217 G5 box; other site 557723000218 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 557723000219 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 557723000220 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557723000221 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 557723000222 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 557723000223 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 557723000224 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 557723000225 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 557723000226 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 557723000227 active site 557723000228 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557723000229 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557723000230 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557723000231 translocation protein TolB; Provisional; Region: tolB; PRK01742 557723000232 TolB amino-terminal domain; Region: TolB_N; cl00639 557723000233 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557723000234 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557723000235 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557723000236 ligand binding site [chemical binding]; other site 557723000237 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 557723000238 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 557723000239 putative metal binding site [ion binding]; other site 557723000240 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 557723000241 HSP70 interaction site [polypeptide binding]; other site 557723000242 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 557723000243 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 557723000244 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 557723000245 FMN binding site [chemical binding]; other site 557723000246 active site 557723000247 catalytic residues [active] 557723000248 substrate binding site [chemical binding]; other site 557723000249 hypothetical protein; Provisional; Region: PRK05415 557723000250 Domain of unknown function (DUF697); Region: DUF697; cl12064 557723000251 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 557723000252 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 557723000253 dimerization interface 3.5A [polypeptide binding]; other site 557723000254 active site 557723000255 ribonuclease G; Provisional; Region: PRK11712 557723000256 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 557723000257 homodimer interface [polypeptide binding]; other site 557723000258 oligonucleotide binding site [chemical binding]; other site 557723000259 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 557723000260 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557723000261 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 557723000262 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 557723000263 OstA-like protein; Region: OstA; cl00844 557723000264 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 557723000265 lipopolysaccharide ABC transporter ATP-binding protein; Provisional; Region: PRK10895 557723000266 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 557723000267 Walker A/P-loop; other site 557723000268 ATP binding site [chemical binding]; other site 557723000269 Q-loop/lid; other site 557723000270 ABC transporter signature motif; other site 557723000271 Walker B; other site 557723000272 D-loop; other site 557723000273 H-loop/switch region; other site 557723000274 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 557723000275 active site 557723000276 phosphorylation site [posttranslational modification] 557723000277 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 557723000278 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000279 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723000280 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 557723000281 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 557723000282 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 557723000283 active site 557723000284 HIGH motif; other site 557723000285 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 557723000286 KMSKS motif; other site 557723000287 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 557723000288 tRNA binding surface [nucleotide binding]; other site 557723000289 anticodon binding site; other site 557723000290 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557723000291 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557723000292 peptide binding site [polypeptide binding]; other site 557723000293 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 557723000294 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 557723000295 homodimer interface [polypeptide binding]; other site 557723000296 maltodextrin phosphorylase; Provisional; Region: PRK14985 557723000297 active site pocket [active] 557723000298 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 557723000299 fatty acid metabolism regulator; Provisional; Region: PRK04984 557723000300 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557723000301 DNA-binding site [nucleotide binding]; DNA binding site 557723000302 FCD domain; Region: FCD; cl11656 557723000303 ApbE family; Region: ApbE; cl00643 557723000304 Protein of unknown function (DUF539); Region: DUF539; cl01129 557723000305 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 557723000306 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 557723000307 active site 557723000308 NTP binding site [chemical binding]; other site 557723000309 metal binding triad [ion binding]; metal-binding site 557723000310 antibiotic binding site [chemical binding]; other site 557723000311 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 557723000312 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 557723000313 Ligand Binding Site [chemical binding]; other site 557723000314 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 557723000315 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 557723000316 TPP-binding site; other site 557723000317 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 557723000318 PYR/PP interface [polypeptide binding]; other site 557723000319 dimer interface [polypeptide binding]; other site 557723000320 TPP binding site [chemical binding]; other site 557723000321 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557723000322 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 557723000323 active site 557723000324 dimerization interface [polypeptide binding]; other site 557723000325 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723000326 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723000327 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723000328 cell division protein MraZ; Reviewed; Region: PRK00326 557723000329 MraZ protein; Region: MraZ; pfam02381 557723000330 MraZ protein; Region: MraZ; pfam02381 557723000331 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 557723000332 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723000333 Septum formation initiator; Region: DivIC; cl11433 557723000334 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 557723000335 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557723000336 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557723000337 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557723000338 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 557723000339 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557723000340 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557723000341 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557723000342 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 557723000343 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557723000344 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557723000345 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557723000346 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 557723000347 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 557723000348 Mg++ binding site [ion binding]; other site 557723000349 putative catalytic motif [active] 557723000350 putative substrate binding site [chemical binding]; other site 557723000351 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03806 557723000352 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557723000353 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557723000354 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 557723000355 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 557723000356 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 557723000357 active site 557723000358 homodimer interface [polypeptide binding]; other site 557723000359 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 557723000360 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557723000361 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557723000362 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557723000363 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 557723000364 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 557723000365 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723000366 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 557723000367 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 557723000368 Cell division protein FtsQ; Region: FtsQ; pfam03799 557723000369 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 557723000370 Cell division protein FtsA; Region: FtsA; cl11496 557723000371 Cell division protein FtsA; Region: FtsA; cl11496 557723000372 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 557723000373 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 557723000374 nucleotide binding site [chemical binding]; other site 557723000375 SulA interaction site; other site 557723000376 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 557723000377 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 557723000378 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 557723000379 GTP-binding protein LepA; Provisional; Region: PRK05433 557723000380 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 557723000381 G1 box; other site 557723000382 putative GEF interaction site [polypeptide binding]; other site 557723000383 GTP/Mg2+ binding site [chemical binding]; other site 557723000384 Switch I region; other site 557723000385 G2 box; other site 557723000386 G3 box; other site 557723000387 Switch II region; other site 557723000388 G4 box; other site 557723000389 G5 box; other site 557723000390 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 557723000391 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 557723000392 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 557723000393 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723000394 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723000395 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723000396 signal peptidase I; Provisional; Region: PRK10861 557723000397 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 557723000398 Catalytic site [active] 557723000399 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 557723000400 ribonuclease III; Reviewed; Region: rnc; PRK00102 557723000401 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 557723000402 dimerization interface [polypeptide binding]; other site 557723000403 active site 557723000404 metal binding site [ion binding]; metal-binding site 557723000405 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 557723000406 dsRNA binding site [nucleotide binding]; other site 557723000407 GTPase Era; Reviewed; Region: era; PRK00089 557723000408 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly...; Region: Era; cd04163 557723000409 G1 box; other site 557723000410 GTP/Mg2+ binding site [chemical binding]; other site 557723000411 Switch I region; other site 557723000412 G2 box; other site 557723000413 Switch II region; other site 557723000414 G3 box; other site 557723000415 G4 box; other site 557723000416 G5 box; other site 557723000417 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 557723000418 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 557723000419 Recombination protein O N terminal; Region: RecO_N; pfam11967 557723000420 Recombination protein O C terminal; Region: RecO_C; pfam02565 557723000421 Transposase IS200 like; Region: Y1_Tnp; cl00848 557723000422 homoserine O-acetyltransferase; Provisional; Region: metX; cl15472 557723000423 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 557723000424 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 557723000425 putative nucleotide binding site [chemical binding]; other site 557723000426 uridine monophosphate binding site [chemical binding]; other site 557723000427 homohexameric interface [polypeptide binding]; other site 557723000428 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 557723000429 dimer interface [polypeptide binding]; other site 557723000430 active site 557723000431 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 557723000432 hinge region; other site 557723000433 YcaO-like family; Region: YcaO; cl09146 557723000434 Permease family; Region: Xan_ur_permease; cl00967 557723000435 Domain of unknown function DUF20; Region: UPF0118; cl00465 557723000436 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK06901 557723000437 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 557723000438 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 557723000439 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 557723000440 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557723000441 TPP binding site [chemical binding]; other site 557723000442 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557723000443 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 557723000444 TPP-binding site [chemical binding]; other site 557723000445 dimer interface [polypeptide binding]; other site 557723000446 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 557723000447 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 557723000448 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 557723000449 active site 557723000450 HIGH motif; other site 557723000451 KMSKS motif; other site 557723000452 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 557723000453 tRNA binding surface [nucleotide binding]; other site 557723000454 anticodon binding site; other site 557723000455 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 557723000456 dimer interface [polypeptide binding]; other site 557723000457 putative tRNA-binding site [nucleotide binding]; other site 557723000458 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 557723000459 active site 557723000460 multimer interface [polypeptide binding]; other site 557723000461 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 557723000462 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 557723000463 dimer interface [polypeptide binding]; other site 557723000464 ADP-ribose binding site [chemical binding]; other site 557723000465 active site 557723000466 nudix motif; other site 557723000467 metal binding site [ion binding]; metal-binding site 557723000468 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557723000469 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 557723000470 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 557723000471 Pyruvate formate lyase 1; Region: PFL1; cd01678 557723000472 coenzyme A binding site [chemical binding]; other site 557723000473 active site 557723000474 catalytic residues [active] 557723000475 glycine loop; other site 557723000476 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 557723000477 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 557723000478 FeS/SAM binding site; other site 557723000479 putative transporter; Validated; Region: PRK03818 557723000480 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 557723000481 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557723000482 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557723000483 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 557723000484 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 557723000485 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 557723000486 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000487 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 557723000488 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 557723000489 23S rRNA interface [nucleotide binding]; other site 557723000490 L3 interface [polypeptide binding]; other site 557723000491 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 557723000492 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 557723000493 trimer interface [polypeptide binding]; other site 557723000494 eyelet of channel; other site 557723000495 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 557723000496 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557723000497 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557723000498 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 557723000499 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 557723000500 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 557723000501 ligand binding site [chemical binding]; other site 557723000502 flexible hinge region; other site 557723000503 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 557723000504 putative switch regulator; other site 557723000505 non-specific DNA interactions [nucleotide binding]; other site 557723000506 DNA binding site [nucleotide binding] 557723000507 sequence specific DNA binding site [nucleotide binding]; other site 557723000508 putative cAMP binding site [chemical binding]; other site 557723000509 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 557723000510 S-adenosylmethionine binding site [chemical binding]; other site 557723000511 replicative DNA helicase; Validated; Region: PRK06904 557723000512 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 557723000513 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 557723000514 Walker A motif; other site 557723000515 ATP binding site [chemical binding]; other site 557723000516 Walker B motif; other site 557723000517 DNA binding loops [nucleotide binding] 557723000518 YcgL domain; Region: YcgL; cl01189 557723000519 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 557723000520 ATP cone domain; Region: ATP-cone; pfam03477 557723000521 quinohemoprotein amine dehydrogenase maturation protein; Region: quino_hemo_SAM; TIGR03906 557723000522 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 557723000523 FeS/SAM binding site; other site 557723000524 elongation factor P; Validated; Region: PRK00529 557723000525 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 557723000526 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 557723000527 RNA binding site [nucleotide binding]; other site 557723000528 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 557723000529 RNA binding site [nucleotide binding]; other site 557723000530 Protein of unknown function (DUF904); Region: DUF904; cl11531 557723000531 Thymidine kinase; Region: TK; cl00631 557723000532 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 557723000533 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 557723000534 active site 557723000535 motif I; other site 557723000536 motif II; other site 557723000537 DNA polymerase I; Provisional; Region: PRK05755 557723000538 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 557723000539 active site 557723000540 metal binding site 1 [ion binding]; metal-binding site 557723000541 putative 5' ssDNA interaction site; other site 557723000542 metal binding site 3; metal-binding site 557723000543 metal binding site 2 [ion binding]; metal-binding site 557723000544 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 557723000545 putative DNA binding site [nucleotide binding]; other site 557723000546 putative metal binding site [ion binding]; other site 557723000547 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 557723000548 active site 557723000549 catalytic site [active] 557723000550 substrate binding site [chemical binding]; other site 557723000551 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 557723000552 active site 557723000553 DNA binding site [nucleotide binding] 557723000554 catalytic site [active] 557723000555 YccA-like proteins; Region: YccA_like; cd10433 557723000556 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 557723000557 Clp amino terminal domain; Region: Clp_N; pfam02861 557723000558 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 557723000559 Walker A motif; other site 557723000560 ATP binding site [chemical binding]; other site 557723000561 Walker B motif; other site 557723000562 arginine finger; other site 557723000563 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 557723000564 Walker A motif; other site 557723000565 ATP binding site [chemical binding]; other site 557723000566 Walker B motif; other site 557723000567 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557723000568 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 557723000569 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 557723000570 dimerization domain [polypeptide binding]; other site 557723000571 dimer interface [polypeptide binding]; other site 557723000572 catalytic residues [active] 557723000573 putative peptidase; Provisional; Region: PRK11649 557723000574 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 557723000575 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 557723000576 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 557723000577 ABC-ATPase subunit interface; other site 557723000578 dimer interface [polypeptide binding]; other site 557723000579 putative PBP binding regions; other site 557723000580 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 557723000581 putative active site [active] 557723000582 putative dimer interface [polypeptide binding]; other site 557723000583 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 557723000584 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 557723000585 active pocket/dimerization site; other site 557723000586 active site 557723000587 phosphorylation site [posttranslational modification] 557723000588 Beta-galactosidase; Region: Glyco_hydro_42; cl03154 557723000589 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 557723000590 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 557723000591 PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_man; cd00001 557723000592 active site 557723000593 phosphorylation site [posttranslational modification] 557723000594 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 557723000595 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 557723000596 dimer interface [polypeptide binding]; other site 557723000597 active site 557723000598 AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases; Region: SIS_AgaS_like; cd05010 557723000599 putative active site [active] 557723000600 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 557723000601 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000602 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557723000603 Putative exonuclease, RdgC; Region: RdgC; cl01122 557723000604 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 557723000605 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 557723000606 dimer interface [polypeptide binding]; other site 557723000607 conserved gate region; other site 557723000608 putative PBP binding loops; other site 557723000609 ABC-ATPase subunit interface; other site 557723000610 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 557723000611 dimer interface [polypeptide binding]; other site 557723000612 conserved gate region; other site 557723000613 putative PBP binding loops; other site 557723000614 ABC-ATPase subunit interface; other site 557723000615 ferric transporter ATP-binding subunit; Provisional; Region: fbpC; PRK11432 557723000616 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000617 Walker A/P-loop; other site 557723000618 ATP binding site [chemical binding]; other site 557723000619 Q-loop/lid; other site 557723000620 ABC transporter signature motif; other site 557723000621 Walker B; other site 557723000622 D-loop; other site 557723000623 H-loop/switch region; other site 557723000624 Uncharacterised BCR, YhbC family COG0779; Region: DUF150; pfam02576 557723000625 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 557723000626 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 557723000627 Sm1 motif; other site 557723000628 predicted subunit interaction site [polypeptide binding]; other site 557723000629 RNA binding pocket [nucleotide binding]; other site 557723000630 Sm2 motif; other site 557723000631 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 557723000632 NusA N-terminal domain; Region: NusA_N; pfam08529 557723000633 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 557723000634 RNA binding site [nucleotide binding]; other site 557723000635 homodimer interface [polypeptide binding]; other site 557723000636 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 557723000637 G-X-X-G motif; other site 557723000638 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 557723000639 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 557723000640 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 557723000641 translation initiation factor IF-2; Region: IF-2; TIGR00487 557723000642 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 557723000643 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases; Region: IF2_eIF5B; cd01887 557723000644 G1 box; other site 557723000645 putative GEF interaction site [polypeptide binding]; other site 557723000646 GTP/Mg2+ binding site [chemical binding]; other site 557723000647 Switch I region; other site 557723000648 G2 box; other site 557723000649 G3 box; other site 557723000650 Switch II region; other site 557723000651 G4 box; other site 557723000652 G5 box; other site 557723000653 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 557723000654 Translation-initiation factor 2; Region: IF-2; pfam11987 557723000655 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 557723000656 LysR family transcriptional regulator; Provisional; Region: PRK14997 557723000657 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000658 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 557723000659 putative effector binding pocket; other site 557723000660 dimerization interface [polypeptide binding]; other site 557723000661 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 557723000662 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 557723000663 active site 557723000664 interdomain interaction site; other site 557723000665 putative metal-binding site [ion binding]; other site 557723000666 nucleotide binding site [chemical binding]; other site 557723000667 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 557723000668 domain I; other site 557723000669 DNA binding groove [nucleotide binding] 557723000670 phosphate binding site [ion binding]; other site 557723000671 domain II; other site 557723000672 domain III; other site 557723000673 nucleotide binding site [chemical binding]; other site 557723000674 catalytic site [active] 557723000675 domain IV; other site 557723000676 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557723000677 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 557723000678 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 557723000679 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 557723000680 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 557723000681 Sulfatase; Region: Sulfatase; cl10460 557723000682 Protein of unknown function (DUF1414); Region: DUF1414; cl01175 557723000683 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557723000684 ATP binding site [chemical binding]; other site 557723000685 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 557723000686 THUMP domain; Region: THUMP; cl12076 557723000687 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 557723000688 Ligand Binding Site [chemical binding]; other site 557723000689 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 557723000690 active site residue [active] 557723000691 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 557723000692 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 557723000693 Substrate binding site; other site 557723000694 Mg++ binding site; other site 557723000695 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 557723000696 active site 557723000697 substrate binding site [chemical binding]; other site 557723000698 CoA binding site [chemical binding]; other site 557723000699 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 557723000700 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 557723000701 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 557723000702 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 557723000703 AmiB activator; Provisional; Region: PRK11637 557723000704 Divergent polysaccharide deacetylase; Region: Polysacc_deac_2; cl04721 557723000705 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 557723000706 Surface antigen; Region: Bac_surface_Ag; cl03097 557723000707 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 557723000708 Family of unknown function (DUF490); Region: DUF490; pfam04357 557723000709 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 557723000710 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557723000711 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000712 Walker A/P-loop; other site 557723000713 ATP binding site [chemical binding]; other site 557723000714 Q-loop/lid; other site 557723000715 ABC transporter signature motif; other site 557723000716 Walker B; other site 557723000717 D-loop; other site 557723000718 H-loop/switch region; other site 557723000719 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 557723000720 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557723000721 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000722 Walker A/P-loop; other site 557723000723 ATP binding site [chemical binding]; other site 557723000724 Q-loop/lid; other site 557723000725 ABC transporter signature motif; other site 557723000726 Walker B; other site 557723000727 D-loop; other site 557723000728 H-loop/switch region; other site 557723000729 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 557723000730 active site 557723000731 8-oxo-dGMP binding site [chemical binding]; other site 557723000732 nudix motif; other site 557723000733 metal binding site [ion binding]; metal-binding site 557723000734 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 557723000735 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000736 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 557723000737 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 557723000738 nucleotide binding region [chemical binding]; other site 557723000739 ATP-binding site [chemical binding]; other site 557723000740 SEC-C motif; Region: SEC-C; pfam02810 557723000741 Protein of unknown function (DUF2547); Region: DUF2547; pfam10818 557723000742 Protein of unknown function (DUF721); Region: DUF721; cl02324 557723000743 Uncharacterized lipoprotein NlpE involved in copper resistance; Region: NlpE; cl01138 557723000744 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 557723000745 catalytic center binding site [active] 557723000746 ATP binding site [chemical binding]; other site 557723000747 poly(A) polymerase I; Provisional; Region: pcnB; PRK11623 557723000748 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 557723000749 active site 557723000750 NTP binding site [chemical binding]; other site 557723000751 metal binding triad [ion binding]; metal-binding site 557723000752 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 557723000753 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 557723000754 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557723000755 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 557723000756 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 557723000757 ABC-type maltose transport systems, permease component [Carbohydrate transport and metabolism]; Region: MalG; COG3833 557723000758 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 557723000759 dimer interface [polypeptide binding]; other site 557723000760 conserved gate region; other site 557723000761 putative PBP binding loops; other site 557723000762 ABC-ATPase subunit interface; other site 557723000763 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 557723000764 dimer interface [polypeptide binding]; other site 557723000765 conserved gate region; other site 557723000766 putative PBP binding loops; other site 557723000767 ABC-ATPase subunit interface; other site 557723000768 maltose ABC transporter periplasmic protein; Reviewed; Region: malE; PRK09474 557723000769 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 557723000770 maltose/maltodextrin transporter ATP-binding protein; Provisional; Region: PRK11000 557723000771 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 557723000772 Walker A/P-loop; other site 557723000773 ATP binding site [chemical binding]; other site 557723000774 Q-loop/lid; other site 557723000775 ABC transporter signature motif; other site 557723000776 Walker B; other site 557723000777 D-loop; other site 557723000778 H-loop/switch region; other site 557723000779 TOBE domain; Region: TOBE_2; cl01440 557723000780 HemN family oxidoreductase; Provisional; Region: PRK05660 557723000781 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 557723000782 FeS/SAM binding site; other site 557723000783 HemN C-terminal region; Region: HemN_C; pfam06969 557723000784 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 557723000785 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 557723000786 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 557723000787 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 557723000788 Trp repressor protein; Region: Trp_repressor; cl01121 557723000789 Transglycosylase; Region: Transgly; cl07896 557723000790 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 557723000791 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 557723000792 dimer interface [polypeptide binding]; other site 557723000793 conserved gate region; other site 557723000794 putative PBP binding loops; other site 557723000795 ABC-ATPase subunit interface; other site 557723000796 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 557723000797 NMT1/THI5 like; Region: NMT1; pfam09084 557723000798 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557723000799 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557723000800 Walker A/P-loop; other site 557723000801 ATP binding site [chemical binding]; other site 557723000802 Q-loop/lid; other site 557723000803 ABC transporter signature motif; other site 557723000804 Walker B; other site 557723000805 D-loop; other site 557723000806 H-loop/switch region; other site 557723000807 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557723000808 active site 557723000809 Uncharacterized conserved protein [Function unknown]; Region: COG2128 557723000810 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557723000811 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 557723000812 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723000813 KicB killing factor; Region: KicB; cl11468 557723000814 MukE-like family; Region: MukE; cl11471 557723000815 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 557723000816 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 557723000817 cofactor binding site; other site 557723000818 DNA binding site [nucleotide binding] 557723000819 substrate interaction site [chemical binding]; other site 557723000820 cell division protein MukB; Provisional; Region: mukB; PRK04863 557723000821 MukB N-terminal; Region: MukB; pfam04310 557723000822 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 557723000823 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 557723000824 active site 557723000825 NTP binding site [chemical binding]; other site 557723000826 metal binding triad [ion binding]; metal-binding site 557723000827 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 557723000828 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557723000829 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 557723000830 dimer interface [polypeptide binding]; other site 557723000831 FMN binding site [chemical binding]; other site 557723000832 Protein of unknown function (DUF406); Region: DUF406; cl11449 557723000833 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 557723000834 Cytolethal distending toxin A/C family; Region: CDtoxinA; pfam03498 557723000835 CdtB, the catalytic DNase I-like subunit of cytolethal distending toxin (CDT) protein; Region: CdtB; cd09081 557723000836 putative catalytic site [active] 557723000837 heterotrimer interface [polypeptide binding]; other site 557723000838 CdtC interface [polypeptide binding]; other site 557723000839 CdtA interface [polypeptide binding]; other site 557723000840 putative metal binding site [ion binding]; other site 557723000841 putative phosphate binding site [ion binding]; other site 557723000842 Cytolethal distending toxin A/C family; Region: CDtoxinA; pfam03498 557723000843 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 557723000844 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557723000845 active site 557723000846 HIGH motif; other site 557723000847 nucleotide binding site [chemical binding]; other site 557723000848 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 557723000849 KMSKS motif; other site 557723000850 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 557723000851 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 557723000852 active site 557723000853 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 557723000854 DHH family; Region: DHH; pfam01368 557723000855 DHHA1 domain; Region: DHHA1; pfam02272 557723000856 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 557723000857 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557723000858 ligand binding site [chemical binding]; other site 557723000859 pyridoxal phosphate (PLP) phosphatase; Provisional; Region: PRK10530 557723000860 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 557723000861 active site 557723000862 motif I; other site 557723000863 motif II; other site 557723000864 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 557723000865 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557723000866 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557723000867 Coenzyme A binding pocket [chemical binding]; other site 557723000868 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 557723000869 dihydrodipicolinate synthase; Region: dapA; TIGR00674 557723000870 dimer interface [polypeptide binding]; other site 557723000871 active site 557723000872 catalytic residue [active] 557723000873 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 557723000874 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 557723000875 dimer interface [polypeptide binding]; other site 557723000876 putative anticodon binding site; other site 557723000877 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 557723000878 motif 1; other site 557723000879 active site 557723000880 motif 2; other site 557723000881 motif 3; other site 557723000882 Protein of unknown function (DUF328); Region: DUF328; cl01143 557723000883 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 557723000884 rRNA interaction site [nucleotide binding]; other site 557723000885 S8 interaction site; other site 557723000886 putative laminin-1 binding site; other site 557723000887 elongation factor Ts; Provisional; Region: tsf; PRK09377 557723000888 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 557723000889 Elongation factor TS; Region: EF_TS; pfam00889 557723000890 Elongation factor TS; Region: EF_TS; pfam00889 557723000891 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 557723000892 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557723000893 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557723000894 molybdopterin cofactor binding site; other site 557723000895 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 557723000896 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 557723000897 molybdopterin cofactor binding site; other site 557723000898 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 557723000899 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 557723000900 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557723000901 glycogen branching enzyme; Provisional; Region: PRK05402 557723000902 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 557723000903 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 557723000904 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 557723000905 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 557723000906 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 557723000907 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 557723000908 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 557723000909 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 557723000910 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 557723000911 ligand binding site; other site 557723000912 oligomer interface; other site 557723000913 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 557723000914 dimer interface [polypeptide binding]; other site 557723000915 N-terminal domain interface [polypeptide binding]; other site 557723000916 sulfate 1 binding site; other site 557723000917 glycogen synthase; Provisional; Region: glgA; PRK00654 557723000918 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 557723000919 ADP-binding pocket [chemical binding]; other site 557723000920 homodimer interface [polypeptide binding]; other site 557723000921 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 557723000922 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 557723000923 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 557723000924 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 557723000925 active site 557723000926 Domain of unknown function (DUF1919); Region: DUF1919; cl01628 557723000927 BRO family, N-terminal domain; Region: Bro-N; cl10591 557723000928 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 557723000929 GMP synthase; Reviewed; Region: guaA; PRK00074 557723000930 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 557723000931 AMP/PPi binding site [chemical binding]; other site 557723000932 candidate oxyanion hole; other site 557723000933 catalytic triad [active] 557723000934 potential glutamine specificity residues [chemical binding]; other site 557723000935 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 557723000936 ATP Binding subdomain [chemical binding]; other site 557723000937 Ligand Binding sites [chemical binding]; other site 557723000938 Dimerization subdomain; other site 557723000939 Flagellin N-methylase; Region: FliB; cl00497 557723000940 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 557723000941 Nuclear pore complex subunit [Intracellular trafficking and secretion]; Region: NUP170; COG5308 557723000942 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 557723000943 Predicted transcriptional regulator [Transcription]; Region: COG2378 557723000944 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000945 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 557723000946 non-specific DNA binding site [nucleotide binding]; other site 557723000947 salt bridge; other site 557723000948 sequence-specific DNA binding site [nucleotide binding]; other site 557723000949 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 557723000950 putative phosphate binding site [ion binding]; other site 557723000951 putative catalytic site [active] 557723000952 active site 557723000953 metal binding site A [ion binding]; metal-binding site 557723000954 DNA binding site [nucleotide binding] 557723000955 putative AP binding site [nucleotide binding]; other site 557723000956 putative metal binding site B [ion binding]; other site 557723000957 Predicted permease [General function prediction only]; Region: COG2056 557723000958 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 557723000959 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 557723000960 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 557723000961 Ligand Binding Site [chemical binding]; other site 557723000962 aromatic acid decarboxylase; Validated; Region: PRK05920 557723000963 Flavoprotein; Region: Flavoprotein; cl08021 557723000964 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557723000965 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 557723000966 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557723000967 metal binding triad; other site 557723000968 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557723000969 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557723000970 metal binding triad; other site 557723000971 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557723000972 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 557723000973 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 557723000974 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 557723000975 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723000976 DNA translocase FtsK; Provisional; Region: PRK10263 557723000977 DNA translocase FtsK; Provisional; Region: PRK10263 557723000978 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723000979 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 557723000980 NeuB family; Region: NeuB; cl00496 557723000981 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557723000982 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 557723000983 Cytolethal distending toxin A/C family; Region: CDtoxinA; pfam03498 557723000984 CdtB, the catalytic DNase I-like subunit of cytolethal distending toxin (CDT) protein; Region: CdtB; cd09081 557723000985 putative catalytic site [active] 557723000986 heterotrimer interface [polypeptide binding]; other site 557723000987 CdtC interface [polypeptide binding]; other site 557723000988 CdtA interface [polypeptide binding]; other site 557723000989 putative metal binding site [ion binding]; other site 557723000990 putative phosphate binding site [ion binding]; other site 557723000991 Cytolethal distending toxin A/C family; Region: CDtoxinA; pfam03498 557723000992 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 557723000993 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 557723000994 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723000995 Mg2+ binding site [ion binding]; other site 557723000996 G-X-G motif; other site 557723000997 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 557723000998 anchoring element; other site 557723000999 dimer interface [polypeptide binding]; other site 557723001000 ATP binding site [chemical binding]; other site 557723001001 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 557723001002 active site 557723001003 putative metal-binding site [ion binding]; other site 557723001004 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 557723001005 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08147 557723001006 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 557723001007 CPxP motif; other site 557723001008 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 557723001009 Protein of unknown function (DUF615); Region: DUF615; cl01147 557723001010 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557723001011 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 557723001012 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 557723001013 substrate binding site [chemical binding]; other site 557723001014 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 557723001015 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 557723001016 substrate binding site [chemical binding]; other site 557723001017 ligand binding site [chemical binding]; other site 557723001018 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 557723001019 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 557723001020 putative substrate translocation pore; other site 557723001021 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 557723001022 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 557723001023 RNA binding surface [nucleotide binding]; other site 557723001024 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 557723001025 active site 557723001026 uracil binding [chemical binding]; other site 557723001027 two-component sensor protein; Provisional; Region: cpxA; PRK09470 557723001028 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 557723001029 dimerization interface [polypeptide binding]; other site 557723001030 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 557723001031 dimer interface [polypeptide binding]; other site 557723001032 phosphorylation site [posttranslational modification] 557723001033 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723001034 ATP binding site [chemical binding]; other site 557723001035 Mg2+ binding site [ion binding]; other site 557723001036 G-X-G motif; other site 557723001037 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557723001038 active site 557723001039 phosphorylation site [posttranslational modification] 557723001040 intermolecular recognition site; other site 557723001041 dimerization interface [polypeptide binding]; other site 557723001042 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; cl02713 557723001043 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 557723001044 DNA binding site [nucleotide binding] 557723001045 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 557723001046 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 557723001047 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 557723001048 proline aminopeptidase P II; Provisional; Region: PRK10879 557723001049 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 557723001050 active site 557723001051 Phd_YefM; Region: PhdYeFM; cl09153 557723001052 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 557723001053 putative active site [active] 557723001054 Aminotransferase class-V; Region: Aminotran_5; pfam00266 557723001055 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 557723001056 homodimer interface [polypeptide binding]; other site 557723001057 substrate-cofactor binding pocket; other site 557723001058 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723001059 catalytic residue [active] 557723001060 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723001061 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723001062 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723001063 HsdM N-terminal domain; Region: HsdM_N; pfam12161 557723001064 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 557723001065 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 557723001066 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723001067 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 557723001068 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 557723001069 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723001070 ATP binding site [chemical binding]; other site 557723001071 putative Mg++ binding site [ion binding]; other site 557723001072 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 557723001073 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 557723001074 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 557723001075 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723001076 homodimer interface [polypeptide binding]; other site 557723001077 catalytic residue [active] 557723001078 DinI-like family; Region: DinI; cl11630 557723001079 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 557723001080 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 557723001081 putative dimer interface [polypeptide binding]; other site 557723001082 putative anticodon binding site; other site 557723001083 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 557723001084 homodimer interface [polypeptide binding]; other site 557723001085 motif 1; other site 557723001086 motif 2; other site 557723001087 active site 557723001088 motif 3; other site 557723001089 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 557723001090 exopolyphosphatase; Provisional; Region: PRK10854 557723001091 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 557723001092 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 557723001093 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 557723001094 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 557723001095 active site 557723001096 hinge; other site 557723001097 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557723001098 DNA-binding site [nucleotide binding]; DNA binding site 557723001099 RNA-binding motif; other site 557723001100 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 557723001101 catalytic triad [active] 557723001102 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 557723001103 active site 557723001104 motif I; other site 557723001105 motif II; other site 557723001106 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723001107 lytic murein transglycosylase; Provisional; Region: PRK11619 557723001108 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557723001109 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557723001110 catalytic residue [active] 557723001111 Cation efflux family; Region: Cation_efflux; cl00316 557723001112 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 557723001113 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723001114 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723001115 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723001116 O-succinylbenzoate synthase; Provisional; Region: PRK05105 557723001117 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 557723001118 active site 557723001119 Uncharacterised protein family (UPF0231); Region: UPF0231; cl11474 557723001120 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 557723001121 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 557723001122 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 557723001123 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 557723001124 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 557723001125 dimer interface [polypeptide binding]; other site 557723001126 ssDNA binding site [nucleotide binding]; other site 557723001127 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557723001128 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 557723001129 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 557723001130 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 557723001131 ATP binding site [chemical binding]; other site 557723001132 Mg++ binding site [ion binding]; other site 557723001133 motif III; other site 557723001134 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 557723001135 nucleotide binding region [chemical binding]; other site 557723001136 ATP-binding site [chemical binding]; other site 557723001137 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 557723001138 non-specific DNA binding site [nucleotide binding]; other site 557723001139 salt bridge; other site 557723001140 sequence-specific DNA binding site [nucleotide binding]; other site 557723001141 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 557723001142 ornithine carbamoyltransferase; Validated; Region: PRK02102 557723001143 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557723001144 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001145 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 557723001146 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 557723001147 dimer interface [polypeptide binding]; other site 557723001148 glycine-pyridoxal phosphate binding site [chemical binding]; other site 557723001149 active site 557723001150 folate binding site [chemical binding]; other site 557723001151 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 557723001152 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 557723001153 generic binding surface II; other site 557723001154 generic binding surface I; other site 557723001155 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 557723001156 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 557723001157 CAP-like domain; other site 557723001158 active site 557723001159 primary dimer interface [polypeptide binding]; other site 557723001160 acyl-CoA esterase; Provisional; Region: PRK10673 557723001161 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557723001162 SeqA protein; Region: SeqA; cl11470 557723001163 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 557723001164 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 557723001165 hypothetical protein; Provisional; Region: PRK11281 557723001166 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 557723001167 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557723001168 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 557723001169 Tetramer interface [polypeptide binding]; other site 557723001170 active site 557723001171 FMN-binding site [chemical binding]; other site 557723001172 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 557723001173 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723001174 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 557723001175 ribonuclease D; Provisional; Region: PRK10829 557723001176 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 557723001177 putative active site [active] 557723001178 catalytic site [active] 557723001179 putative substrate binding site [chemical binding]; other site 557723001180 HRDC domain; Region: HRDC; cl02578 557723001181 Acetokinase family; Region: Acetate_kinase; cl01029 557723001182 phosphate acetyltransferase; Reviewed; Region: PRK05632 557723001183 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723001184 DRTGG domain; Region: DRTGG; cl12147 557723001185 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 557723001186 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 557723001187 zinc binding site [ion binding]; other site 557723001188 putative ligand binding site [chemical binding]; other site 557723001189 Stringent starvation protein B; Region: SspB; cl01120 557723001190 stringent starvation protein A; Provisional; Region: sspA; PRK09481 557723001191 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 557723001192 C-terminal domain interface [polypeptide binding]; other site 557723001193 putative GSH binding site (G-site) [chemical binding]; other site 557723001194 dimer interface [polypeptide binding]; other site 557723001195 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 557723001196 dimer interface [polypeptide binding]; other site 557723001197 N-terminal domain interface [polypeptide binding]; other site 557723001198 Protein of unknown function (DUF496); Region: DUF496; cl09955 557723001199 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 557723001200 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557723001201 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 557723001202 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 557723001203 PemK-like protein; Region: PemK; cl00995 557723001204 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 557723001205 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 557723001206 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 557723001207 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723001208 homodimer interface [polypeptide binding]; other site 557723001209 catalytic residue [active] 557723001210 EamA-like transporter family; Region: EamA; cl01037 557723001211 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001212 flavoprotein, HI0933 family; Region: TIGR00275 557723001213 N-acetylneuraminate lyase; Region: nanA; TIGR00683 557723001214 N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL); Region: NAL; cd00954 557723001215 inhibitor site; inhibition site 557723001216 active site 557723001217 dimer interface [polypeptide binding]; other site 557723001218 catalytic residue [active] 557723001219 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 557723001220 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 557723001221 putative active site [active] 557723001222 Domain of unknown function (DUF386); Region: DUF386; cl01047 557723001223 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 557723001224 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 557723001225 non-specific DNA binding site [nucleotide binding]; other site 557723001226 salt bridge; other site 557723001227 sequence-specific DNA binding site [nucleotide binding]; other site 557723001228 Phage minor tail protein L; Region: Phage_tail_L; cl01908 557723001229 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 557723001230 T5orf172 domain; Region: T5orf172; cl11176 557723001231 Phage minor tail protein; Region: Phage_min_tail; cl01940 557723001232 Preprotein translocase SecG subunit; Region: SecG; cl09123 557723001233 DNA topoisomerase III; Provisional; Region: PRK07726 557723001234 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 557723001235 active site 557723001236 putative interdomain interaction site [polypeptide binding]; other site 557723001237 putative metal-binding site [ion binding]; other site 557723001238 putative nucleotide binding site [chemical binding]; other site 557723001239 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 557723001240 domain I; other site 557723001241 DNA binding groove [nucleotide binding] 557723001242 phosphate binding site [ion binding]; other site 557723001243 domain II; other site 557723001244 domain III; other site 557723001245 nucleotide binding site [chemical binding]; other site 557723001246 catalytic site [active] 557723001247 domain IV; other site 557723001248 Penicillin-insensitive murein endopeptidase; Region: Peptidase_M74; cl01538 557723001249 Murein endopeptidase [Cell envelope biogenesis, outer membrane]; Region: MepA; COG3770 557723001250 Protein of unknown function (DUF423); Region: DUF423; cl01008 557723001251 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 557723001252 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723001253 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 557723001254 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 557723001255 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 557723001256 FeS/SAM binding site; other site 557723001257 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 557723001258 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 557723001259 trimer interface [polypeptide binding]; other site 557723001260 dimer interface [polypeptide binding]; other site 557723001261 putative active site [active] 557723001262 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 557723001263 MoaE interaction surface [polypeptide binding]; other site 557723001264 MoeB interaction surface [polypeptide binding]; other site 557723001265 thiocarboxylated glycine; other site 557723001266 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 557723001267 MoaE homodimer interface [polypeptide binding]; other site 557723001268 MoaD interaction [polypeptide binding]; other site 557723001269 active site residues [active] 557723001270 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 557723001271 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]; Region: COG1444 557723001272 Putative ATPase (DUF699); Region: DUF699; pfam05127 557723001273 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557723001274 Coenzyme A binding pocket [chemical binding]; other site 557723001275 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 557723001276 Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Region: PBP1_GGBP; cd01539 557723001277 ligand binding site [chemical binding]; other site 557723001278 calcium binding site [ion binding]; other site 557723001279 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 557723001280 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional; Region: PRK10982 557723001281 Walker A/P-loop; other site 557723001282 ATP binding site [chemical binding]; other site 557723001283 Q-loop/lid; other site 557723001284 ABC transporter signature motif; other site 557723001285 Walker B; other site 557723001286 D-loop; other site 557723001287 H-loop/switch region; other site 557723001288 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 557723001289 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 557723001290 TM-ABC transporter signature motif; other site 557723001291 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 557723001292 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 557723001293 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 557723001294 dimer interface [polypeptide binding]; other site 557723001295 conserved gate region; other site 557723001296 ABC-ATPase subunit interface; other site 557723001297 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 557723001298 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 557723001299 Walker A/P-loop; other site 557723001300 ATP binding site [chemical binding]; other site 557723001301 Q-loop/lid; other site 557723001302 ABC transporter signature motif; other site 557723001303 Walker B; other site 557723001304 D-loop; other site 557723001305 H-loop/switch region; other site 557723001306 NIL domain; Region: NIL; cl09633 557723001307 MarC family integral membrane protein; Region: MarC; cl00919 557723001308 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 557723001309 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 557723001310 peptide binding site [polypeptide binding]; other site 557723001311 antiporter inner membrane protein; Provisional; Region: PRK11670 557723001312 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 557723001313 acetylornithine deacetylase; Provisional; Region: PRK05111 557723001314 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 557723001315 metal binding site [ion binding]; metal-binding site 557723001316 putative dimer interface [polypeptide binding]; other site 557723001317 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 557723001318 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 557723001319 ATP binding site [chemical binding]; other site 557723001320 substrate interface [chemical binding]; other site 557723001321 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cd00474 557723001322 Predicted RNA interaction site [nucleotide binding]; other site 557723001323 putative binding site; other site 557723001324 Mutations affecting start-site selection; other site 557723001325 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 557723001326 active site 557723001327 dimer interface [polypeptide binding]; other site 557723001328 tetratricopeptide repeat protein; Provisional; Region: PRK11788 557723001329 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 557723001330 binding surface 557723001331 TPR motif; other site 557723001332 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 557723001333 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 557723001334 IHF dimer interface [polypeptide binding]; other site 557723001335 IHF - DNA interface [nucleotide binding]; other site 557723001336 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 557723001337 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 557723001338 RNA binding site [nucleotide binding]; other site 557723001339 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 557723001340 RNA binding site [nucleotide binding]; other site 557723001341 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 557723001342 RNA binding site [nucleotide binding]; other site 557723001343 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557723001344 RNA binding site [nucleotide binding]; other site 557723001345 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 557723001346 RNA binding site [nucleotide binding]; other site 557723001347 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 557723001348 RNA binding site [nucleotide binding]; other site 557723001349 cytidylate kinase; Provisional; Region: cmk; PRK00023 557723001350 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 557723001351 CMP-binding site; other site 557723001352 The sites determining sugar specificity; other site 557723001353 serine endoprotease; Provisional; Region: PRK10898 557723001354 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 557723001355 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 557723001356 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 557723001357 active site 557723001358 tetramer interface; other site 557723001359 Global regulator protein family; Region: CsrA; cl00670 557723001360 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 557723001361 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 557723001362 motif 1; other site 557723001363 active site 557723001364 motif 2; other site 557723001365 motif 3; other site 557723001366 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 557723001367 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 557723001368 Ligand Binding Site [chemical binding]; other site 557723001369 ComEC family competence protein; Provisional; Region: PRK11539 557723001370 Competence protein; Region: Competence; cl00471 557723001371 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557723001372 YCII-related domain; Region: YCII; cl00999 557723001373 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 557723001374 Intracellular septation protein A; Region: IspA; cl01098 557723001375 Protein of unknown function, DUF412; Region: DUF412; cl01183 557723001376 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 557723001377 nucleoside/Zn binding site; other site 557723001378 dimer interface [polypeptide binding]; other site 557723001379 catalytic motif [active] 557723001380 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 557723001381 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 557723001382 ATP binding site [chemical binding]; other site 557723001383 Mg++ binding site [ion binding]; other site 557723001384 motif III; other site 557723001385 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 557723001386 nucleotide binding region [chemical binding]; other site 557723001387 ATP-binding site [chemical binding]; other site 557723001388 DbpA RNA binding domain; Region: DbpA; pfam03880 557723001389 lipoprotein NlpI; Provisional; Region: PRK11189 557723001390 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 557723001391 binding surface 557723001392 TPR motif; other site 557723001393 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 557723001394 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 557723001395 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 557723001396 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 557723001397 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 557723001398 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 557723001399 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 557723001400 putative nucleic acid binding region [nucleotide binding]; other site 557723001401 G-X-X-G motif; other site 557723001402 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 557723001403 RNA binding site [nucleotide binding]; other site 557723001404 domain interface; other site 557723001405 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 557723001406 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 557723001407 active site 557723001408 metal binding site [ion binding]; metal-binding site 557723001409 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 557723001410 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 557723001411 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 557723001412 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557723001413 putative active site [active] 557723001414 heme pocket [chemical binding]; other site 557723001415 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 557723001416 dimer interface [polypeptide binding]; other site 557723001417 phosphorylation site [posttranslational modification] 557723001418 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723001419 ATP binding site [chemical binding]; other site 557723001420 Mg2+ binding site [ion binding]; other site 557723001421 G-X-G motif; other site 557723001422 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557723001423 active site 557723001424 phosphorylation site [posttranslational modification] 557723001425 intermolecular recognition site; other site 557723001426 dimerization interface [polypeptide binding]; other site 557723001427 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 557723001428 putative binding surface; other site 557723001429 active site 557723001430 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 557723001431 OstA-like protein; Region: OstA; cl00844 557723001432 Organic solvent tolerance protein; Region: OstA_C; pfam04453 557723001433 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 557723001434 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 557723001435 FeS/SAM binding site; other site 557723001436 HemN C-terminal region; Region: HemN_C; pfam06969 557723001437 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 557723001438 Protein of unknown function, DUF414; Region: DUF414; cl01172 557723001439 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 557723001440 putative active site [active] 557723001441 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 557723001442 EamA-like transporter family; Region: EamA; cl01037 557723001443 EamA-like transporter family; Region: EamA; cl01037 557723001444 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 557723001445 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 557723001446 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 557723001447 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 557723001448 RNA binding site [nucleotide binding]; other site 557723001449 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 557723001450 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001451 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001452 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557723001453 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 557723001454 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 557723001455 E3 interaction surface; other site 557723001456 lipoyl attachment site [posttranslational modification]; other site 557723001457 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 557723001458 E3 interaction surface; other site 557723001459 lipoyl attachment site [posttranslational modification]; other site 557723001460 e3 binding domain; Region: E3_binding; pfam02817 557723001461 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 557723001462 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 557723001463 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 557723001464 dimer interface [polypeptide binding]; other site 557723001465 TPP-binding site [chemical binding]; other site 557723001466 AIR carboxylase; Region: AIRC; cl00310 557723001467 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 557723001468 active site 557723001469 homodimer interface [polypeptide binding]; other site 557723001470 homotetramer interface [polypeptide binding]; other site 557723001471 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 557723001472 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723001473 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 557723001474 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 557723001475 substrate binding site [chemical binding]; other site 557723001476 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 557723001477 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 557723001478 S-adenosylmethionine binding site [chemical binding]; other site 557723001479 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 557723001480 S-adenosylmethionine synthetase; Validated; Region: PRK05250 557723001481 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 557723001482 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 557723001483 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 557723001484 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723001485 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001486 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 557723001487 Uncharacterized conserved protein [Function unknown]; Region: COG0327 557723001488 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 557723001489 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 557723001490 dimer interface [polypeptide binding]; other site 557723001491 putative functional site; other site 557723001492 putative MPT binding site; other site 557723001493 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723001494 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723001495 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723001496 MarC family integral membrane protein; Region: MarC; cl00919 557723001497 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 557723001498 FtsH Extracellular; Region: FtsH_ext; pfam06480 557723001499 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 557723001500 Walker A motif; other site 557723001501 ATP binding site [chemical binding]; other site 557723001502 Walker B motif; other site 557723001503 arginine finger; other site 557723001504 Peptidase family M41; Region: Peptidase_M41; pfam01434 557723001505 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 557723001506 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 557723001507 S-adenosylmethionine binding site [chemical binding]; other site 557723001508 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 557723001509 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 557723001510 NAD binding site [chemical binding]; other site 557723001511 homotetramer interface [polypeptide binding]; other site 557723001512 homodimer interface [polypeptide binding]; other site 557723001513 substrate binding site [chemical binding]; other site 557723001514 active site 557723001515 Fic/DOC family; Region: Fic; cl00960 557723001516 Predicted transcriptional regulator [Transcription]; Region: COG2944 557723001517 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 557723001518 non-specific DNA binding site [nucleotide binding]; other site 557723001519 salt bridge; other site 557723001520 sequence-specific DNA binding site [nucleotide binding]; other site 557723001521 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 557723001522 exoribonuclease II; Provisional; Region: PRK05054 557723001523 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557723001524 RNB domain; Region: RNB; pfam00773 557723001525 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557723001526 RNA binding site [nucleotide binding]; other site 557723001527 murein transglycosylase A; Provisional; Region: mltA; PRK11162 557723001528 MltA specific insert domain; Region: MltA; cl08398 557723001529 3D domain; Region: 3D; cl01439 557723001530 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 557723001531 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557723001532 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 557723001533 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557723001534 DNA binding site [nucleotide binding] 557723001535 domain linker motif; other site 557723001536 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 557723001537 dimerization interface [polypeptide binding]; other site 557723001538 ligand binding site [chemical binding]; other site 557723001539 HemK family putative methylases; Region: hemK_fam; TIGR00536 557723001540 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 557723001541 S-adenosylmethionine binding site [chemical binding]; other site 557723001542 hypothetical protein; Provisional; Region: PRK04946 557723001543 Smr domain; Region: Smr; cl02619 557723001544 Amino acid permease; Region: AA_permease; cl00524 557723001545 Amino acid permease; Region: AA_permease; cl00524 557723001546 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 557723001547 catalytic residues [active] 557723001548 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 557723001549 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 557723001550 SelR domain; Region: SelR; cl00369 557723001551 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557723001552 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 557723001553 DNA binding residues [nucleotide binding] 557723001554 capsid-scaffolding protein; Provisional; Region: O; PHA02529 557723001555 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; pfam05929 557723001556 terminase endonuclease subunit; Provisional; Region: M; PHA02537 557723001557 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 557723001558 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 557723001559 catalytic residues [active] 557723001560 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 557723001561 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557723001562 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 557723001563 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 557723001564 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557723001565 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 557723001566 phage tail tape measure protein, lambda family; Region: tape_meas_lam_C; TIGR01541 557723001567 YcfA-like protein; Region: YcfA; cl00752 557723001568 Uncharacterised protein family (UPF0150); Region: UPF0150; cl00691 557723001569 ECF sigma factor; Region: Sigma70_ECF; pfam07638 557723001570 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 557723001571 NinB protein; Region: NinB; cl14671 557723001572 Replication protein P; Region: Phage_lambda_P; pfam06992 557723001573 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 557723001574 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 557723001575 non-specific DNA binding site [nucleotide binding]; other site 557723001576 salt bridge; other site 557723001577 sequence-specific DNA binding site [nucleotide binding]; other site 557723001578 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 557723001579 Catalytic site [active] 557723001580 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557723001581 YcfA-like protein; Region: YcfA; cl00752 557723001582 Uncharacterised protein family (UPF0150); Region: UPF0150; cl00691 557723001583 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 557723001584 Domain of unknown function (DUF3560); Region: DUF3560; pfam12083 557723001585 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 557723001586 active site 557723001587 RecT family; Region: RecT; cl04285 557723001588 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 557723001589 dimer interface [polypeptide binding]; other site 557723001590 ssDNA binding site [nucleotide binding]; other site 557723001591 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557723001592 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 557723001593 LexA regulated protein; Provisional; Region: PRK11675 557723001594 Phage-related protein, tail component [Function unknown]; Region: COG4733 557723001595 hypothetical protein; Validated; Region: PRK09039 557723001596 Domain of unknown function (DUF1983); Region: DUF1983; pfam09327 557723001597 Prophage antirepressor [Transcription]; Region: COG3617 557723001598 BRO family, N-terminal domain; Region: Bro-N; cl10591 557723001599 Bacteriophage lambda tail assembly protein I; Region: Lambda_tail_I; cl01945 557723001600 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; Region: MPN_NLPC_P60; cd08073 557723001601 MPN+ (JAMM) motif; other site 557723001602 Zinc-binding site [ion binding]; other site 557723001603 NlpC/P60 family; Region: NLPC_P60; cl11438 557723001604 Phage minor tail protein L; Region: Phage_tail_L; cl01908 557723001605 Phage minor tail protein; Region: Phage_min_tail; cl01940 557723001606 tape measure domain; Region: tape_meas_nterm; TIGR02675 557723001607 Phage-related minor tail protein [Function unknown]; Region: COG5281 557723001608 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 557723001609 RelB antitoxin; Region: RelB; cl01171 557723001610 Phage minor tail protein U; Region: Phage_tail_U; pfam06141 557723001611 Prophage minor tail protein Z (GPZ); Region: Minor_tail_Z; pfam06763 557723001612 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 557723001613 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 557723001614 oligomer interface [polypeptide binding]; other site 557723001615 active site residues [active] 557723001616 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 557723001617 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 557723001618 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 557723001619 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 557723001620 Protein of unknown function (DUF1441); Region: DUF1441; pfam07278 557723001621 Protein of unknown function (DUF2570); Region: DUF2570; pfam10828 557723001622 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 557723001623 catalytic residues [active] 557723001624 ECF sigma factor; Region: Sigma70_ECF; pfam07638 557723001625 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 557723001626 NinB protein; Region: NinB; cl14671 557723001627 Replication protein P; Region: Phage_lambda_P; pfam06992 557723001628 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 557723001629 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 557723001630 non-specific DNA binding site [nucleotide binding]; other site 557723001631 Predicted transcriptional regulator [Transcription]; Region: COG2932 557723001632 salt bridge; other site 557723001633 sequence-specific DNA binding site [nucleotide binding]; other site 557723001634 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 557723001635 Catalytic site [active] 557723001636 KilA-N domain; Region: KilA-N; pfam04383 557723001637 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723001638 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 557723001639 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 557723001640 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723001641 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 557723001642 Domain of unknown function (DUF3560); Region: DUF3560; pfam12083 557723001643 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 557723001644 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 557723001645 active site 557723001646 metal binding site [ion binding]; metal-binding site 557723001647 lytic murein transglycosylase; Region: MltB_2; TIGR02283 557723001648 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557723001649 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 557723001650 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 557723001651 RNA binding site [nucleotide binding]; other site 557723001652 active site 557723001653 Ribosome-binding factor A; Region: RBFA; cl00542 557723001654 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 557723001655 putative active site [active] 557723001656 catalytic triad [active] 557723001657 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 557723001658 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; cl15373 557723001659 Autotransporter beta-domain; Region: Autotransporter; cl02365 557723001660 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 557723001661 5S rRNA interface [nucleotide binding]; other site 557723001662 CTC domain interface [polypeptide binding]; other site 557723001663 L16 interface [polypeptide binding]; other site 557723001664 glycogen phosphorylase; Provisional; Region: PRK14986 557723001665 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 557723001666 homodimer interface [polypeptide binding]; other site 557723001667 active site pocket [active] 557723001668 LysE type translocator; Region: LysE; cl00565 557723001669 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 557723001670 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 557723001671 TPP-binding site [chemical binding]; other site 557723001672 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 557723001673 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 557723001674 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 557723001675 E3 interaction surface; other site 557723001676 lipoyl attachment site [posttranslational modification]; other site 557723001677 e3 binding domain; Region: E3_binding; pfam02817 557723001678 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 557723001679 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 557723001680 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723001681 CoA-ligase; Region: Ligase_CoA; pfam00549 557723001682 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 557723001683 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001684 CoA-ligase; Region: Ligase_CoA; pfam00549 557723001685 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 557723001686 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557723001687 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001688 seryl-tRNA synthetase; Provisional; Region: PRK05431 557723001689 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 557723001690 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 557723001691 dimer interface [polypeptide binding]; other site 557723001692 active site 557723001693 motif 1; other site 557723001694 motif 2; other site 557723001695 motif 3; other site 557723001696 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 557723001697 putative active site [active] 557723001698 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 557723001699 SmpB-tmRNA interface; other site 557723001700 YcjX-like family, DUF463; Region: DUF463; cl01193 557723001701 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001702 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 557723001703 selenophosphate synthetase; Provisional; Region: PRK00943 557723001704 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 557723001705 dimerization interface [polypeptide binding]; other site 557723001706 putative ATP binding site [chemical binding]; other site 557723001707 Domain of unknown function; Region: DUF331; cl01149 557723001708 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 557723001709 S-adenosylmethionine binding site [chemical binding]; other site 557723001710 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 557723001711 Domain of unknown function DUF20; Region: UPF0118; cl00465 557723001712 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 557723001713 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 557723001714 formate dehydrogenase accessory protein FdhE; Provisional; Region: PRK03564; cl11689 557723001715 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 557723001716 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 557723001717 Sulfatase; Region: Sulfatase; cl10460 557723001718 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 557723001719 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 557723001720 MOSC domain; Region: MOSC; pfam03473 557723001721 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 557723001722 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 557723001723 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 557723001724 substrate binding pocket [chemical binding]; other site 557723001725 chain length determination region; other site 557723001726 substrate-Mg2+ binding site; other site 557723001727 catalytic residues [active] 557723001728 aspartate-rich region 1; other site 557723001729 active site lid residues [active] 557723001730 aspartate-rich region 2; other site 557723001731 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339; cl15420 557723001732 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 557723001733 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 557723001734 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 557723001735 substrate binding site [chemical binding]; other site 557723001736 oxyanion hole (OAH) forming residues; other site 557723001737 trimer interface [polypeptide binding]; other site 557723001738 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723001739 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557723001740 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 557723001741 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557723001742 dimer interface [polypeptide binding]; other site 557723001743 active site 557723001744 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 557723001745 iron-sulfur cluster-binding protein; Region: TIGR00273 557723001746 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 557723001747 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 557723001748 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 557723001749 Cysteine-rich domain; Region: CCG; pfam02754 557723001750 Cysteine-rich domain; Region: CCG; pfam02754 557723001751 L-lactate permease; Region: Lactate_perm; cl00701 557723001752 glycolate transporter; Provisional; Region: PRK09695 557723001753 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 557723001754 folate binding site [chemical binding]; other site 557723001755 NADP+ binding site [chemical binding]; other site 557723001756 gamma-glutamyl kinase; Provisional; Region: PRK05429 557723001757 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 557723001758 nucleotide binding site [chemical binding]; other site 557723001759 homotetrameric interface [polypeptide binding]; other site 557723001760 putative phosphate binding site [ion binding]; other site 557723001761 putative allosteric binding site; other site 557723001762 PUA domain; Region: PUA; cl00607 557723001763 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557723001764 endonuclease III; Provisional; Region: PRK10702 557723001765 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557723001766 minor groove reading motif; other site 557723001767 helix-hairpin-helix signature motif; other site 557723001768 substrate binding pocket [chemical binding]; other site 557723001769 active site 557723001770 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 557723001771 SH3 domain protein [Signal transduction mechanisms]; Region: COG3103 557723001772 Bacterial SH3 domain; Region: SH3_3; cl02551 557723001773 Phosphate transporter family; Region: PHO4; cl00396 557723001774 Phosphate transporter family; Region: PHO4; cl00396 557723001775 Protein of unknown function DUF47; Region: PhoU_div; pfam01865 557723001776 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 557723001777 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 557723001778 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 557723001779 dimer interface [polypeptide binding]; other site 557723001780 motif 1; other site 557723001781 active site 557723001782 motif 2; other site 557723001783 motif 3; other site 557723001784 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 557723001785 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 557723001786 putative tRNA-binding site [nucleotide binding]; other site 557723001787 B3/4 domain; Region: B3_4; cl11458 557723001788 tRNA synthetase B5 domain; Region: B5; cl08394 557723001789 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 557723001790 dimer interface [polypeptide binding]; other site 557723001791 motif 1; other site 557723001792 motif 3; other site 557723001793 motif 2; other site 557723001794 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 557723001795 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 557723001796 IHF dimer interface [polypeptide binding]; other site 557723001797 IHF - DNA interface [nucleotide binding]; other site 557723001798 NlpC/P60 family; Region: NLPC_P60; cl11438 557723001799 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 557723001800 Sugar specificity; other site 557723001801 Pyrimidine base specificity; other site 557723001802 ATP-binding site [chemical binding]; other site 557723001803 2'-deoxycytidine 5'-triphosphate deaminase (DCD); Region: DCD; pfam06559 557723001804 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 557723001805 trimer interface [polypeptide binding]; other site 557723001806 active site 557723001807 amidophosphoribosyltransferase; Provisional; Region: PRK09246 557723001808 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 557723001809 active site 557723001810 tetramer interface [polypeptide binding]; other site 557723001811 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723001812 Colicin V production protein; Region: Colicin_V; cl00567 557723001813 L-aspartate oxidase; Region: nadB; TIGR00551 557723001814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001815 domain; Region: Succ_DH_flav_C; pfam02910 557723001816 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 557723001817 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 557723001818 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 557723001819 homotrimer interaction site [polypeptide binding]; other site 557723001820 putative active site [active] 557723001821 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 557723001822 Nucleoid-associated protein [General function prediction only]; Region: COG3081 557723001823 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 557723001824 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 557723001825 Uncharacterised protein family (UPF0075); Region: UPF0075; cl04217 557723001826 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 557723001827 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 557723001828 putative active site [active] 557723001829 Domain of unknown function, DUF446; Region: DUF446; cl01187 557723001830 tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not...; Region: PseudoU_synth_TruC; cd02563 557723001831 probable active site [active] 557723001832 Uncharacterised protein family (UPF0181); Region: UPF0181; cl11477 557723001833 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl03735 557723001834 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 557723001835 putative coenzyme Q binding site [chemical binding]; other site 557723001836 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 557723001837 homotrimer interaction site [polypeptide binding]; other site 557723001838 zinc binding site [ion binding]; other site 557723001839 CDP-binding sites; other site 557723001840 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 557723001841 substrate binding site; other site 557723001842 dimer interface; other site 557723001843 Septum formation initiator; Region: DivIC; cl11433 557723001844 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 557723001845 active site 557723001846 substrate-binding site [chemical binding]; other site 557723001847 metal-binding site [ion binding] 557723001848 ATP binding site [chemical binding]; other site 557723001849 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 557723001850 putative active site [active] 557723001851 putative metal binding residues [ion binding]; other site 557723001852 signature motif; other site 557723001853 putative triphosphate binding site [ion binding]; other site 557723001854 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseA; COG3073 557723001855 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 557723001856 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 557723001857 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 557723001858 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557723001859 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 557723001860 DNA binding residues [nucleotide binding] 557723001861 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 557723001862 HsdM N-terminal domain; Region: HsdM_N; pfam12161 557723001863 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723001864 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 557723001865 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723001866 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723001867 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 557723001868 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 557723001869 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 557723001870 ATP binding site [chemical binding]; other site 557723001871 putative Mg++ binding site [ion binding]; other site 557723001872 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 557723001873 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 557723001874 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 557723001875 putative active site [active] 557723001876 catalytic triad [active] 557723001877 putative dimer interface [polypeptide binding]; other site 557723001878 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 557723001879 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 557723001880 Transporter associated domain; Region: CorC_HlyC; cl08393 557723001881 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 557723001882 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 557723001883 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 557723001884 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 557723001885 Protein of unknown function (DUF3791); Region: DUF3791; pfam12668 557723001886 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 557723001887 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 557723001888 synthetase active site [active] 557723001889 NTP binding site [chemical binding]; other site 557723001890 metal binding site [ion binding]; metal-binding site 557723001891 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 557723001892 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 557723001893 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 557723001894 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 557723001895 tRNA; other site 557723001896 putative tRNA binding site [nucleotide binding]; other site 557723001897 putative NADP binding site [chemical binding]; other site 557723001898 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 557723001899 GTP-binding protein Der; Reviewed; Region: PRK00093 557723001900 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA1; cd01894 557723001901 G1 box; other site 557723001902 GTP/Mg2+ binding site [chemical binding]; other site 557723001903 Switch I region; other site 557723001904 G2 box; other site 557723001905 Switch II region; other site 557723001906 G3 box; other site 557723001907 G4 box; other site 557723001908 G5 box; other site 557723001909 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA2; cd01895 557723001910 G1 box; other site 557723001911 GTP/Mg2+ binding site [chemical binding]; other site 557723001912 Switch I region; other site 557723001913 G2 box; other site 557723001914 G3 box; other site 557723001915 Switch II region; other site 557723001916 G4 box; other site 557723001917 G5 box; other site 557723001918 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 557723001919 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 557723001920 putative ribose interaction site [chemical binding]; other site 557723001921 putative ADP binding site [chemical binding]; other site 557723001922 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557723001923 active site 557723001924 nucleotide binding site [chemical binding]; other site 557723001925 HIGH motif; other site 557723001926 KMSKS motif; other site 557723001927 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 557723001928 SurA N-terminal domain; Region: SurA_N; pfam09312 557723001929 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557723001930 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723001931 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 557723001932 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 557723001933 hinge; other site 557723001934 active site 557723001935 BolA-like protein; Region: BolA; cl00386 557723001936 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 557723001937 anti sigma factor interaction site; other site 557723001938 regulatory phosphorylation site [posttranslational modification]; other site 557723001939 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 557723001940 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 557723001941 mce related protein; Region: MCE; cl15431 557723001942 Domain of unknown function DUF140; Region: DUF140; cl00510 557723001943 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 557723001944 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 557723001945 Walker A/P-loop; other site 557723001946 ATP binding site [chemical binding]; other site 557723001947 Q-loop/lid; other site 557723001948 ABC transporter signature motif; other site 557723001949 Walker B; other site 557723001950 D-loop; other site 557723001951 H-loop/switch region; other site 557723001952 BON domain; Region: BON; cl02771 557723001953 BON domain; Region: BON; cl02771 557723001954 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 557723001955 dimer interface [polypeptide binding]; other site 557723001956 active site 557723001957 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 557723001958 LppC putative lipoprotein; Region: LppC; pfam04348 557723001959 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 557723001960 putative ligand binding site [chemical binding]; other site 557723001961 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 557723001962 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 557723001963 Ferritin-like domain; Region: Ferritin; pfam00210 557723001964 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 557723001965 dimerization interface [polypeptide binding]; other site 557723001966 DPS ferroxidase diiron center [ion binding]; other site 557723001967 ion pore; other site 557723001968 Protein of unknown function DUF72; Region: DUF72; cl00777 557723001969 Autotransporter beta-domain; Region: Autotransporter; cl02365 557723001970 adenylosuccinate lyase; Provisional; Region: PRK09285 557723001971 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 557723001972 tetramer interface [polypeptide binding]; other site 557723001973 active site 557723001974 glycerate dehydrogenase; Provisional; Region: PRK06932 557723001975 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723001976 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 557723001977 E-class dimer interface [polypeptide binding]; other site 557723001978 P-class dimer interface [polypeptide binding]; other site 557723001979 active site 557723001980 Cu2+ binding site [ion binding]; other site 557723001981 Zn2+ binding site [ion binding]; other site 557723001982 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 557723001983 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 557723001984 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 557723001985 Uncharacterized phage-associated protein [Function unknown]; Region: GepA; COG3600 557723001986 GTP-binding protein YchF; Reviewed; Region: PRK09601 557723001987 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 557723001988 G1 box; other site 557723001989 GTP/Mg2+ binding site [chemical binding]; other site 557723001990 Switch I region; other site 557723001991 G2 box; other site 557723001992 Switch II region; other site 557723001993 G3 box; other site 557723001994 G4 box; other site 557723001995 G5 box; other site 557723001996 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 557723001997 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 557723001998 putative active site [active] 557723001999 catalytic residue [active] 557723002000 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557723002001 Dehydratase family; Region: ILVD_EDD; cl00340 557723002002 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3514 557723002003 Protein of unknown function (DUF497); Region: DUF497; cl01108 557723002004 Domain of unknown function (DUF927); Region: DUF927; cl12098 557723002005 Terminase small subunit; Region: Terminase_2; cl01513 557723002006 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557723002007 integrase; Provisional; Region: PRK09692 557723002008 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 557723002009 active site 557723002010 Int/Topo IB signature motif; other site 557723002011 UbiA prenyltransferase family; Region: UbiA; cl00337 557723002012 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 557723002013 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723002014 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557723002015 NeuB family; Region: NeuB; cl00496 557723002016 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557723002017 hypothetical protein; Provisional; Region: PRK10941 557723002018 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 557723002019 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 557723002020 R.HinP1I restriction endonuclease; Region: R-HINP1I; pfam11463 557723002021 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 557723002022 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 557723002023 cofactor binding site; other site 557723002024 DNA binding site [nucleotide binding] 557723002025 substrate interaction site [chemical binding]; other site 557723002026 peptide chain release factor 1; Validated; Region: prfA; PRK00591 557723002027 RF-1 domain; Region: RF-1; cl02875 557723002028 RF-1 domain; Region: RF-1; cl02875 557723002029 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 557723002030 IHF dimer interface [polypeptide binding]; other site 557723002031 IHF - DNA interface [nucleotide binding]; other site 557723002032 Protein of unknown function (DUF416); Region: DUF416; cl01166 557723002033 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 557723002034 substrate binding site [chemical binding]; other site 557723002035 active site 557723002036 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 557723002037 active site 557723002038 phosphate binding residues; other site 557723002039 catalytic residues [active] 557723002040 argininosuccinate lyase; Provisional; Region: PRK04833 557723002041 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 557723002042 active sites [active] 557723002043 tetramer interface [polypeptide binding]; other site 557723002044 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 557723002045 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required...; Region: ABC_PotA_N; cd03300 557723002046 Walker A/P-loop; other site 557723002047 ATP binding site [chemical binding]; other site 557723002048 Q-loop/lid; other site 557723002049 ABC transporter signature motif; other site 557723002050 Walker B; other site 557723002051 D-loop; other site 557723002052 H-loop/switch region; other site 557723002053 TOBE domain; Region: TOBE_2; cl01440 557723002054 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 557723002055 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 557723002056 dimer interface [polypeptide binding]; other site 557723002057 conserved gate region; other site 557723002058 putative PBP binding loops; other site 557723002059 ABC-ATPase subunit interface; other site 557723002060 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 557723002061 dimer interface [polypeptide binding]; other site 557723002062 conserved gate region; other site 557723002063 putative PBP binding loops; other site 557723002064 ABC-ATPase subunit interface; other site 557723002065 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 557723002066 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 557723002067 dimer interface [polypeptide binding]; other site 557723002068 motif 1; other site 557723002069 active site 557723002070 motif 2; other site 557723002071 motif 3; other site 557723002072 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 557723002073 anticodon binding site; other site 557723002074 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 557723002075 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 557723002076 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 557723002077 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002078 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 557723002079 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 557723002080 putative substrate translocation pore; other site 557723002081 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 557723002082 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723002083 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 557723002084 amidase catalytic site [active] 557723002085 Zn binding residues [ion binding]; other site 557723002086 substrate binding site [chemical binding]; other site 557723002087 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 557723002088 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 557723002089 active site 557723002090 DNA polymerase IV; Validated; Region: PRK02406 557723002091 DNA binding site [nucleotide binding] 557723002092 Peptidase family M48; Region: Peptidase_M48; cl12018 557723002093 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 557723002094 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 557723002095 GIY-YIG motif/motif A; other site 557723002096 active site 557723002097 catalytic site [active] 557723002098 putative DNA binding site [nucleotide binding]; other site 557723002099 metal binding site [ion binding]; metal-binding site 557723002100 UvrB/uvrC motif; Region: UVR; pfam02151 557723002101 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 557723002102 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 557723002103 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 557723002104 dimer interface [polypeptide binding]; other site 557723002105 conserved gate region; other site 557723002106 putative PBP binding loops; other site 557723002107 ABC-ATPase subunit interface; other site 557723002108 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 557723002109 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002110 Walker A/P-loop; other site 557723002111 ATP binding site [chemical binding]; other site 557723002112 Q-loop/lid; other site 557723002113 ABC transporter signature motif; other site 557723002114 Walker B; other site 557723002115 D-loop; other site 557723002116 H-loop/switch region; other site 557723002117 TOBE domain; Region: TOBE_2; cl01440 557723002118 superoxide dismutase; Provisional; Region: PRK10925 557723002119 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 557723002120 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 557723002121 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557723002122 GIY-YIG domain of uncharacterized proteins from bacteria and their eukaryotic homologs; Region: GIY-YIG_COG3680; cd10440 557723002123 GIY-YIG motif/motif A; other site 557723002124 putative active site [active] 557723002125 putative metal binding site [ion binding]; other site 557723002126 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 557723002127 non-specific DNA binding site [nucleotide binding]; other site 557723002128 salt bridge; other site 557723002129 sequence-specific DNA binding site [nucleotide binding]; other site 557723002130 integrase; Provisional; Region: PRK09692 557723002131 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 557723002132 active site 557723002133 Int/Topo IB signature motif; other site 557723002134 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723002135 transcription termination factor Rho; Provisional; Region: rho; PRK09376 557723002136 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 557723002137 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 557723002138 RNA binding site [nucleotide binding]; other site 557723002139 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 557723002140 multimer interface [polypeptide binding]; other site 557723002141 Walker A motif; other site 557723002142 ATP binding site [chemical binding]; other site 557723002143 Walker B motif; other site 557723002144 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 557723002145 RNA binding surface [nucleotide binding]; other site 557723002146 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 557723002147 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 557723002148 dimerization interface [polypeptide binding]; other site 557723002149 domain crossover interface; other site 557723002150 redox-dependent activation switch; other site 557723002151 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 557723002152 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 557723002153 active site 557723002154 substrate binding site [chemical binding]; other site 557723002155 catalytic site [active] 557723002156 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002157 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 557723002158 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 557723002159 Transposase IS200 like; Region: Y1_Tnp; cl00848 557723002160 Protein of unknown function (DUF1304); Region: DUF1304; cl01533 557723002161 Protein of unknown function (DUF1016); Region: DUF1016; cl01979 557723002162 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 557723002163 putative active site [active] 557723002164 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 557723002165 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 557723002166 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 557723002167 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 cysteine...; Region: CysQ; cd01638 557723002168 active site 557723002169 RF-1 domain; Region: RF-1; cl02875 557723002170 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 557723002171 RF-1 domain; Region: RF-1; cl02875 557723002172 tRNA mo(5)U34 methyltransferase; Provisional; Region: PRK15068 557723002173 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 557723002174 S-adenosylmethionine binding site [chemical binding]; other site 557723002175 Transposase [DNA replication, recombination, and repair]; Region: COG5433 557723002176 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 557723002177 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 557723002178 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 557723002179 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 557723002180 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 557723002181 putative active site [active] 557723002182 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557723002183 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 557723002184 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 557723002185 active site 557723002186 substrate binding site [chemical binding]; other site 557723002187 metal binding site [ion binding]; metal-binding site 557723002188 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 557723002189 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 557723002190 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557723002191 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 557723002192 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 557723002193 substrate binding pocket [chemical binding]; other site 557723002194 chain length determination region; other site 557723002195 substrate-Mg2+ binding site; other site 557723002196 catalytic residues [active] 557723002197 aspartate-rich region 1; other site 557723002198 active site lid residues [active] 557723002199 aspartate-rich region 2; other site 557723002200 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 557723002201 Acyl transferase domain; Region: Acyl_transf_1; cl08282 557723002202 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 557723002203 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 557723002204 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 557723002205 NAD(P) binding site [chemical binding]; other site 557723002206 homotetramer interface [polypeptide binding]; other site 557723002207 homodimer interface [polypeptide binding]; other site 557723002208 active site 557723002209 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 557723002210 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 557723002211 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 557723002212 DNA binding site [nucleotide binding] 557723002213 catalytic residue [active] 557723002214 H2TH interface [polypeptide binding]; other site 557723002215 putative catalytic residues [active] 557723002216 turnover-facilitating residue; other site 557723002217 intercalation triad [nucleotide binding]; other site 557723002218 8OG recognition residue [nucleotide binding]; other site 557723002219 putative reading head residues; other site 557723002220 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 557723002221 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 557723002222 Mor transcription activator family; Region: Mor; cl02360 557723002223 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 557723002224 Bacteriophage Mu Gam like protein; Region: Phage_Mu_Gam; cl01825 557723002225 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 557723002226 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002227 Integrase core domain; Region: rve; cl01316 557723002228 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723002229 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 557723002230 Predicted lysozyme (DUF847); Region: DUF847; pfam05838 557723002231 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 557723002232 Protein of unknown function (DUF2644); Region: DUF2644; pfam10841 557723002233 Protein of unknown function (DUF2681); Region: DUF2681; pfam10883 557723002234 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 557723002235 Ribonuclease R winged-helix domain; Region: HTH_12; pfam08461 557723002236 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 557723002237 Terminase-like family; Region: Terminase_6; pfam03237 557723002238 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 557723002239 Protein of unknown function (DUF935); Region: DUF935; cl15409 557723002240 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 557723002241 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 557723002242 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 557723002243 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 557723002244 Gp37 protein; Region: Gp37; pfam09646 557723002245 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 557723002246 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 557723002247 Phage tail tube protein FII; Region: Phage_tube; cl01390 557723002248 Phage P2 GpE; Region: Phage_P2_GpE; pfam06528 557723002249 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 557723002250 Phage-related protein [Function unknown]; Region: COG5412 557723002251 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 557723002252 Phage Tail Protein X; Region: Phage_tail_X; cl02088 557723002253 Phage protein D [General function prediction only]; Region: COG3500; cl12180 557723002254 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 557723002255 Phage P2 baseplate assembly protein gpV [General function prediction only]; Region: gpV; COG4540 557723002256 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557723002257 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557723002258 Baseplate J-like protein; Region: Baseplate_J; cl01294 557723002259 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 557723002260 Phage tail fibre repeat; Region: Phage_fiber_2; pfam03406 557723002261 Tail fiber protein gp37 C terminal; Region: gp37_C; pfam12604 557723002262 Phage-related protein, tail component [Function unknown]; Region: COG4733 557723002263 Domain of unknown function (DUF1983); Region: DUF1983; pfam09327 557723002264 Transferrin binding protein-like solute binding protein; Region: Lipoprotein_5; pfam01298 557723002265 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 557723002266 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 557723002267 metal binding site [ion binding]; metal-binding site 557723002268 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 557723002269 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 557723002270 domain interface [polypeptide binding]; other site 557723002271 putative active site [active] 557723002272 catalytic site [active] 557723002273 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 557723002274 domain interface [polypeptide binding]; other site 557723002275 putative active site [active] 557723002276 catalytic site [active] 557723002277 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 557723002278 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557723002279 active site 557723002280 HIGH motif; other site 557723002281 nucleotide binding site [chemical binding]; other site 557723002282 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 557723002283 active site 557723002284 KMSKS motif; other site 557723002285 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 557723002286 tRNA binding surface [nucleotide binding]; other site 557723002287 anticodon binding site; other site 557723002288 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 557723002289 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002290 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 557723002291 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 557723002292 active site 557723002293 Riboflavin kinase; Region: Flavokinase; cl03312 557723002294 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 557723002295 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 557723002296 dimerization interface [polypeptide binding]; other site 557723002297 putative ATP binding site [chemical binding]; other site 557723002298 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723002299 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723002300 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723002301 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 557723002302 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 557723002303 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 557723002304 RNA binding surface [nucleotide binding]; other site 557723002305 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 557723002306 active site 557723002307 BolA-like protein; Region: BolA; cl00386 557723002308 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 557723002309 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 557723002310 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 557723002311 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 557723002312 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557723002313 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 557723002314 TRAM domain; Region: TRAM; cl01282 557723002315 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 557723002316 S-adenosylmethionine binding site [chemical binding]; other site 557723002317 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557723002318 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557723002319 peptide binding site [polypeptide binding]; other site 557723002320 dipeptide transporter permease DppB; Provisional; Region: PRK10914 557723002321 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 557723002322 dimer interface [polypeptide binding]; other site 557723002323 conserved gate region; other site 557723002324 putative PBP binding loops; other site 557723002325 ABC-ATPase subunit interface; other site 557723002326 dipeptide transporter; Provisional; Region: PRK10913 557723002327 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 557723002328 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 557723002329 dimer interface [polypeptide binding]; other site 557723002330 conserved gate region; other site 557723002331 putative PBP binding loops; other site 557723002332 ABC-ATPase subunit interface; other site 557723002333 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 557723002334 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723002335 Walker A/P-loop; other site 557723002336 ATP binding site [chemical binding]; other site 557723002337 Q-loop/lid; other site 557723002338 ABC transporter signature motif; other site 557723002339 Walker B; other site 557723002340 D-loop; other site 557723002341 H-loop/switch region; other site 557723002342 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723002343 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 557723002344 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723002345 Walker A/P-loop; other site 557723002346 ATP binding site [chemical binding]; other site 557723002347 Q-loop/lid; other site 557723002348 ABC transporter signature motif; other site 557723002349 Walker B; other site 557723002350 D-loop; other site 557723002351 H-loop/switch region; other site 557723002352 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723002353 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 557723002354 active site 557723002355 putative DNA-binding cleft [nucleotide binding]; other site 557723002356 dimer interface [polypeptide binding]; other site 557723002357 Domain of unknown function DUF28; Region: DUF28; cl00361 557723002358 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 557723002359 nudix motif; other site 557723002360 Outer membrane efflux protein; Region: OEP; pfam02321 557723002361 dihydropteroate synthase; Region: DHPS; TIGR01496 557723002362 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 557723002363 substrate binding pocket [chemical binding]; other site 557723002364 dimer interface [polypeptide binding]; other site 557723002365 inhibitor binding site; inhibition site 557723002366 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 557723002367 ArsC family; Region: ArsC; pfam03960 557723002368 putative catalytic residues [active] 557723002369 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 557723002370 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 557723002371 CoA-binding site [chemical binding]; other site 557723002372 ATP-binding [chemical binding]; other site 557723002373 Domain of unknown function (DUF329); Region: DUF329; cl01144 557723002374 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 557723002375 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 557723002376 Lipopolysaccharide-assembly; Region: LptE; cl01125 557723002377 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 557723002378 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 557723002379 HIGH motif; other site 557723002380 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557723002381 active site 557723002382 KMSKS motif; other site 557723002383 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 557723002384 tRNA binding surface [nucleotide binding]; other site 557723002385 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723002386 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 557723002387 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 557723002388 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 557723002389 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 557723002390 active site 557723002391 dimer interface [polypeptide binding]; other site 557723002392 motif 1; other site 557723002393 motif 2; other site 557723002394 motif 3; other site 557723002395 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 557723002396 anticodon binding site; other site 557723002397 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 557723002398 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 557723002399 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 557723002400 FeS/SAM binding site; other site 557723002401 TRAM domain; Region: TRAM; cl01282 557723002402 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_glc; cl00162 557723002403 HPr interaction site; other site 557723002404 glycerol kinase (GK) interaction site [polypeptide binding]; other site 557723002405 active site 557723002406 phosphorylation site [posttranslational modification] 557723002407 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 557723002408 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 557723002409 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 557723002410 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557723002411 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 557723002412 dimerization domain swap beta strand [polypeptide binding]; other site 557723002413 regulatory protein interface [polypeptide binding]; other site 557723002414 active site 557723002415 regulatory phosphorylation site [posttranslational modification]; other site 557723002416 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 557723002417 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002418 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 557723002419 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 557723002420 C2 domain; Region: C2; cl14603 557723002421 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 557723002422 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 557723002423 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 557723002424 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 557723002425 Protein export membrane protein; Region: SecD_SecF; cl14618 557723002426 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 557723002427 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 557723002428 Protein export membrane protein; Region: SecD_SecF; cl14618 557723002429 Preprotein translocase subunit; Region: YajC; cl00806 557723002430 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; cl01158 557723002431 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 557723002432 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 557723002433 Ligand Binding Site [chemical binding]; other site 557723002434 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 557723002435 catalytic core [active] 557723002436 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 557723002437 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 557723002438 Ligand binding site; other site 557723002439 oligomer interface; other site 557723002440 Protein of unknown function, DUF462; Region: DUF462; cl01190 557723002441 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 557723002442 putative FMN binding site [chemical binding]; other site 557723002443 transketolase; Reviewed; Region: PRK12753 557723002444 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 557723002445 TPP-binding site [chemical binding]; other site 557723002446 dimer interface [polypeptide binding]; other site 557723002447 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 557723002448 PYR/PP interface [polypeptide binding]; other site 557723002449 dimer interface [polypeptide binding]; other site 557723002450 TPP binding site [chemical binding]; other site 557723002451 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557723002452 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 557723002453 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 557723002454 putative active site [active] 557723002455 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557723002456 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 557723002457 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 557723002458 NAD binding site [chemical binding]; other site 557723002459 substrate binding site [chemical binding]; other site 557723002460 homodimer interface [polypeptide binding]; other site 557723002461 active site 557723002462 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002463 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 557723002464 NAD(P) binding site [chemical binding]; other site 557723002465 active site 557723002466 arginine repressor; Provisional; Region: PRK05066 557723002467 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 557723002468 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 557723002469 malate dehydrogenase; Provisional; Region: PRK05086 557723002470 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 557723002471 NAD binding site [chemical binding]; other site 557723002472 dimerization interface [polypeptide binding]; other site 557723002473 Substrate binding site [chemical binding]; other site 557723002474 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 557723002475 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 557723002476 thioredoxin reductase; Provisional; Region: PRK10262 557723002477 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002478 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 557723002479 putative metal binding site; other site 557723002480 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 557723002481 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 557723002482 adenylate cyclase; Provisional; Region: cyaA; PRK09450 557723002483 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 557723002484 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 557723002485 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557723002486 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002487 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 557723002488 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 557723002489 Walker A motif; other site 557723002490 ATP binding site [chemical binding]; other site 557723002491 Walker B motif; other site 557723002492 arginine finger; other site 557723002493 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 557723002494 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 557723002495 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 557723002496 peptide binding site [polypeptide binding]; other site 557723002497 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 557723002498 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 557723002499 dimer interface [polypeptide binding]; other site 557723002500 conserved gate region; other site 557723002501 putative PBP binding loops; other site 557723002502 ABC-ATPase subunit interface; other site 557723002503 oligopeptide ABC transporter permease OppC; Provisional; Region: PRK15406 557723002504 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 557723002505 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 557723002506 dimer interface [polypeptide binding]; other site 557723002507 conserved gate region; other site 557723002508 ABC-ATPase subunit interface; other site 557723002509 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 557723002510 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723002511 Walker A/P-loop; other site 557723002512 ATP binding site [chemical binding]; other site 557723002513 Q-loop/lid; other site 557723002514 ABC transporter signature motif; other site 557723002515 Walker B; other site 557723002516 D-loop; other site 557723002517 H-loop/switch region; other site 557723002518 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723002519 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723002520 Walker A/P-loop; other site 557723002521 ATP binding site [chemical binding]; other site 557723002522 Q-loop/lid; other site 557723002523 ABC transporter signature motif; other site 557723002524 Walker B; other site 557723002525 D-loop; other site 557723002526 H-loop/switch region; other site 557723002527 ABC transporter ATPase component; Reviewed; Region: PRK11147 557723002528 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002529 Walker A/P-loop; other site 557723002530 ATP binding site [chemical binding]; other site 557723002531 ABC transporter signature motif; other site 557723002532 Walker B; other site 557723002533 D-loop; other site 557723002534 H-loop/switch region; other site 557723002535 ABC transporter; Region: ABC_tran_2; pfam12848 557723002536 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557723002537 transcriptional regulator MalT; Provisional; Region: PRK04841 557723002538 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 557723002539 DNA binding residues [nucleotide binding] 557723002540 dimerization interface [polypeptide binding]; other site 557723002541 Protein of unknown function, DUF440; Region: DUF440; cl11472 557723002542 hemY protein; Region: hemY_coli; TIGR00540 557723002543 HemY protein N-terminus; Region: HemY_N; pfam07219 557723002544 ribonuclease E; Reviewed; Region: rne; PRK10811 557723002545 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemX; COG2959 557723002546 HemX; Region: HemX; cl14667 557723002547 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 557723002548 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 557723002549 active site 557723002550 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 557723002551 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 557723002552 domain interfaces; other site 557723002553 active site 557723002554 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 557723002555 PTS system, sucrose-specific IIBC component; Region: PTS-II-BC-sucr; TIGR01996 557723002556 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 557723002557 active site turn [active] 557723002558 phosphorylation site [posttranslational modification] 557723002559 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 557723002560 protease3; Provisional; Region: PRK15101 557723002561 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 557723002562 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557723002563 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557723002564 Protein of unknown function (DUF489); Region: DUF489; cl01097 557723002565 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 557723002566 Found in ATP-dependent protease La (LON); Region: LON; smart00464 557723002567 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 557723002568 Walker A motif; other site 557723002569 ATP binding site [chemical binding]; other site 557723002570 Walker B motif; other site 557723002571 arginine finger; other site 557723002572 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 557723002573 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723002574 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 557723002575 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 557723002576 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 557723002577 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002578 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002579 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002580 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723002581 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 557723002582 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723002583 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 557723002584 putative dimerization interface [polypeptide binding]; other site 557723002585 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 557723002586 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 557723002587 putative active site [active] 557723002588 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 557723002589 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 557723002590 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 557723002591 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557723002592 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 557723002593 putative ADP-binding pocket [chemical binding]; other site 557723002594 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 557723002595 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 557723002596 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 557723002597 Transposase [DNA replication, recombination, and repair]; Region: COG5433 557723002598 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 557723002599 poxB regulator PoxA; Provisional; Region: PRK09350 557723002600 motif 1; other site 557723002601 dimer interface [polypeptide binding]; other site 557723002602 active site 557723002603 motif 2; other site 557723002604 motif 3; other site 557723002605 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557723002606 active site 557723002607 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 557723002608 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557723002609 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 557723002610 putative active site [active] 557723002611 putative metal binding site [ion binding]; other site 557723002612 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 557723002613 active site 557723002614 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557723002615 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 557723002616 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 557723002617 synthetase active site [active] 557723002618 NTP binding site [chemical binding]; other site 557723002619 metal binding site [ion binding]; metal-binding site 557723002620 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 557723002621 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 557723002622 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 557723002623 transaldolase-like protein; Provisional; Region: PTZ00411 557723002624 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 557723002625 active site 557723002626 dimer interface [polypeptide binding]; other site 557723002627 catalytic residue [active] 557723002628 muropeptide transporter; Validated; Region: ampG; PRK11010 557723002629 AmpG-related permease; Region: 2A0125; TIGR00901 557723002630 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 557723002631 UDP-glucose 4-epimerase; Region: PLN02240 557723002632 NAD binding site [chemical binding]; other site 557723002633 homodimer interface [polypeptide binding]; other site 557723002634 active site 557723002635 substrate binding site [chemical binding]; other site 557723002636 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 557723002637 pseudouridine synthase; Region: TIGR00093 557723002638 active site 557723002639 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 557723002640 recombination protein RecR; Reviewed; Region: recR; PRK00076 557723002641 RecR protein; Region: RecR; pfam02132 557723002642 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 557723002643 putative active site [active] 557723002644 putative metal-binding site [ion binding]; other site 557723002645 tetramer interface [polypeptide binding]; other site 557723002646 CTP synthetase; Validated; Region: pyrG; PRK05380 557723002647 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 557723002648 Catalytic site [active] 557723002649 active site 557723002650 UTP binding site [chemical binding]; other site 557723002651 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 557723002652 active site 557723002653 putative oxyanion hole; other site 557723002654 catalytic triad [active] 557723002655 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 557723002656 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723002657 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 557723002658 L-serine binding site [chemical binding]; other site 557723002659 ACT domain interface; other site 557723002660 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 557723002661 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557723002662 active site 557723002663 dimer interface [polypeptide binding]; other site 557723002664 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 557723002665 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 557723002666 active site 557723002667 substrate binding site [chemical binding]; other site 557723002668 metal binding site [ion binding]; metal-binding site 557723002669 threonine dehydratase; Reviewed; Region: PRK09224 557723002670 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 557723002671 tetramer interface [polypeptide binding]; other site 557723002672 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723002673 catalytic residue [active] 557723002674 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 557723002675 putative Ile/Val binding site [chemical binding]; other site 557723002676 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 557723002677 putative Ile/Val binding site [chemical binding]; other site 557723002678 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557723002679 Protein of unknown function (DUF541); Region: SIMPL; cl01077 557723002680 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 557723002681 homodimer interaction site [polypeptide binding]; other site 557723002682 cofactor binding site; other site 557723002683 UbiA prenyltransferase family; Region: UbiA; cl00337 557723002684 Trm112p-like protein; Region: Trm112p; cl01066 557723002685 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 557723002686 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 557723002687 ChuX-like family; Region: DUF1008; cl01509 557723002688 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557723002689 glycerol kinase; Provisional; Region: glpK; PRK00047 557723002690 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 557723002691 N- and C-terminal domain interface [polypeptide binding]; other site 557723002692 active site 557723002693 MgATP binding site [chemical binding]; other site 557723002694 catalytic site [active] 557723002695 metal binding site [ion binding]; metal-binding site 557723002696 glycerol binding site [chemical binding]; other site 557723002697 homotetramer interface [polypeptide binding]; other site 557723002698 homodimer interface [polypeptide binding]; other site 557723002699 FBP binding site [chemical binding]; other site 557723002700 protein IIAGlc interface [polypeptide binding]; other site 557723002701 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 557723002702 amphipathic channel; other site 557723002703 Asn-Pro-Ala signature motifs; other site 557723002704 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 557723002705 WzyE protein; Region: WzyE; cl11643 557723002706 4-alpha-L-fucosyltransferase (Fuc4NAc transferase); Region: Fuc4NAc_transf; cl07929 557723002707 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 557723002708 Transglycosylase; Region: Transgly; cl07896 557723002709 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557723002710 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557723002711 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 557723002712 dimer interface [polypeptide binding]; other site 557723002713 conserved gate region; other site 557723002714 putative PBP binding loops; other site 557723002715 ABC-ATPase subunit interface; other site 557723002716 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 557723002717 dimer interface [polypeptide binding]; other site 557723002718 conserved gate region; other site 557723002719 putative PBP binding loops; other site 557723002720 ABC-ATPase subunit interface; other site 557723002721 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 557723002722 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 557723002723 substrate binding pocket [chemical binding]; other site 557723002724 membrane-bound complex binding site; other site 557723002725 hinge residues; other site 557723002726 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 557723002727 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557723002728 Walker A/P-loop; other site 557723002729 ATP binding site [chemical binding]; other site 557723002730 Q-loop/lid; other site 557723002731 ABC transporter signature motif; other site 557723002732 Walker B; other site 557723002733 D-loop; other site 557723002734 H-loop/switch region; other site 557723002735 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 557723002736 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002737 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723002738 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 557723002739 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 557723002740 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 557723002741 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 557723002742 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 557723002743 dimer interface [polypeptide binding]; other site 557723002744 ssDNA binding site [nucleotide binding]; other site 557723002745 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557723002746 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 557723002747 metabolite-proton symporter; Region: 2A0106; TIGR00883 557723002748 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 557723002749 putative substrate translocation pore; other site 557723002750 Choline Kinase (ChoK). The ChoK subfamily 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: ChoK; cd05151 557723002751 active site 557723002752 ATP binding site [chemical binding]; other site 557723002753 substrate binding site [chemical binding]; other site 557723002754 dimer interface [polypeptide binding]; other site 557723002755 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 557723002756 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 557723002757 putative dimer interface [polypeptide binding]; other site 557723002758 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 557723002759 nucleotide binding site/active site [active] 557723002760 HIT family signature motif; other site 557723002761 catalytic residue [active] 557723002762 Transposase [DNA replication, recombination, and repair]; Region: COG5433 557723002763 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557723002764 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 557723002765 NifU-like domain; Region: NifU; cl00484 557723002766 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 557723002767 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 557723002768 E3 interaction surface; other site 557723002769 lipoyl attachment site [posttranslational modification]; other site 557723002770 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 557723002771 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 557723002772 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 557723002773 FMN-binding domain; Region: FMN_bind; cl01081 557723002774 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557723002775 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557723002776 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 557723002777 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 557723002778 FAD binding pocket [chemical binding]; other site 557723002779 FAD binding motif [chemical binding]; other site 557723002780 phosphate binding motif [ion binding]; other site 557723002781 beta-alpha-beta structure motif; other site 557723002782 NAD binding pocket [chemical binding]; other site 557723002783 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 557723002784 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 557723002785 active site 557723002786 NTP binding site [chemical binding]; other site 557723002787 metal binding triad [ion binding]; metal-binding site 557723002788 antibiotic binding site [chemical binding]; other site 557723002789 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 557723002790 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 557723002791 dimer interface [polypeptide binding]; other site 557723002792 conserved gate region; other site 557723002793 putative PBP binding loops; other site 557723002794 ABC-ATPase subunit interface; other site 557723002795 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 557723002796 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; cl10556 557723002797 Formate-dependent nitrite reductase, periplasmic cytochrome c552 subunit [Inorganic ion transport and metabolism]; Region: NrfA; COG3303 557723002798 cytochrome c nitrite reductase pentaheme subunit; Provisional; Region: PRK11659 557723002799 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 557723002800 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 557723002801 Polysulphide reductase, NrfD; Region: NrfD; cl01295 557723002802 Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane]; Region: OCH1; COG3774 557723002803 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 557723002804 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 557723002805 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 557723002806 rRNA binding site [nucleotide binding]; other site 557723002807 predicted 30S ribosome binding site; other site 557723002808 Predicted GTPases [General function prediction only]; Region: COG1162 557723002809 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs...; Region: YjeQ_engC; cd01854 557723002810 GTPase/OB domain interface [polypeptide binding]; other site 557723002811 GTPase/Zn-binding domain interface [polypeptide binding]; other site 557723002812 GTP/Mg2+ binding site [chemical binding]; other site 557723002813 G4 box; other site 557723002814 G5 box; other site 557723002815 G1 box; other site 557723002816 Switch I region; other site 557723002817 G2 box; other site 557723002818 G3 box; other site 557723002819 Switch II region; other site 557723002820 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 557723002821 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 557723002822 metal binding site [ion binding]; metal-binding site 557723002823 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 557723002824 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 557723002825 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 557723002826 ABC-ATPase subunit interface; other site 557723002827 dimer interface [polypeptide binding]; other site 557723002828 putative PBP binding regions; other site 557723002829 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 557723002830 ABC-ATPase subunit interface; other site 557723002831 dimer interface [polypeptide binding]; other site 557723002832 putative PBP binding regions; other site 557723002833 Uncharacterized protein conserved in bacteria (DUF2251); Region: DUF2251; cl01770 557723002834 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 557723002835 non-specific DNA binding site [nucleotide binding]; other site 557723002836 salt bridge; other site 557723002837 sequence-specific DNA binding site [nucleotide binding]; other site 557723002838 Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]; Region: SacC; COG1621 557723002839 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 557723002840 substrate binding [chemical binding]; other site 557723002841 active site 557723002842 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 557723002843 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 557723002844 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 557723002845 PhnA protein; Region: PhnA; pfam03831 557723002846 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 557723002847 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 557723002848 active site 557723002849 substrate binding site [chemical binding]; other site 557723002850 cosubstrate binding site; other site 557723002851 catalytic site [active] 557723002852 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 557723002853 Aspartase; Region: Aspartase; cd01357 557723002854 active sites [active] 557723002855 tetramer interface [polypeptide binding]; other site 557723002856 heat shock protein 90; Provisional; Region: PRK05218 557723002857 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723002858 ATP binding site [chemical binding]; other site 557723002859 Mg2+ binding site [ion binding]; other site 557723002860 G-X-G motif; other site 557723002861 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl15297 557723002862 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 557723002863 domain; Region: GreA_GreB_N; pfam03449 557723002864 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557723002865 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 557723002866 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723002867 Walker A/P-loop; other site 557723002868 ATP binding site [chemical binding]; other site 557723002869 Q-loop/lid; other site 557723002870 ABC transporter signature motif; other site 557723002871 Walker B; other site 557723002872 D-loop; other site 557723002873 H-loop/switch region; other site 557723002874 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723002875 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 557723002876 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 557723002877 dimer interface [polypeptide binding]; other site 557723002878 conserved gate region; other site 557723002879 putative PBP binding loops; other site 557723002880 ABC-ATPase subunit interface; other site 557723002881 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 557723002882 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723002883 Walker A/P-loop; other site 557723002884 ATP binding site [chemical binding]; other site 557723002885 Q-loop/lid; other site 557723002886 ABC transporter signature motif; other site 557723002887 Walker B; other site 557723002888 D-loop; other site 557723002889 H-loop/switch region; other site 557723002890 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723002891 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 557723002892 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 557723002893 dimer interface [polypeptide binding]; other site 557723002894 conserved gate region; other site 557723002895 ABC-ATPase subunit interface; other site 557723002896 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 557723002897 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 557723002898 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 557723002899 RNA/DNA hybrid binding site [nucleotide binding]; other site 557723002900 active site 557723002901 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 557723002902 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 557723002903 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 557723002904 putative active site [active] 557723002905 putative substrate binding site [chemical binding]; other site 557723002906 putative cosubstrate binding site; other site 557723002907 catalytic site [active] 557723002908 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 557723002909 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 557723002910 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 557723002911 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 557723002912 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557723002913 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557723002914 Cytochrome C biogenesis protein; Region: CcmH; cl01179 557723002915 formate-dependent nitrite reductase complex subunit NrfG; Provisional; Region: PRK10370 557723002916 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557723002917 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 557723002918 Walker A/P-loop; other site 557723002919 ATP binding site [chemical binding]; other site 557723002920 Q-loop/lid; other site 557723002921 ABC transporter signature motif; other site 557723002922 Walker B; other site 557723002923 D-loop; other site 557723002924 H-loop/switch region; other site 557723002925 TOBE domain; Region: TOBE_2; cl01440 557723002926 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 557723002927 dimer interface [polypeptide binding]; other site 557723002928 conserved gate region; other site 557723002929 putative PBP binding loops; other site 557723002930 ABC-ATPase subunit interface; other site 557723002931 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 557723002932 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 557723002933 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 557723002934 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 557723002935 16S/18S rRNA binding site [nucleotide binding]; other site 557723002936 S13e-L30e interaction site [polypeptide binding]; other site 557723002937 25S rRNA binding site [nucleotide binding]; other site 557723002938 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 557723002939 periplasmic folding chaperone; Provisional; Region: PRK10788 557723002940 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557723002941 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 557723002942 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 557723002943 catalytic motif [active] 557723002944 Zn binding site [ion binding]; other site 557723002945 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 557723002946 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 557723002947 Lumazine binding domain; Region: Lum_binding; pfam00677 557723002948 Lumazine binding domain; Region: Lum_binding; pfam00677 557723002949 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 557723002950 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 557723002951 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 557723002952 dimerization interface [polypeptide binding]; other site 557723002953 active site 557723002954 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 557723002955 homopentamer interface [polypeptide binding]; other site 557723002956 active site 557723002957 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 557723002958 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 557723002959 Walker A/P-loop; other site 557723002960 ATP binding site [chemical binding]; other site 557723002961 Q-loop/lid; other site 557723002962 ABC transporter signature motif; other site 557723002963 Walker B; other site 557723002964 D-loop; other site 557723002965 H-loop/switch region; other site 557723002966 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 557723002967 TM-ABC transporter signature motif; other site 557723002968 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 557723002969 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 557723002970 substrate binding pocket [chemical binding]; other site 557723002971 membrane-bound complex binding site; other site 557723002972 hinge residues; other site 557723002973 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557723002974 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557723002975 catalytic residue [active] 557723002976 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 557723002977 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 557723002978 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 557723002979 homodimer interface [polypeptide binding]; other site 557723002980 NADP binding site [chemical binding]; other site 557723002981 substrate binding site [chemical binding]; other site 557723002982 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 557723002983 Phage integrase family; Region: Phage_integrase; pfam00589 557723002984 DNA binding site [nucleotide binding] 557723002985 Int/Topo IB signature motif; other site 557723002986 active site 557723002987 BRO family, N-terminal domain; Region: Bro-N; cl10591 557723002988 ORF6C domain; Region: ORF6C; pfam10552 557723002989 Transposase [DNA replication, recombination, and repair]; Region: COG5433 557723002990 Predicted membrane protein (DUF2335); Region: DUF2335; cl02210 557723002991 PemK-like protein; Region: PemK; cl00995 557723002992 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 557723002993 RecT family; Region: RecT; cl04285 557723002994 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 557723002995 Protein of unknown function (DUF560); Region: DUF560; pfam04575 557723002996 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 557723002997 Cell division protein ZapA; Region: ZapA; cl01146 557723002998 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 557723002999 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08271 557723003000 Class III ribonucleotide reductase; Region: RNR_III; cd01675 557723003001 effector binding site; other site 557723003002 active site 557723003003 Zn binding site [ion binding]; other site 557723003004 glycine loop; other site 557723003005 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15367 557723003006 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557723003007 Glutamine amidotransferase class-I; Region: GATase; pfam00117 557723003008 glutamine binding [chemical binding]; other site 557723003009 catalytic triad [active] 557723003010 RmuC family; Region: RmuC; pfam02646 557723003011 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 557723003012 dimer interface [polypeptide binding]; other site 557723003013 allosteric magnesium binding site [ion binding]; other site 557723003014 active site 557723003015 aspartate-rich active site metal binding site; other site 557723003016 Schiff base residues; other site 557723003017 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 557723003018 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 557723003019 ligand binding site [chemical binding]; other site 557723003020 flexible hinge region; other site 557723003021 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723003022 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 557723003023 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 557723003024 FeS/SAM binding site; other site 557723003025 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 557723003026 ATP-dependent helicase HepA; Validated; Region: PRK04914 557723003027 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 557723003028 ATP binding site [chemical binding]; other site 557723003029 putative Mg++ binding site [ion binding]; other site 557723003030 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 557723003031 nucleotide binding region [chemical binding]; other site 557723003032 ATP-binding site [chemical binding]; other site 557723003033 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 557723003034 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 557723003035 active site 557723003036 dimer interface [polypeptide binding]; other site 557723003037 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 557723003038 dimer interface [polypeptide binding]; other site 557723003039 active site 557723003040 Membrane fusogenic activity; Region: BMFP; cl01115 557723003041 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 557723003042 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 557723003043 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 557723003044 shikimate binding site; other site 557723003045 NAD(P) binding site [chemical binding]; other site 557723003046 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 557723003047 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557723003048 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 557723003049 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557723003050 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557723003051 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as...; Region: ASCH_yqfb_like; cd06552 557723003052 RecX family; Region: RecX; cl00936 557723003053 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 557723003054 protein RecA; Region: tigrfam_recA; TIGR02012 557723003055 hexamer interface [polypeptide binding]; other site 557723003056 Walker A motif; other site 557723003057 ATP binding site [chemical binding]; other site 557723003058 Walker B motif; other site 557723003059 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 557723003060 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557723003061 tellurite resistance protein TehB; Provisional; Region: PRK12335 557723003062 Domain of unknown function (DUF1971); Region: DUF1971; cl01451 557723003063 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 557723003064 S-adenosylmethionine binding site [chemical binding]; other site 557723003065 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 557723003066 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 557723003067 FMN binding site [chemical binding]; other site 557723003068 active site 557723003069 catalytic residues [active] 557723003070 substrate binding site [chemical binding]; other site 557723003071 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 557723003072 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 557723003073 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557723003074 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 557723003075 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557723003076 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557723003077 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 557723003078 DNA binding residues [nucleotide binding] 557723003079 DNA primase; Validated; Region: dnaG; PRK05667 557723003080 CHC2 zinc finger; Region: zf-CHC2; cl15369 557723003081 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 557723003082 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 557723003083 active site 557723003084 metal binding site [ion binding]; metal-binding site 557723003085 interdomain interaction site; other site 557723003086 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 557723003087 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 557723003088 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 557723003089 ribonuclease E; Reviewed; Region: rne; PRK10811 557723003090 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 557723003091 homodimer interface [polypeptide binding]; other site 557723003092 oligonucleotide binding site [chemical binding]; other site 557723003093 ribonuclease E; Reviewed; Region: rne; PRK10811 557723003094 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 557723003095 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557723003096 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557723003097 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557723003098 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 557723003099 AMP binding site [chemical binding]; other site 557723003100 metal binding site [ion binding]; metal-binding site 557723003101 active site 557723003102 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557723003103 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557723003104 peptide binding site [polypeptide binding]; other site 557723003105 D-fructose-responsive transcription factor; Region: fruct_sucro_rep; TIGR02417 557723003106 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557723003107 DNA binding site [nucleotide binding] 557723003108 domain linker motif; other site 557723003109 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 557723003110 dimerization interface [polypeptide binding]; other site 557723003111 ligand binding site [chemical binding]; other site 557723003112 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 557723003113 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 557723003114 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 557723003115 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 557723003116 Walker A motif; other site 557723003117 ATP binding site [chemical binding]; other site 557723003118 Walker B motif; other site 557723003119 arginine finger; other site 557723003120 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557723003121 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 557723003122 peptide binding site [polypeptide binding]; other site 557723003123 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapB; COG4168 557723003124 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 557723003125 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 557723003126 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 557723003127 catalytic residues [active] 557723003128 central insert; other site 557723003129 Cytochrome C biogenesis protein; Region: CcmH; cl01179 557723003130 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 557723003131 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 557723003132 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 557723003133 binding surface 557723003134 TPR motif; other site 557723003135 IPP transferase; Region: IPPT; cl00403 557723003136 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 557723003137 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 557723003138 Sm1 motif; other site 557723003139 intra - hexamer interaction site; other site 557723003140 inter - hexamer interaction site [polypeptide binding]; other site 557723003141 nucleotide binding pocket [chemical binding]; other site 557723003142 Sm2 motif; other site 557723003143 GTPase HflX; Provisional; Region: PRK11058 557723003144 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 557723003145 G1 box; other site 557723003146 GTP/Mg2+ binding site [chemical binding]; other site 557723003147 Switch I region; other site 557723003148 G2 box; other site 557723003149 G3 box; other site 557723003150 Switch II region; other site 557723003151 G4 box; other site 557723003152 G5 box; other site 557723003153 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 557723003154 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557723003155 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 557723003156 motif II; other site 557723003157 N-acetylmannosamine kinase; Provisional; Region: PRK05082 557723003158 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 557723003159 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 557723003160 N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of...; Region: NanE; cd04729 557723003161 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional; Region: PRK01130 557723003162 putative active site cavity [active] 557723003163 Indigoidine synthase A like protein; Region: Indigoidine_A; cl00983 557723003164 putative kinase; Provisional; Region: PRK09954 557723003165 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723003166 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 557723003167 substrate binding site [chemical binding]; other site 557723003168 ATP binding site [chemical binding]; other site 557723003169 nucleoside transporter; Region: nupC; TIGR00804 557723003170 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 557723003171 Nucleoside recognition; Region: Gate; cl00486 557723003172 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 557723003173 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 557723003174 intersubunit interface [polypeptide binding]; other site 557723003175 active site 557723003176 catalytic residue [active] 557723003177 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 557723003178 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 557723003179 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_4; cd07268 557723003180 putative metal binding site [ion binding]; other site 557723003181 arginyl-tRNA synthetase; Region: argS; TIGR00456 557723003182 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 557723003183 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 557723003184 active site 557723003185 HIGH motif; other site 557723003186 KMSK motif region; other site 557723003187 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 557723003188 tRNA binding surface [nucleotide binding]; other site 557723003189 anticodon binding site; other site 557723003190 elongation factor Tu; Reviewed; Region: PRK00049 557723003191 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 557723003192 G1 box; other site 557723003193 GEF interaction site [polypeptide binding]; other site 557723003194 GTP/Mg2+ binding site [chemical binding]; other site 557723003195 Switch I region; other site 557723003196 G2 box; other site 557723003197 G3 box; other site 557723003198 Switch II region; other site 557723003199 G4 box; other site 557723003200 G5 box; other site 557723003201 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 557723003202 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 557723003203 Antibiotic Binding Site [chemical binding]; other site 557723003204 pantothenate kinase; Provisional; Region: PRK05439 557723003205 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 557723003206 ATP-binding site [chemical binding]; other site 557723003207 CoA-binding site [chemical binding]; other site 557723003208 Mg2+-binding site [ion binding]; other site 557723003209 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 557723003210 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 557723003211 S-adenosylmethionine binding site [chemical binding]; other site 557723003212 lipoyl synthase; Provisional; Region: PRK05481 557723003213 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 557723003214 FeS/SAM binding site; other site 557723003215 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 557723003216 Protein of unknown function (DUF493); Region: DUF493; cl01102 557723003217 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 557723003218 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 557723003219 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 557723003220 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 557723003221 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 557723003222 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557723003223 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557723003224 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 557723003225 Domain of unknown function DUF143; Region: DUF143; cl00519 557723003226 Sugar fermentation stimulation protein; Region: SfsA; cl00647 557723003227 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 557723003228 active site 557723003229 HslU subunit interaction site [polypeptide binding]; other site 557723003230 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 557723003231 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 557723003232 Walker A motif; other site 557723003233 ATP binding site [chemical binding]; other site 557723003234 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723003235 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557723003236 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 557723003237 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 557723003238 dimer interface [polypeptide binding]; other site 557723003239 tetramer interface [polypeptide binding]; other site 557723003240 PYR/PP interface [polypeptide binding]; other site 557723003241 TPP binding site [chemical binding]; other site 557723003242 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 557723003243 TPP-binding site; other site 557723003244 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Provisional; Region: PRK11126 557723003245 Protein of unknown function, DUF399; Region: DUF399; cl01139 557723003246 Uncharacterised protein family UPF0547; Region: UPF0547; pfam10571 557723003247 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 557723003248 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723003249 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 557723003250 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 557723003251 primosome assembly protein PriA; Validated; Region: PRK05580 557723003252 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 557723003253 ATP binding site [chemical binding]; other site 557723003254 putative Mg++ binding site [ion binding]; other site 557723003255 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723003256 Predicted permeases [General function prediction only]; Region: RarD; COG2962 557723003257 Predicted permeases [General function prediction only]; Region: RarD; COG2962 557723003258 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 557723003259 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 557723003260 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723003261 homodimer interface [polypeptide binding]; other site 557723003262 catalytic residue [active] 557723003263 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 557723003264 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557723003265 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 557723003266 active site 557723003267 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 557723003268 fructokinase; Reviewed; Region: PRK09557 557723003269 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557723003270 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 557723003271 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 557723003272 catalytic residue [active] 557723003273 putative FPP diphosphate binding site; other site 557723003274 putative FPP binding hydrophobic cleft; other site 557723003275 dimer interface [polypeptide binding]; other site 557723003276 putative IPP diphosphate binding site; other site 557723003277 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 557723003278 zinc metallopeptidase RseP; Provisional; Region: PRK10779 557723003279 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 557723003280 active site 557723003281 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 557723003282 protein binding site [polypeptide binding]; other site 557723003283 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 557723003284 protein binding site [polypeptide binding]; other site 557723003285 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 557723003286 putative substrate binding region [chemical binding]; other site 557723003287 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 557723003288 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557723003289 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557723003290 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557723003291 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557723003292 Surface antigen; Region: Bac_surface_Ag; cl03097 557723003293 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 557723003294 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 557723003295 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 557723003296 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 557723003297 trimer interface [polypeptide binding]; other site 557723003298 active site 557723003299 UDP-GlcNAc binding site [chemical binding]; other site 557723003300 lipid binding site [chemical binding]; lipid-binding site 557723003301 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 557723003302 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 557723003303 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 557723003304 active site 557723003305 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 557723003306 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 557723003307 putative catalytic residues [active] 557723003308 putative nucleotide binding site [chemical binding]; other site 557723003309 putative aspartate binding site [chemical binding]; other site 557723003310 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 557723003311 dimer interface [polypeptide binding]; other site 557723003312 putative threonine allosteric regulatory site; other site 557723003313 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 557723003314 putative threonine allosteric regulatory site; other site 557723003315 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003316 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 557723003317 homoserine kinase; Provisional; Region: PRK01212 557723003318 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 557723003319 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 557723003320 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 557723003321 Chorismate mutase type II; Region: CM_2; cl00693 557723003322 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003323 NeuB family; Region: NeuB; cl00496 557723003324 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557723003325 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 557723003326 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 557723003327 putative active site [active] 557723003328 DsrC like protein; Region: DsrC; cl01101 557723003329 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 557723003330 High-affinity nickel-transport protein; Region: NicO; cl00964 557723003331 Protein of unknown function (DUF1007); Region: DUF1007; cl01487 557723003332 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 557723003333 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 557723003334 active site 557723003335 Zn binding site [ion binding]; other site 557723003336 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 557723003337 Chorismate mutase type II; Region: CM_2; cl00693 557723003338 Prephenate dehydratase; Region: PDT; pfam00800 557723003339 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 557723003340 putative L-Phe binding site [chemical binding]; other site 557723003341 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 557723003342 ligand binding site [chemical binding]; other site 557723003343 active site 557723003344 UGI interface [polypeptide binding]; other site 557723003345 catalytic site [active] 557723003346 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 557723003347 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 557723003348 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557723003349 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723003350 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557723003351 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 557723003352 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 557723003353 carboxyltransferase (CT) interaction site; other site 557723003354 biotinylation site [posttranslational modification]; other site 557723003355 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 557723003356 active site 557723003357 trimer interface [polypeptide binding]; other site 557723003358 dimer interface [polypeptide binding]; other site 557723003359 biotin synthetase; Region: bioB; TIGR00433 557723003360 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 557723003361 FeS/SAM binding site; other site 557723003362 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 557723003363 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 557723003364 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 557723003365 trimer interface [polypeptide binding]; other site 557723003366 active site 557723003367 substrate binding site [chemical binding]; other site 557723003368 CoA binding site [chemical binding]; other site 557723003369 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 557723003370 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 557723003371 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 557723003372 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 557723003373 inhibitor-cofactor binding pocket; inhibition site 557723003374 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723003375 catalytic residue [active] 557723003376 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 557723003377 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 557723003378 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723003379 catalytic residue [active] 557723003380 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 557723003381 ribonuclease PH; Reviewed; Region: rph; PRK00173 557723003382 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 557723003383 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 557723003384 hypothetical protein; Provisional; Region: PRK11820 557723003385 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 557723003386 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 557723003387 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 557723003388 FAD binding domain; Region: FAD_binding_4; pfam01565 557723003389 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 557723003390 birA, biotin-[acetyl-CoA-carboxylase] ligase region; Region: birA_ligase; TIGR00121 557723003391 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 557723003392 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 557723003393 Protein of unknown function (DUF454); Region: DUF454; cl01063 557723003394 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 557723003395 MPT binding site; other site 557723003396 trimer interface [polypeptide binding]; other site 557723003397 Nitrogen regulatory protein P-II; Region: P-II; cl00412 557723003398 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 557723003399 LytB protein; Region: LYTB; cl00507 557723003400 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 557723003401 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 557723003402 endonuclease III; Region: ENDO3c; smart00478 557723003403 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557723003404 helix-hairpin-helix signature motif; other site 557723003405 substrate binding pocket [chemical binding]; other site 557723003406 active site 557723003407 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 557723003408 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 557723003409 DNA binding and oxoG recognition site [nucleotide binding] 557723003410 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 557723003411 murein transglycosylase C; Provisional; Region: mltC; PRK11671 557723003412 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 557723003413 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557723003414 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557723003415 catalytic residue [active] 557723003416 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 557723003417 glycerol-3-phosphate dehydrogenase, anaerobic, C subunit; Region: glycerol3P_GlpC; TIGR03379 557723003418 Cysteine-rich domain; Region: CCG; pfam02754 557723003419 Cysteine-rich domain; Region: CCG; pfam02754 557723003420 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 557723003421 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl10040 557723003422 sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional; Region: glpA; PRK11101 557723003423 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003424 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557723003425 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 557723003426 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 557723003427 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 557723003428 active site 557723003429 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557723003430 Peptidase family M48; Region: Peptidase_M48; cl12018 557723003431 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 557723003432 dimer interface [polypeptide binding]; other site 557723003433 substrate binding site [chemical binding]; other site 557723003434 metal binding sites [ion binding]; metal-binding site 557723003435 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 557723003436 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 557723003437 ATP binding site [chemical binding]; other site 557723003438 putative Mg++ binding site [ion binding]; other site 557723003439 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 557723003440 nucleotide binding region [chemical binding]; other site 557723003441 ATP-binding site [chemical binding]; other site 557723003442 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557723003443 Fic family protein [Function unknown]; Region: COG3177 557723003444 Fic/DOC family; Region: Fic; cl00960 557723003445 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 557723003446 ATP binding site [chemical binding]; other site 557723003447 putative Mg++ binding site [ion binding]; other site 557723003448 ketol-acid reductoisomerase; Validated; Region: PRK05225 557723003449 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003450 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 557723003451 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 557723003452 Sodium:solute symporter family; Region: SSF; cl00456 557723003453 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 557723003454 Proline dehydrogenase; Region: Pro_dh; cl03282 557723003455 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 557723003456 Glutamate binding site [chemical binding]; other site 557723003457 NAD binding site [chemical binding]; other site 557723003458 catalytic residues [active] 557723003459 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 557723003460 dimer interface [polypeptide binding]; other site 557723003461 putative radical transfer pathway; other site 557723003462 diiron center [ion binding]; other site 557723003463 tyrosyl radical; other site 557723003464 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 557723003465 Class I ribonucleotide reductase; Region: RNR_I; cd01679 557723003466 active site 557723003467 dimer interface [polypeptide binding]; other site 557723003468 catalytic residues [active] 557723003469 effector binding site; other site 557723003470 R2 peptide binding site; other site 557723003471 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557723003472 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 557723003473 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 557723003474 RuvA N terminal domain; Region: RuvA_N; pfam01330 557723003475 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 557723003476 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 557723003477 SprT homologues; Region: SprT; cl01182 557723003478 SprT-like family; Region: SprT-like; pfam10263 557723003479 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 557723003480 B1 nucleotide binding pocket [chemical binding]; other site 557723003481 B2 nucleotide binding pocket [chemical binding]; other site 557723003482 CAS motifs; other site 557723003483 active site 557723003484 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557723003485 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 557723003486 dimer interface [polypeptide binding]; other site 557723003487 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723003488 catalytic residue [active] 557723003489 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 557723003490 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 557723003491 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 557723003492 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723003493 ATP binding site [chemical binding]; other site 557723003494 Mg2+ binding site [ion binding]; other site 557723003495 G-X-G motif; other site 557723003496 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 557723003497 ATP binding site [chemical binding]; other site 557723003498 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 557723003499 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 557723003500 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 557723003501 THF binding site; other site 557723003502 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 557723003503 substrate binding site [chemical binding]; other site 557723003504 THF binding site; other site 557723003505 zinc-binding site [ion binding]; other site 557723003506 recombination and repair protein; Provisional; Region: PRK10869 557723003507 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 557723003508 Walker A/P-loop; other site 557723003509 ATP binding site [chemical binding]; other site 557723003510 Q-loop/lid; other site 557723003511 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 557723003512 Q-loop/lid; other site 557723003513 ABC transporter signature motif; other site 557723003514 Walker B; other site 557723003515 D-loop; other site 557723003516 H-loop/switch region; other site 557723003517 Transferrin binding protein-like solute binding protein; Region: Lipoprotein_5; pfam01298 557723003518 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 557723003519 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 557723003520 putative DNA-binding cleft [nucleotide binding]; other site 557723003521 putative DNA clevage site; other site 557723003522 molecular lever; other site 557723003523 Integral membrane protein TerC family; Region: TerC; cl10468 557723003524 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723003525 thiamine ABC transporter, ATP-binding protein; Region: thiQ; TIGR01277 557723003526 Walker A/P-loop; other site 557723003527 ATP binding site [chemical binding]; other site 557723003528 Q-loop/lid; other site 557723003529 ABC transporter signature motif; other site 557723003530 Walker B; other site 557723003531 D-loop; other site 557723003532 H-loop/switch region; other site 557723003533 cell division protein FtsN; Provisional; Region: PRK12757 557723003534 Sporulation related domain; Region: SPOR; cl10051 557723003535 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 557723003536 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557723003537 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557723003538 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557723003539 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 557723003540 active site residue [active] 557723003541 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 557723003542 putative inner membrane peptidase; Provisional; Region: PRK11778 557723003543 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 557723003544 tandem repeat interface [polypeptide binding]; other site 557723003545 oligomer interface [polypeptide binding]; other site 557723003546 active site residues [active] 557723003547 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 557723003548 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 557723003549 FMN binding site [chemical binding]; other site 557723003550 active site 557723003551 catalytic residues [active] 557723003552 substrate binding site [chemical binding]; other site 557723003553 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723003554 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 557723003555 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 557723003556 S-adenosylmethionine binding site [chemical binding]; other site 557723003557 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 557723003558 SCP-2 sterol transfer family; Region: SCP2; cl01225 557723003559 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 557723003560 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557723003561 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 557723003562 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 557723003563 Ligand Binding Site [chemical binding]; other site 557723003564 TilS substrate binding domain; Region: TilS; pfam09179 557723003565 B3/4 domain; Region: B3_4; cl11458 557723003566 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 557723003567 putative active site [active] 557723003568 dimerization interface [polypeptide binding]; other site 557723003569 putative tRNAtyr binding site [nucleotide binding]; other site 557723003570 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 557723003571 Mac 1; Region: Mac-1; pfam09028 557723003572 Autotransporter beta-domain; Region: Autotransporter; cl02365 557723003573 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 557723003574 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 557723003575 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723003576 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 557723003577 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 557723003578 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 557723003579 putative catalytic cysteine [active] 557723003580 Autotransporter beta-domain; Region: Autotransporter; cl02365 557723003581 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 557723003582 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723003583 Walker A/P-loop; other site 557723003584 ATP binding site [chemical binding]; other site 557723003585 Q-loop/lid; other site 557723003586 ABC transporter signature motif; other site 557723003587 Walker B; other site 557723003588 D-loop; other site 557723003589 H-loop/switch region; other site 557723003590 ABC transporter; Region: ABC_tran_2; pfam12848 557723003591 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557723003592 glutathione reductase; Validated; Region: PRK06116 557723003593 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003594 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557723003595 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 557723003596 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 557723003597 FeS/SAM binding site; other site 557723003598 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 557723003599 active site 557723003600 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 557723003601 Ligand Binding Site [chemical binding]; other site 557723003602 Pirin-related protein [General function prediction only]; Region: COG1741 557723003603 Cupin domain; Region: Cupin_2; cl09118 557723003604 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 557723003605 aminopeptidase B; Provisional; Region: PRK05015 557723003606 Peptidase; Region: DUF3663; pfam12404 557723003607 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 557723003608 interface (dimer of trimers) [polypeptide binding]; other site 557723003609 Substrate-binding/catalytic site; other site 557723003610 Zn-binding sites [ion binding]; other site 557723003611 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723003612 Rrf2 family protein; Region: rrf2_super; TIGR00738 557723003613 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 557723003614 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 557723003615 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 557723003616 membrane protein insertase; Provisional; Region: PRK01318 557723003617 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 557723003618 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723003619 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 557723003620 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 557723003621 Int/Topo IB signature motif; other site 557723003622 active site 557723003623 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 557723003624 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 557723003625 dimer interface [polypeptide binding]; other site 557723003626 ADP-ribose binding site [chemical binding]; other site 557723003627 active site 557723003628 nudix motif; other site 557723003629 metal binding site [ion binding]; metal-binding site 557723003630 Phosphate-starvation-inducible E; Region: PsiE; cl01264 557723003631 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 557723003632 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 557723003633 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 557723003634 core dimer interface [polypeptide binding]; other site 557723003635 peripheral dimer interface [polypeptide binding]; other site 557723003636 L10 interface [polypeptide binding]; other site 557723003637 L11 interface [polypeptide binding]; other site 557723003638 putative EF-Tu interaction site [polypeptide binding]; other site 557723003639 putative EF-G interaction site [polypeptide binding]; other site 557723003640 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 557723003641 23S rRNA interface [nucleotide binding]; other site 557723003642 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 557723003643 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 557723003644 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 557723003645 active site 557723003646 (T/H)XGH motif; other site 557723003647 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 557723003648 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 557723003649 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 557723003650 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 557723003651 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 557723003652 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 557723003653 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 557723003654 generic binding surface II; other site 557723003655 generic binding surface I; other site 557723003656 cysteinyl-tRNA synthetase; Provisional; Region: cysS; PRK14535 557723003657 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723003658 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 557723003659 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 557723003660 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 557723003661 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 557723003662 multifunctional aminopeptidase A; Provisional; Region: PRK00913 557723003663 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 557723003664 interface (dimer of trimers) [polypeptide binding]; other site 557723003665 Substrate-binding/catalytic site; other site 557723003666 Zn-binding sites [ion binding]; other site 557723003667 putative protease; Provisional; Region: PRK15452 557723003668 Peptidase family U32; Region: Peptidase_U32; cl03113 557723003669 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 557723003670 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 557723003671 active site 557723003672 Zn binding site [ion binding]; other site 557723003673 dihydroxynaphthoic acid synthetase; Validated; Region: PRK07396 557723003674 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 557723003675 substrate binding site [chemical binding]; other site 557723003676 oxyanion hole (OAH) forming residues; other site 557723003677 trimer interface [polypeptide binding]; other site 557723003678 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557723003679 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 557723003680 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 557723003681 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 557723003682 alphaNTD homodimer interface [polypeptide binding]; other site 557723003683 alphaNTD - beta interaction site [polypeptide binding]; other site 557723003684 alphaNTD - beta' interaction site [polypeptide binding]; other site 557723003685 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 557723003686 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 557723003687 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 557723003688 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 557723003689 RNA binding surface [nucleotide binding]; other site 557723003690 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 557723003691 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 557723003692 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 557723003693 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 557723003694 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 557723003695 SecY translocase; Region: SecY; pfam00344 557723003696 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 557723003697 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 557723003698 23S rRNA binding site [nucleotide binding]; other site 557723003699 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 557723003700 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 557723003701 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 557723003702 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 557723003703 23S rRNA interface [nucleotide binding]; other site 557723003704 L21e interface [polypeptide binding]; other site 557723003705 5S rRNA interface [nucleotide binding]; other site 557723003706 L27 interface [polypeptide binding]; other site 557723003707 L5 interface [polypeptide binding]; other site 557723003708 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 557723003709 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 557723003710 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 557723003711 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 557723003712 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 557723003713 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 557723003714 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 557723003715 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 557723003716 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 557723003717 KOW motif; Region: KOW; cl00354 557723003718 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 557723003719 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 557723003720 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 557723003721 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723003722 Walker A/P-loop; other site 557723003723 ATP binding site [chemical binding]; other site 557723003724 Q-loop/lid; other site 557723003725 ABC transporter signature motif; other site 557723003726 Walker B; other site 557723003727 D-loop; other site 557723003728 H-loop/switch region; other site 557723003729 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723003730 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723003731 Walker A/P-loop; other site 557723003732 ATP binding site [chemical binding]; other site 557723003733 Q-loop/lid; other site 557723003734 ABC transporter signature motif; other site 557723003735 Walker B; other site 557723003736 D-loop; other site 557723003737 H-loop/switch region; other site 557723003738 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 557723003739 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 557723003740 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 557723003741 dimer interface [polypeptide binding]; other site 557723003742 conserved gate region; other site 557723003743 putative PBP binding loops; other site 557723003744 ABC-ATPase subunit interface; other site 557723003745 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557723003746 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 557723003747 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 557723003748 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723003749 TOBE domain; Region: TOBE_2; cl01440 557723003750 TOBE domain; Region: TOBE_2; cl01440 557723003751 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 557723003752 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 557723003753 dimerization interface [polypeptide binding]; other site 557723003754 active site 557723003755 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 557723003756 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 557723003757 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 557723003758 ATP binding site [chemical binding]; other site 557723003759 active site 557723003760 substrate binding site [chemical binding]; other site 557723003761 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 557723003762 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 557723003763 metal binding site [ion binding]; metal-binding site 557723003764 dimer interface [polypeptide binding]; other site 557723003765 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723003766 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723003767 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723003768 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723003769 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557723003770 diaminopimelate decarboxylase; Region: lysA; TIGR01048 557723003771 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 557723003772 active site 557723003773 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557723003774 substrate binding site [chemical binding]; other site 557723003775 catalytic residues [active] 557723003776 dimer interface [polypeptide binding]; other site 557723003777 Amino acid permease; Region: AA_permease; cl00524 557723003778 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 557723003779 MutS domain I; Region: MutS_I; pfam01624 557723003780 MutS domain II; Region: MutS_II; pfam05188 557723003781 MutS family domain IV; Region: MutS_IV; pfam05190 557723003782 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 557723003783 Walker A/P-loop; other site 557723003784 ATP binding site [chemical binding]; other site 557723003785 Q-loop/lid; other site 557723003786 ABC transporter signature motif; other site 557723003787 Walker B; other site 557723003788 D-loop; other site 557723003789 H-loop/switch region; other site 557723003790 YeeE/YedE family (DUF395); Region: DUF395; cl01018 557723003791 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 557723003792 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 557723003793 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 557723003794 protein binding site [polypeptide binding]; other site 557723003795 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 557723003796 Carbon starvation protein CstA; Region: CstA; cl00856 557723003797 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 557723003798 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723003799 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 557723003800 SecA binding site; other site 557723003801 Preprotein binding site; other site 557723003802 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 557723003803 active site residue [active] 557723003804 trigger factor; Provisional; Region: tig; PRK01490 557723003805 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557723003806 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 557723003807 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 557723003808 active site 557723003809 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 557723003810 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 557723003811 glutaminase active site [active] 557723003812 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 557723003813 dimer interface [polypeptide binding]; other site 557723003814 active site 557723003815 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 557723003816 dimer interface [polypeptide binding]; other site 557723003817 active site 557723003818 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 557723003819 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723003820 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557723003821 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 557723003822 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 557723003823 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 557723003824 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 557723003825 generic binding surface II; other site 557723003826 ssDNA binding site; other site 557723003827 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 557723003828 ATP binding site [chemical binding]; other site 557723003829 putative Mg++ binding site [ion binding]; other site 557723003830 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 557723003831 nucleotide binding region [chemical binding]; other site 557723003832 ATP-binding site [chemical binding]; other site 557723003833 Uncharacterized conserved protein [Function unknown]; Region: COG2850 557723003834 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 557723003835 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 557723003836 conserved cys residue [active] 557723003837 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 557723003838 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 557723003839 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 557723003840 active site 557723003841 motif I; other site 557723003842 motif II; other site 557723003843 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 557723003844 motif II; other site 557723003845 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557723003846 DNA utilization protein GntX; Provisional; Region: PRK11595 557723003847 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723003848 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557723003849 active site 557723003850 ribonuclease R; Region: RNase_R; TIGR02063 557723003851 Ribonuclease R winged-helix domain; Region: HTH_12; pfam08461 557723003852 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557723003853 RNB domain; Region: RNB; pfam00773 557723003854 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 557723003855 RNA binding site [nucleotide binding]; other site 557723003856 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 557723003857 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 557723003858 hypothetical protein; Validated; Region: PRK06672 557723003859 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 557723003860 Walker B motif; other site 557723003861 arginine finger; other site 557723003862 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 557723003863 DnaA box-binding interface [nucleotide binding]; other site 557723003864 DNA polymerase III subunit beta; Validated; Region: PRK05643 557723003865 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 557723003866 putative DNA binding surface [nucleotide binding]; other site 557723003867 dimer interface [polypeptide binding]; other site 557723003868 beta-clamp/clamp loader binding surface; other site 557723003869 beta-clamp/translesion DNA polymerase binding surface; other site 557723003870 YGGT family; Region: YGGT; cl00508 557723003871 YGGT family; Region: YGGT; cl00508 557723003872 Uncharacterised ACR, YggU family COG1872; Region: DUF167; cl00811 557723003873 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557723003874 hypothetical protein; Provisional; Region: PRK11573 557723003875 Domain of unknown function DUF21; Region: DUF21; pfam01595 557723003876 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 557723003877 Transporter associated domain; Region: CorC_HlyC; cl08393 557723003878 signal recognition particle protein; Provisional; Region: PRK10867 557723003879 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 557723003880 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 557723003881 P loop; other site 557723003882 GTP binding site [chemical binding]; other site 557723003883 Signal peptide binding domain; Region: SRP_SPB; pfam02978 557723003884 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557723003885 serine acetyltransferase; Provisional; Region: cysE; PRK11132 557723003886 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 557723003887 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 557723003888 trimer interface [polypeptide binding]; other site 557723003889 active site 557723003890 substrate binding site [chemical binding]; other site 557723003891 CoA binding site [chemical binding]; other site 557723003892 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003893 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 557723003894 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 557723003895 two-component response regulator; Provisional; Region: PRK11173 557723003896 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557723003897 active site 557723003898 phosphorylation site [posttranslational modification] 557723003899 intermolecular recognition site; other site 557723003900 dimerization interface [polypeptide binding]; other site 557723003901 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 557723003902 DNA binding site [nucleotide binding] 557723003903 cytidine deaminase; Provisional; Region: PRK09027 557723003904 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 557723003905 active site 557723003906 catalytic motif [active] 557723003907 Zn binding site [ion binding]; other site 557723003908 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 557723003909 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 557723003910 homooctamer interface [polypeptide binding]; other site 557723003911 active site 557723003912 Domain of unknown function (DUF205); Region: DUF205; cl00410 557723003913 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 557723003914 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 557723003915 S-adenosylmethionine binding site [chemical binding]; other site 557723003916 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 557723003917 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 557723003918 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335; cl15440 557723003919 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 557723003920 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557723003921 DNA-binding site [nucleotide binding]; DNA binding site 557723003922 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557723003923 Putative bacterial lipoprotein (DUF799); Region: DUF799; cl01813 557723003924 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 557723003925 TolB amino-terminal domain; Region: TolB_N; cl00639 557723003926 L-fucose isomerase; Provisional; Region: fucI; PRK10991 557723003927 L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose...; Region: L-fuc_L-ara-isomerases; cl00947 557723003928 hexamer (dimer of trimers) interface [polypeptide binding]; other site 557723003929 trimer interface [polypeptide binding]; other site 557723003930 substrate binding site [chemical binding]; other site 557723003931 Mn binding site [ion binding]; other site 557723003932 L-fuculokinase; Provisional; Region: PRK10331 557723003933 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 557723003934 N- and C-terminal domain interface [polypeptide binding]; other site 557723003935 active site 557723003936 MgATP binding site [chemical binding]; other site 557723003937 catalytic site [active] 557723003938 metal binding site [ion binding]; metal-binding site 557723003939 carbohydrate binding site [chemical binding]; other site 557723003940 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 557723003941 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cd00398 557723003942 intersubunit interface [polypeptide binding]; other site 557723003943 active site 557723003944 Zn2+ binding site [ion binding]; other site 557723003945 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 557723003946 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 557723003947 putative active site [active] 557723003948 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557723003949 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 557723003950 substrate binding site [chemical binding]; other site 557723003951 ATP binding site [chemical binding]; other site 557723003952 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 557723003953 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 557723003954 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557723003955 PYR/PP interface [polypeptide binding]; other site 557723003956 dimer interface [polypeptide binding]; other site 557723003957 TPP binding site [chemical binding]; other site 557723003958 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557723003959 Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism; Region: TPP_IolD; cd02003 557723003960 TPP-binding site; other site 557723003961 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 557723003962 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 557723003963 Metal-binding active site; metal-binding site 557723003964 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003965 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 557723003966 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 557723003967 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 557723003968 Phosphotransferase system, EIIC; Region: PTS_EIIC; pfam02378 557723003969 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 557723003970 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 557723003971 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723003972 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 557723003973 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 557723003974 TM-ABC transporter signature motif; other site 557723003975 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 557723003976 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 557723003977 Walker A/P-loop; other site 557723003978 ATP binding site [chemical binding]; other site 557723003979 Q-loop/lid; other site 557723003980 ABC transporter signature motif; other site 557723003981 Walker B; other site 557723003982 D-loop; other site 557723003983 H-loop/switch region; other site 557723003984 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 557723003985 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 557723003986 Periplasmic binding proteins specific to rhizopines; Region: PBP1_rhizopine_binding_like; cd06301 557723003987 putative ligand binding site [chemical binding]; other site 557723003988 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 557723003989 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557723003990 tetrameric interface [polypeptide binding]; other site 557723003991 NAD binding site [chemical binding]; other site 557723003992 catalytic residues [active] 557723003993 KduI/IolB family; Region: KduI; cl01508 557723003994 DsrE/DsrF-like family; Region: DrsE; cl00672 557723003995 DsrE/DsrF-like family; Region: DrsE; cl00672 557723003996 DsrE/DsrF-like family; Region: DrsE; cl00672 557723003997 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 557723003998 YheO-like PAS domain; Region: PAS_6; pfam08348 557723003999 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 557723004000 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 557723004001 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557723004002 SlyX; Region: SlyX; cl01090 557723004003 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557723004004 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 557723004005 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 557723004006 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 557723004007 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 557723004008 FeS/SAM binding site; other site 557723004009 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 557723004010 dimer interface [polypeptide binding]; other site 557723004011 motif 1; other site 557723004012 active site 557723004013 motif 2; other site 557723004014 motif 3; other site 557723004015 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557723004016 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 557723004017 putative active site [active] 557723004018 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 557723004019 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06173 557723004020 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 557723004021 inhibitor-cofactor binding pocket; inhibition site 557723004022 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723004023 catalytic residue [active] 557723004024 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 557723004025 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 557723004026 substrate-cofactor binding pocket; other site 557723004027 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723004028 catalytic residue [active] 557723004029 Protein of unknown function (DUF452); Region: DUF452; cl01062 557723004030 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 557723004031 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 557723004032 S-adenosylmethionine binding site [chemical binding]; other site 557723004033 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004034 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004035 sexual stage antigen; Provisional; Region: PTZ00360 557723004036 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 557723004037 Phage integrase family; Region: Phage_integrase; pfam00589 557723004038 DNA binding site [nucleotide binding] 557723004039 Int/Topo IB signature motif; other site 557723004040 active site 557723004041 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 557723004042 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557723004043 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557723004044 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl15358 557723004045 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 557723004046 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 557723004047 N-terminal plug; other site 557723004048 ligand-binding site [chemical binding]; other site 557723004049 Protein of unknown function, DUF399; Region: DUF399; cl01139 557723004050 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 557723004051 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 557723004052 Walker A/P-loop; other site 557723004053 ATP binding site [chemical binding]; other site 557723004054 Q-loop/lid; other site 557723004055 ABC transporter signature motif; other site 557723004056 Walker B; other site 557723004057 D-loop; other site 557723004058 H-loop/switch region; other site 557723004059 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 557723004060 ABC-ATPase subunit interface; other site 557723004061 dimer interface [polypeptide binding]; other site 557723004062 putative PBP binding regions; other site 557723004063 ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ChuT; COG4558 557723004064 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 557723004065 putative hemin binding site; other site 557723004066 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 557723004067 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 557723004068 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 557723004069 active site 557723004070 catalytic residues [active] 557723004071 metal binding site [ion binding]; metal-binding site 557723004072 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 557723004073 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 557723004074 NADP binding site [chemical binding]; other site 557723004075 homopentamer interface [polypeptide binding]; other site 557723004076 substrate binding site [chemical binding]; other site 557723004077 active site 557723004078 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 557723004079 non-specific DNA binding site [nucleotide binding]; other site 557723004080 salt bridge; other site 557723004081 sequence-specific DNA binding site [nucleotide binding]; other site 557723004082 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 557723004083 Domain of unknown function (DUF927); Region: DUF927; cl12098 557723004084 Terminase small subunit; Region: Terminase_2; cl01513 557723004085 integrase; Provisional; Region: PRK09692 557723004086 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 557723004087 active site 557723004088 Int/Topo IB signature motif; other site 557723004089 selenocysteine synthase; Provisional; Region: PRK04311 557723004090 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 557723004091 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 557723004092 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 557723004093 SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB...; Region: SelB; cd04171 557723004094 G1 box; other site 557723004095 putative GEF interaction site [polypeptide binding]; other site 557723004096 GTP/Mg2+ binding site [chemical binding]; other site 557723004097 Switch I region; other site 557723004098 G2 box; other site 557723004099 G3 box; other site 557723004100 Switch II region; other site 557723004101 G4 box; other site 557723004102 G5 box; other site 557723004103 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 557723004104 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 557723004105 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 557723004106 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 557723004107 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 557723004108 non-specific DNA binding site [nucleotide binding]; other site 557723004109 salt bridge; other site 557723004110 sequence-specific DNA binding site [nucleotide binding]; other site 557723004111 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 557723004112 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 557723004113 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 557723004114 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 557723004115 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 557723004116 RPB11 interaction site [polypeptide binding]; other site 557723004117 RPB12 interaction site [polypeptide binding]; other site 557723004118 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 557723004119 RPB1 interaction site [polypeptide binding]; other site 557723004120 RPB11 interaction site [polypeptide binding]; other site 557723004121 RPB10 interaction site [polypeptide binding]; other site 557723004122 RPB3 interaction site [polypeptide binding]; other site 557723004123 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 557723004124 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 557723004125 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 557723004126 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 557723004127 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 557723004128 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 557723004129 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 557723004130 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 557723004131 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 557723004132 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 557723004133 DNA binding site [nucleotide binding] 557723004134 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 557723004135 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 557723004136 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004137 Walker A/P-loop; other site 557723004138 ATP binding site [chemical binding]; other site 557723004139 Q-loop/lid; other site 557723004140 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004141 ABC transporter signature motif; other site 557723004142 Walker B; other site 557723004143 D-loop; other site 557723004144 H-loop/switch region; other site 557723004145 Protein with unknown function (DUF469); Region: DUF469; cl01237 557723004146 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004147 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 557723004148 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 557723004149 dimer interface [polypeptide binding]; other site 557723004150 active site 557723004151 CoA binding pocket [chemical binding]; other site 557723004152 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723004153 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723004154 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723004155 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723004156 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723004157 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723004158 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723004159 fumarate hydratase; Reviewed; Region: fumC; PRK00485 557723004160 Class II fumarases; Region: Fumarase_classII; cd01362 557723004161 active site 557723004162 tetramer interface [polypeptide binding]; other site 557723004163 TfoX N-terminal domain; Region: TfoX_N; cl01167 557723004164 TfoX N-terminal domain; Region: TfoX_N; cl01167 557723004165 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 557723004166 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 557723004167 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 557723004168 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 557723004169 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 557723004170 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 557723004171 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 557723004172 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 557723004173 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 557723004174 protein-rRNA interface [nucleotide binding]; other site 557723004175 putative translocon binding site; other site 557723004176 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 557723004177 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 557723004178 G-X-X-G motif; other site 557723004179 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 557723004180 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 557723004181 23S rRNA interface [nucleotide binding]; other site 557723004182 5S rRNA interface [nucleotide binding]; other site 557723004183 putative antibiotic binding site [chemical binding]; other site 557723004184 L25 interface [polypeptide binding]; other site 557723004185 L27 interface [polypeptide binding]; other site 557723004186 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 557723004187 23S rRNA interface [nucleotide binding]; other site 557723004188 putative translocon interaction site; other site 557723004189 signal recognition particle (SRP54) interaction site; other site 557723004190 L23 interface [polypeptide binding]; other site 557723004191 trigger factor interaction site; other site 557723004192 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 557723004193 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cd00260 557723004194 Neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: NanH; COG4409 557723004195 Asp-box motif; other site 557723004196 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 557723004197 transmembrane helices; other site 557723004198 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 557723004199 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557723004200 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557723004201 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 557723004202 ATP synthase I chain; Region: ATP_synt_I; cl09170 557723004203 ATP synthase A chain; Region: ATP-synt_A; cl00413 557723004204 ATP synthase subunit C; Region: ATP-synt_C; cl00466 557723004205 Plant ATP synthase F0; Region: YMF19; cl07975 557723004206 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 557723004207 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl15360 557723004208 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 557723004209 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 557723004210 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 557723004211 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 557723004212 beta subunit interaction interface [polypeptide binding]; other site 557723004213 Walker A motif; other site 557723004214 ATP binding site [chemical binding]; other site 557723004215 Walker B motif; other site 557723004216 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 557723004217 ATP synthase; Region: ATP-synt; cl00365 557723004218 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 557723004219 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 557723004220 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 557723004221 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 557723004222 alpha subunit interaction interface [polypeptide binding]; other site 557723004223 Walker A motif; other site 557723004224 ATP binding site [chemical binding]; other site 557723004225 Walker B motif; other site 557723004226 inhibitor binding site; inhibition site 557723004227 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 557723004228 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 557723004229 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 557723004230 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 557723004231 transcriptional repressor RbsR; Provisional; Region: PRK10423 557723004232 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557723004233 DNA binding site [nucleotide binding] 557723004234 domain linker motif; other site 557723004235 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 557723004236 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 557723004237 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 557723004238 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 557723004239 Walker A/P-loop; other site 557723004240 ATP binding site [chemical binding]; other site 557723004241 Q-loop/lid; other site 557723004242 ABC transporter signature motif; other site 557723004243 Walker B; other site 557723004244 D-loop; other site 557723004245 H-loop/switch region; other site 557723004246 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 557723004247 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 557723004248 TM-ABC transporter signature motif; other site 557723004249 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 557723004250 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 557723004251 ligand binding site [chemical binding]; other site 557723004252 dimerization interface [polypeptide binding]; other site 557723004253 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557723004254 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 557723004255 substrate binding site [chemical binding]; other site 557723004256 dimer interface [polypeptide binding]; other site 557723004257 ATP binding site [chemical binding]; other site 557723004258 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 557723004259 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557723004260 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004261 NAD(P) binding site [chemical binding]; other site 557723004262 active site 557723004263 Cupin domain; Region: Cupin_2; cl09118 557723004264 Helix-turn-helix domain; Region: HTH_18; pfam12833 557723004265 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557723004266 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557723004267 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004268 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 557723004269 putative effector binding pocket; other site 557723004270 dimerization interface [polypeptide binding]; other site 557723004271 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 557723004272 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004273 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004274 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 557723004275 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 557723004276 dimer interface [polypeptide binding]; other site 557723004277 anticodon binding site; other site 557723004278 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 557723004279 homodimer interface [polypeptide binding]; other site 557723004280 motif 1; other site 557723004281 active site 557723004282 motif 2; other site 557723004283 GAD domain; Region: GAD; pfam02938 557723004284 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 557723004285 active site 557723004286 motif 3; other site 557723004287 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 557723004288 dimer interface [polypeptide binding]; other site 557723004289 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 557723004290 Protein of unknown function (DUF441); Region: DUF441; cl01041 557723004291 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 557723004292 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 557723004293 ATP binding site [chemical binding]; other site 557723004294 putative Mg++ binding site [ion binding]; other site 557723004295 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 557723004296 nucleotide binding region [chemical binding]; other site 557723004297 ATP-binding site [chemical binding]; other site 557723004298 Helicase associated domain (HA2); Region: HA2; cl04503 557723004299 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 557723004300 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 557723004301 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 557723004302 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 557723004303 active site 557723004304 HIGH motif; other site 557723004305 dimer interface [polypeptide binding]; other site 557723004306 KMSKS motif; other site 557723004307 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 557723004308 alanine racemase; Reviewed; Region: alr; PRK00053 557723004309 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 557723004310 active site 557723004311 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557723004312 substrate binding site [chemical binding]; other site 557723004313 catalytic residues [active] 557723004314 dimer interface [polypeptide binding]; other site 557723004315 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 557723004316 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 557723004317 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 557723004318 Permease family; Region: Xan_ur_permease; cl00967 557723004319 Permease family; Region: Xan_ur_permease; cl00967 557723004320 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 557723004321 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 557723004322 putative NAD(P) binding site [chemical binding]; other site 557723004323 homodimer interface [polypeptide binding]; other site 557723004324 homotetramer interface [polypeptide binding]; other site 557723004325 active site 557723004326 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 557723004327 active site clefts [active] 557723004328 zinc binding site [ion binding]; other site 557723004329 dimer interface [polypeptide binding]; other site 557723004330 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723004331 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723004332 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723004333 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 557723004334 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 557723004335 Walker A/P-loop; other site 557723004336 ATP binding site [chemical binding]; other site 557723004337 Q-loop/lid; other site 557723004338 ABC transporter signature motif; other site 557723004339 Walker B; other site 557723004340 D-loop; other site 557723004341 H-loop/switch region; other site 557723004342 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 557723004343 FtsX-like permease family; Region: FtsX; pfam02687 557723004344 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 557723004345 active site 557723004346 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 557723004347 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 557723004348 putative ATP binding site [chemical binding]; other site 557723004349 putative substrate interface [chemical binding]; other site 557723004350 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 557723004351 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004352 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 557723004353 S-adenosylmethionine binding site [chemical binding]; other site 557723004354 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 557723004355 putative acyl-acceptor binding pocket; other site 557723004356 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557723004357 Transposase IS200 like; Region: Y1_Tnp; cl00848 557723004358 FMN-binding domain; Region: FMN_bind; cl01081 557723004359 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 557723004360 Predicted membrane protein [Function unknown]; Region: COG2860 557723004361 UPF0126 domain; Region: UPF0126; pfam03458 557723004362 UPF0126 domain; Region: UPF0126; pfam03458 557723004363 electron transport complex protein RnfC; Provisional; Region: PRK05035 557723004364 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 557723004365 SLBB domain; Region: SLBB; pfam10531 557723004366 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 557723004367 electron transport complex protein RnfB; Provisional; Region: PRK05113 557723004368 Putative Fe-S cluster; Region: FeS; pfam04060 557723004369 4Fe-4S binding domain; Region: Fer4; cl02805 557723004370 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557723004371 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 557723004372 dimer interface [polypeptide binding]; other site 557723004373 pyridoxal binding site [chemical binding]; other site 557723004374 ATP binding site [chemical binding]; other site 557723004375 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723004376 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723004377 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723004378 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004379 prolyl-tRNA synthetase; Provisional; Region: PRK09194 557723004380 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 557723004381 dimer interface [polypeptide binding]; other site 557723004382 motif 1; other site 557723004383 active site 557723004384 motif 2; other site 557723004385 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 557723004386 putative deacylase active site [active] 557723004387 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 557723004388 active site 557723004389 motif 3; other site 557723004390 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 557723004391 anticodon binding site; other site 557723004392 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557723004393 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557723004394 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 557723004395 putative substrate binding site [chemical binding]; other site 557723004396 putative ATP binding site [chemical binding]; other site 557723004397 CutC family; Region: CutC; cl01218 557723004398 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 557723004399 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 557723004400 active site 557723004401 catalytic residues [active] 557723004402 galactokinase; Provisional; Region: PRK05101 557723004403 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 557723004404 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 557723004405 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 557723004406 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 557723004407 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 557723004408 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 557723004409 endonuclease IV; Provisional; Region: PRK01060 557723004410 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 557723004411 AP (apurinic/apyrimidinic) site pocket; other site 557723004412 DNA interaction; other site 557723004413 Metal-binding active site; metal-binding site 557723004414 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 557723004415 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 557723004416 23S rRNA interface [nucleotide binding]; other site 557723004417 L7/L12 interface [polypeptide binding]; other site 557723004418 putative thiostrepton binding site; other site 557723004419 L25 interface [polypeptide binding]; other site 557723004420 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 557723004421 mRNA/rRNA interface [nucleotide binding]; other site 557723004422 DoxX; Region: DoxX; cl00976 557723004423 HsdM N-terminal domain; Region: HsdM_N; pfam12161 557723004424 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 557723004425 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004426 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004427 Domain of unknown function DUF1828; Region: DUF1828; pfam08861 557723004428 Domain of unknown function DUF1829; Region: DUF1829; pfam08862 557723004429 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 557723004430 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 557723004431 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 557723004432 ATP binding site [chemical binding]; other site 557723004433 putative Mg++ binding site [ion binding]; other site 557723004434 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 557723004435 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004436 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 557723004437 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_2; cd06310 557723004438 putative ligand binding site [chemical binding]; other site 557723004439 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 557723004440 TM-ABC transporter signature motif; other site 557723004441 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 557723004442 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 557723004443 Walker A/P-loop; other site 557723004444 ATP binding site [chemical binding]; other site 557723004445 Q-loop/lid; other site 557723004446 ABC transporter signature motif; other site 557723004447 Walker B; other site 557723004448 D-loop; other site 557723004449 H-loop/switch region; other site 557723004450 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 557723004451 Phosphomannose isomerase type I; Region: PMI_typeI; cl15429 557723004452 mannose-6-phosphate isomerase; Region: PLN02288 557723004453 Protein of unknown function (DUF986); Region: DUF986; cl01983 557723004454 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 557723004455 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 557723004456 PTS system mannose-specific transporter subunits IIAB; Provisional; Region: PRK15088 557723004457 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 557723004458 active pocket/dimerization site; other site 557723004459 active site 557723004460 phosphorylation site [posttranslational modification] 557723004461 PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_man; cd00001 557723004462 active site 557723004463 phosphorylation site [posttranslational modification] 557723004464 ferrochelatase; Reviewed; Region: hemH; PRK00035 557723004465 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 557723004466 C-terminal domain interface [polypeptide binding]; other site 557723004467 active site 557723004468 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 557723004469 active site 557723004470 N-terminal domain interface [polypeptide binding]; other site 557723004471 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; cl15476 557723004472 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 557723004473 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 557723004474 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004475 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 557723004476 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004477 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 557723004478 HicB family; Region: HicB; pfam05534 557723004479 Mg chelatase-related protein; Region: TIGR00368 557723004480 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 557723004481 Walker A motif; other site 557723004482 ATP binding site [chemical binding]; other site 557723004483 Walker B motif; other site 557723004484 arginine finger; other site 557723004485 DNA polymerase III subunit delta'; Validated; Region: PRK06871 557723004486 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004487 DNA polymerase III, delta subunit, C terminal; Region: DNApol3-delta_C; pfam09115 557723004488 thymidylate kinase; Validated; Region: tmk; PRK00698 557723004489 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 557723004490 TMP-binding site; other site 557723004491 ATP-binding site [chemical binding]; other site 557723004492 YceG-like family; Region: YceG; pfam02618 557723004493 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 557723004494 dimerization interface [polypeptide binding]; other site 557723004495 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 557723004496 substrate binding site [chemical binding]; other site 557723004497 dimer interface [polypeptide binding]; other site 557723004498 catalytic triad [active] 557723004499 Survival protein SurE; Region: SurE; cl00448 557723004500 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557723004501 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557723004502 putative peptidoglycan binding site; other site 557723004503 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 557723004504 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557723004505 putative peptidoglycan binding site; other site 557723004506 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 557723004507 integral membrane protein, PqiA family; Region: pqiA_fam; TIGR00155 557723004508 Paraquat-inducible protein A; Region: PqiA; pfam04403 557723004509 Paraquat-inducible protein A; Region: PqiA; pfam04403 557723004510 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 557723004511 RNA/DNA hybrid binding site [nucleotide binding]; other site 557723004512 active site 557723004513 putative global regulator; Reviewed; Region: PRK09559 557723004514 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 557723004515 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004516 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 557723004517 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004518 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723004519 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723004520 Virulence protein [General function prediction only]; Region: COG3943 557723004521 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 557723004522 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 557723004523 inhibitor-cofactor binding pocket; inhibition site 557723004524 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723004525 catalytic residue [active] 557723004526 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 557723004527 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 557723004528 Mg++ binding site [ion binding]; other site 557723004529 putative catalytic motif [active] 557723004530 substrate binding site [chemical binding]; other site 557723004531 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 557723004532 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 557723004533 homodimer interface [polypeptide binding]; other site 557723004534 active site 557723004535 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 557723004536 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004537 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 557723004538 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004539 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 557723004540 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 557723004541 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 557723004542 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 557723004543 DsbD alpha interface [polypeptide binding]; other site 557723004544 catalytic residues [active] 557723004545 short chain dehydrogenase; Provisional; Region: PRK05693 557723004546 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 557723004547 NADP binding site [chemical binding]; other site 557723004548 active site 557723004549 steroid binding site; other site 557723004550 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 557723004551 KorB domain; Region: KorB; pfam08535 557723004552 Integrase core domain; Region: rve; cl01316 557723004553 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 557723004554 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 557723004555 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004556 GTP/Mg2+ binding site [chemical binding]; other site 557723004557 G4 box; other site 557723004558 G5 box; other site 557723004559 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 557723004560 G1 box; other site 557723004561 G1 box; other site 557723004562 GTP/Mg2+ binding site [chemical binding]; other site 557723004563 Switch I region; other site 557723004564 Switch I region; other site 557723004565 G2 box; other site 557723004566 G2 box; other site 557723004567 Switch II region; other site 557723004568 G3 box; other site 557723004569 G3 box; other site 557723004570 Switch II region; other site 557723004571 G4 box; other site 557723004572 G5 box; other site 557723004573 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 557723004574 Protein of unknown function (DUF805); Region: DUF805; cl01224 557723004575 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 557723004576 active site 557723004577 trimer interface [polypeptide binding]; other site 557723004578 dimer interface [polypeptide binding]; other site 557723004579 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 557723004580 active site 557723004581 dimer interface [polypeptide binding]; other site 557723004582 magnesium binding site [ion binding]; other site 557723004583 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 557723004584 active site 557723004585 phosphorylation site [posttranslational modification] 557723004586 PTS system ascorbate-specific transporter subunits IICB; Provisional; Region: PRK09548 557723004587 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 557723004588 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 557723004589 P-loop; other site 557723004590 active site 557723004591 phosphorylation site [posttranslational modification] 557723004592 putative L-xylulose 5-phosphate 3-epimerase; Reviewed; Region: PRK13210 557723004593 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 557723004594 AP (apurinic/apyrimidinic) site pocket; other site 557723004595 DNA interaction; other site 557723004596 Metal-binding active site; metal-binding site 557723004597 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 557723004598 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cd00398 557723004599 intersubunit interface [polypeptide binding]; other site 557723004600 active site 557723004601 Zn2+ binding site [ion binding]; other site 557723004602 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 557723004603 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 557723004604 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 557723004605 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 557723004606 GntP family permease; Region: GntP_permease; cl15264 557723004607 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 557723004608 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 557723004609 ATP-binding site [chemical binding]; other site 557723004610 Gluconate-6-phosphate binding site [chemical binding]; other site 557723004611 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 557723004612 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557723004613 DNA binding site [nucleotide binding] 557723004614 domain linker motif; other site 557723004615 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 557723004616 putative ligand binding site [chemical binding]; other site 557723004617 putative dimerization interface [polypeptide binding]; other site 557723004618 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 557723004619 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 557723004620 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 557723004621 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 557723004622 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557723004623 4Fe-4S binding domain; Region: Fer4; cl02805 557723004624 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 557723004625 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 557723004626 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 557723004627 [4Fe-4S] binding site [ion binding]; other site 557723004628 molybdopterin cofactor binding site; other site 557723004629 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 557723004630 molybdopterin cofactor binding site; other site 557723004631 NapD protein; Region: NapD; cl01163 557723004632 ferredoxin-type protein; Provisional; Region: PRK10194 557723004633 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 557723004634 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 557723004635 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 557723004636 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 557723004637 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 557723004638 substrate binding site [chemical binding]; other site 557723004639 hexamer interface [polypeptide binding]; other site 557723004640 metal binding site [ion binding]; metal-binding site 557723004641 Sulfatase; Region: Sulfatase; cl10460 557723004642 Sodium:solute symporter family; Region: SSF; cl00456 557723004643 putative transporter; Provisional; Region: PRK10484 557723004644 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557723004645 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557723004646 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 557723004647 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004648 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 557723004649 dimerization interface [polypeptide binding]; other site 557723004650 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 557723004651 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004652 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 557723004653 catalytic residues [active] 557723004654 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 557723004655 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 557723004656 catalytic residues [active] 557723004657 hinge region; other site 557723004658 alpha helical domain; other site 557723004659 Protein of unknown function (DUF1040); Region: DUF1040; cl01176 557723004660 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional; Region: PRK14489 557723004661 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 557723004662 GTP binding site; other site 557723004663 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 557723004664 Walker A motif; other site 557723004665 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004666 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557723004667 Bacterial transcriptional regulator; Region: IclR; pfam01614 557723004668 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 557723004669 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 557723004670 L-xylulose kinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_L-XK; cd07802 557723004671 putative N- and C-terminal domain interface [polypeptide binding]; other site 557723004672 putative active site [active] 557723004673 putative MgATP binding site [chemical binding]; other site 557723004674 catalytic site [active] 557723004675 metal binding site [ion binding]; metal-binding site 557723004676 putative xylulose binding site [chemical binding]; other site 557723004677 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 557723004678 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 557723004679 putative homodimer interface [polypeptide binding]; other site 557723004680 KOW motif; Region: KOW; cl00354 557723004681 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 557723004682 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557723004683 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 557723004684 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557723004685 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 557723004686 non-specific DNA binding site [nucleotide binding]; other site 557723004687 salt bridge; other site 557723004688 sequence-specific DNA binding site [nucleotide binding]; other site 557723004689 HipA N-terminal domain; Region: couple_hipA; TIGR03071 557723004690 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 557723004691 HipA-like N-terminal domain; Region: HipA_N; pfam07805 557723004692 HipA-like C-terminal domain; Region: HipA_C; pfam07804 557723004693 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 557723004694 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 557723004695 catalytic residues [active] 557723004696 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557723004697 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004698 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 557723004699 dimerization interface [polypeptide binding]; other site 557723004700 putative effector binding pocket; other site 557723004701 type III restriction-modification system StyLTI enzyme res; Provisional; Region: PRK15483 557723004702 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004703 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004704 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004705 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 557723004706 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 557723004707 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 557723004708 DNA binding residues [nucleotide binding] 557723004709 dimer interface [polypeptide binding]; other site 557723004710 putative metal binding site [ion binding]; other site 557723004711 Cation efflux family; Region: Cation_efflux; cl00316 557723004712 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 557723004713 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 557723004714 DNA binding residues [nucleotide binding] 557723004715 dimer interface [polypeptide binding]; other site 557723004716 copper binding site [ion binding]; other site 557723004717 Domain of unknown function (DUF305); Region: DUF305; pfam03713 557723004718 Domain of unknown function (DUF305); Region: DUF305; pfam03713 557723004719 putative enoyl-(acyl-carrier-protein) reductase II; Region: enACPred_II; TIGR03151 557723004720 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 557723004721 FMN binding site [chemical binding]; other site 557723004722 substrate binding site [chemical binding]; other site 557723004723 putative catalytic residue [active] 557723004724 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea; Region: GIY-YIG_unchar_2; cd10447 557723004725 GIY-YIG motif/motif A; other site 557723004726 putative active site [active] 557723004727 putative metal binding site [ion binding]; other site 557723004728 Protein of unknown function (DUF1016); Region: DUF1016; cl01979 557723004729 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 557723004730 active site 557723004731 thiamine phosphate binding site [chemical binding]; other site 557723004732 pyrophosphate binding site [ion binding]; other site 557723004733 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 557723004734 dimer interface [polypeptide binding]; other site 557723004735 substrate binding site [chemical binding]; other site 557723004736 ATP binding site [chemical binding]; other site 557723004737 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 557723004738 substrate binding site [chemical binding]; other site 557723004739 multimerization interface [polypeptide binding]; other site 557723004740 ATP binding site [chemical binding]; other site 557723004741 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557723004742 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 557723004743 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557723004744 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 557723004745 non-specific DNA binding site [nucleotide binding]; other site 557723004746 salt bridge; other site 557723004747 sequence-specific DNA binding site [nucleotide binding]; other site 557723004748 HipA N-terminal domain; Region: couple_hipA; TIGR03071 557723004749 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 557723004750 HipA-like N-terminal domain; Region: HipA_N; pfam07805 557723004751 HipA-like C-terminal domain; Region: HipA_C; pfam07804 557723004752 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557723004753 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 557723004754 S-adenosylmethionine binding site [chemical binding]; other site 557723004755 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 557723004756 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 557723004757 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 557723004758 P loop; other site 557723004759 GTP binding site [chemical binding]; other site 557723004760 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723004761 Walker A/P-loop; other site 557723004762 ATP binding site [chemical binding]; other site 557723004763 Q-loop/lid; other site 557723004764 ABC transporter signature motif; other site 557723004765 Walker B; other site 557723004766 D-loop; other site 557723004767 H-loop/switch region; other site 557723004768 glutathionine S-transferase; Provisional; Region: PRK10542 557723004769 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 557723004770 C-terminal domain interface [polypeptide binding]; other site 557723004771 GSH binding site (G-site) [chemical binding]; other site 557723004772 dimer interface [polypeptide binding]; other site 557723004773 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 557723004774 N-terminal domain interface [polypeptide binding]; other site 557723004775 dimer interface [polypeptide binding]; other site 557723004776 substrate binding pocket (H-site) [chemical binding]; other site 557723004777 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557723004778 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 557723004779 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 557723004780 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004781 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557723004782 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557723004783 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004784 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 557723004785 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 557723004786 intersubunit interface [polypeptide binding]; other site 557723004787 active site 557723004788 Zn2+ binding site [ion binding]; other site 557723004789 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 557723004790 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 557723004791 Metal-binding active site; metal-binding site 557723004792 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557723004793 Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs; Region: Gne_like_SDR_e; cd05238 557723004794 putative NAD(P) binding site [chemical binding]; other site 557723004795 active site 557723004796 putative substrate binding site [chemical binding]; other site 557723004797 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 557723004798 GntP family permease; Region: GntP_permease; cl15264 557723004799 Predicted peptidase [General function prediction only]; Region: COG4099 557723004800 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557723004801 D-lactate dehydrogenase; Provisional; Region: PRK11183 557723004802 FAD binding domain; Region: FAD_binding_4; pfam01565 557723004803 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 557723004804 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 557723004805 UTRA domain; Region: UTRA; cl01230 557723004806 NnaC (CMP-NeuNAc synthetase) _like subfamily of SGNH_hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: NnaC_like; cd01841 557723004807 active site 557723004808 catalytic triad [active] 557723004809 oxyanion hole [active] 557723004810 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 557723004811 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 557723004812 active site 557723004813 HIGH motif; other site 557723004814 dimer interface [polypeptide binding]; other site 557723004815 KMSKS motif; other site 557723004816 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 557723004817 chaperone protein DnaJ; Provisional; Region: PRK10767 557723004818 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 557723004819 HSP70 interaction site [polypeptide binding]; other site 557723004820 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 557723004821 substrate binding site [polypeptide binding]; other site 557723004822 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 557723004823 Zn binding sites [ion binding]; other site 557723004824 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 557723004825 dimer interface [polypeptide binding]; other site 557723004826 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 557723004827 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 557723004828 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 557723004829 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 557723004830 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 557723004831 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 557723004832 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 557723004833 catalytic site [active] 557723004834 subunit interface [polypeptide binding]; other site 557723004835 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 557723004836 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557723004837 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723004838 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557723004839 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 557723004840 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 557723004841 IMP binding site; other site 557723004842 dimer interface [polypeptide binding]; other site 557723004843 interdomain contacts; other site 557723004844 partial ornithine binding site; other site 557723004845 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 557723004846 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 557723004847 Ribonuclease P; Region: Ribonuclease_P; cl00457 557723004848 Domain of unknown function DUF37; Region: DUF37; cl00506 557723004849 hypothetical protein; Provisional; Region: PRK11568 557723004850 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 557723004851 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 557723004852 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 557723004853 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 557723004854 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 557723004855 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 557723004856 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 557723004857 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 557723004858 Ligand Binding Site [chemical binding]; other site 557723004859 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 557723004860 active site 557723004861 NTP binding site [chemical binding]; other site 557723004862 metal binding triad [ion binding]; metal-binding site 557723004863 antibiotic binding site [chemical binding]; other site 557723004864 Protein of unknown function (DUF1016); Region: DUF1016; cl01979 557723004865 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 557723004866 non-specific DNA binding site [nucleotide binding]; other site 557723004867 salt bridge; other site 557723004868 sequence-specific DNA binding site [nucleotide binding]; other site 557723004869 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 557723004870 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 557723004871 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 557723004872 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 557723004873 oligomeric interface; other site 557723004874 putative active site [active] 557723004875 homodimer interface [polypeptide binding]; other site 557723004876 Phd_YefM; Region: PhdYeFM; cl09153 557723004877 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 557723004878 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 557723004879 putative active site [active] 557723004880 substrate binding site [chemical binding]; other site 557723004881 putative cosubstrate binding site; other site 557723004882 catalytic site [active] 557723004883 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 557723004884 substrate binding site [chemical binding]; other site 557723004885 16S rRNA methyltransferase B; Provisional; Region: PRK10901 557723004886 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 557723004887 putative RNA binding site [nucleotide binding]; other site 557723004888 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 557723004889 S-adenosylmethionine binding site [chemical binding]; other site 557723004890 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 557723004891 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004892 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557723004893 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004894 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557723004895 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 557723004896 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 557723004897 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723004898 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 557723004899 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 557723004900 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 557723004901 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 557723004902 AlwI restriction endonuclease; Region: RE_AlwI; pfam09491 557723004903 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 557723004904 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004905 cofactor binding site; other site 557723004906 DNA binding site [nucleotide binding] 557723004907 substrate interaction site [chemical binding]; other site 557723004908 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 557723004909 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 557723004910 cofactor binding site; other site 557723004911 DNA binding site [nucleotide binding] 557723004912 substrate interaction site [chemical binding]; other site 557723004913 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 557723004914 salt bridge; other site 557723004915 non-specific DNA binding site [nucleotide binding]; other site 557723004916 sequence-specific DNA binding site [nucleotide binding]; other site 557723004917 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 557723004918 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 557723004919 Cation transport protein; Region: TrkH; cl10514 557723004920 putative hydrolase; Provisional; Region: PRK10976 557723004921 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 557723004922 active site 557723004923 motif I; other site 557723004924 motif II; other site 557723004925 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 557723004926 2-isopropylmalate synthase; Validated; Region: PRK00915 557723004927 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 557723004928 active site 557723004929 metal binding site [ion binding]; metal-binding site 557723004930 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 557723004931 peptidase T; Region: peptidase-T; TIGR01882 557723004932 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 557723004933 metal binding site [ion binding]; metal-binding site 557723004934 dimer interface [polypeptide binding]; other site 557723004935 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 557723004936 23S rRNA binding site [nucleotide binding]; other site 557723004937 L21 binding site [polypeptide binding]; other site 557723004938 L13 binding site [polypeptide binding]; other site 557723004939 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 557723004940 translation initiation factor IF-3; Region: infC; TIGR00168 557723004941 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 557723004942 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 557723004943 UGMP family protein; Validated; Region: PRK09604 557723004944 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 557723004945 shikimate 5-dehydrogenase; Reviewed; Region: PRK12550 557723004946 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 557723004947 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 557723004948 shikimate binding site; other site 557723004949 NAD(P) binding site [chemical binding]; other site 557723004950 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 557723004951 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 557723004952 putative substrate translocation pore; other site 557723004953 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 557723004954 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 557723004955 ATP binding site [chemical binding]; other site 557723004956 substrate interface [chemical binding]; other site 557723004957 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 557723004958 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 557723004959 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 557723004960 RimM N-terminal domain; Region: RimM; pfam01782 557723004961 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 557723004962 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 557723004963 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 557723004964 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 557723004965 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 557723004966 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723004967 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723004968 TIR domain; Region: TIR; cl02060 557723004969 Protein of unknown function DUF45; Region: DUF45; cl00636 557723004970 Protein of unknown function DUF262; Region: DUF262; cl14890 557723004971 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 557723004972 active site 557723004973 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723004974 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557723004975 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 557723004976 dimer interface [polypeptide binding]; other site 557723004977 active site 557723004978 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723004979 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 557723004980 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 557723004981 Protein of unknown function, DUF; Region: DUF413; cl10479 557723004982 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723004983 tRNA (Uracil-5-)-methyltransferase; Region: tRNA_U5-meth_tr; pfam05958 557723004984 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 557723004985 S17 interaction site [polypeptide binding]; other site 557723004986 S8 interaction site; other site 557723004987 16S rRNA interaction site [nucleotide binding]; other site 557723004988 streptomycin interaction site [chemical binding]; other site 557723004989 23S rRNA interaction site [nucleotide binding]; other site 557723004990 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 557723004991 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 557723004992 elongation factor G; Reviewed; Region: PRK00007 557723004993 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so...; Region: EF-G; cd01886 557723004994 G1 box; other site 557723004995 putative GEF interaction site [polypeptide binding]; other site 557723004996 GTP/Mg2+ binding site [chemical binding]; other site 557723004997 Switch I region; other site 557723004998 G2 box; other site 557723004999 G3 box; other site 557723005000 Switch II region; other site 557723005001 G4 box; other site 557723005002 G5 box; other site 557723005003 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 557723005004 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 557723005005 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 557723005006 elongation factor Tu; Reviewed; Region: PRK00049 557723005007 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 557723005008 G1 box; other site 557723005009 GEF interaction site [polypeptide binding]; other site 557723005010 GTP/Mg2+ binding site [chemical binding]; other site 557723005011 Switch I region; other site 557723005012 G2 box; other site 557723005013 G3 box; other site 557723005014 Switch II region; other site 557723005015 G4 box; other site 557723005016 G5 box; other site 557723005017 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 557723005018 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 557723005019 Antibiotic Binding Site [chemical binding]; other site 557723005020 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 557723005021 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 557723005022 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557723005023 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 557723005024 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 557723005025 G1 box; other site 557723005026 putative GEF interaction site [polypeptide binding]; other site 557723005027 GTP/Mg2+ binding site [chemical binding]; other site 557723005028 Switch I region; other site 557723005029 G2 box; other site 557723005030 G3 box; other site 557723005031 Switch II region; other site 557723005032 G4 box; other site 557723005033 G5 box; other site 557723005034 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 557723005035 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557723005036 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 557723005037 active site 557723005038 metal binding site [ion binding]; metal-binding site 557723005039 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional; Region: PRK08099 557723005040 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557723005041 active site 557723005042 nucleotide binding site [chemical binding]; other site 557723005043 HIGH motif; other site 557723005044 KMSKS motif; other site 557723005045 Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]; Region: NadR; cl01238 557723005046 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557723005047 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557723005048 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 557723005049 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 557723005050 dimerization interface [polypeptide binding]; other site 557723005051 ATP binding site [chemical binding]; other site 557723005052 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 557723005053 dimerization interface [polypeptide binding]; other site 557723005054 ATP binding site [chemical binding]; other site 557723005055 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 557723005056 putative active site [active] 557723005057 catalytic triad [active] 557723005058 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 557723005059 Transposase, Mutator family; Region: Transposase_mut; pfam00872 557723005060 Protein of unknown function (DUF535); Region: DUF535; cl01128 557723005061 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 557723005062 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557723005063 HIGH motif; other site 557723005064 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 557723005065 active site 557723005066 KMSKS motif; other site 557723005067 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 557723005068 tRNA binding surface [nucleotide binding]; other site 557723005069 anticodon binding site; other site 557723005070 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 557723005071 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723005072 Fic family protein [Function unknown]; Region: COG3177 557723005073 Fic/DOC family; Region: Fic; cl00960 557723005074 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 557723005075 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 557723005076 substrate binding site [chemical binding]; other site 557723005077 active site 557723005078 catalytic residues [active] 557723005079 heterodimer interface [polypeptide binding]; other site 557723005080 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 557723005081 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557723005082 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723005083 catalytic residue [active] 557723005084 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 557723005085 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 557723005086 active site 557723005087 ribulose/triose binding site [chemical binding]; other site 557723005088 phosphate binding site [ion binding]; other site 557723005089 substrate (anthranilate) binding pocket [chemical binding]; other site 557723005090 product (indole) binding pocket [chemical binding]; other site 557723005091 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 557723005092 active site 557723005093 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 557723005094 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 557723005095 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 557723005096 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557723005097 Glutamine amidotransferase class-I; Region: GATase; pfam00117 557723005098 glutamine binding [chemical binding]; other site 557723005099 catalytic triad [active] 557723005100 anthranilate synthase component I; Provisional; Region: PRK13564 557723005101 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 557723005102 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557723005103 Sulfatase; Region: Sulfatase; cl10460 557723005104 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 557723005105 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 557723005106 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 557723005107 probable active site [active] 557723005108 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 557723005109 Fe-S metabolism associated domain; Region: SufE; cl00951 557723005110 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 557723005111 oligomer interface [polypeptide binding]; other site 557723005112 active site residues [active] 557723005113 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 557723005114 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 557723005115 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 557723005116 Walker A motif; other site 557723005117 ATP binding site [chemical binding]; other site 557723005118 Walker B motif; other site 557723005119 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557723005120 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 557723005121 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 557723005122 metal binding site [ion binding]; metal-binding site 557723005123 dimer interface [polypeptide binding]; other site 557723005124 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 557723005125 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 557723005126 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 557723005127 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 557723005128 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 557723005129 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005130 Walker A motif; other site 557723005131 ATP binding site [chemical binding]; other site 557723005132 Walker B motif; other site 557723005133 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 557723005134 putative active site [active] 557723005135 putative major pilin subunit; Provisional; Region: PRK10574 557723005136 DNA repair protein RadA; Provisional; Region: PRK11823 557723005137 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 557723005138 Walker A motif/ATP binding site; other site 557723005139 ATP binding site [chemical binding]; other site 557723005140 Walker B motif; other site 557723005141 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 557723005142 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 557723005143 catalytic site [active] 557723005144 G-X2-G-X-G-K; other site 557723005145 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723005146 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723005147 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723005148 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 557723005149 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005150 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557723005151 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 557723005152 THUMP domain; Region: THUMP; cl12076 557723005153 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723005154 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723005155 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 557723005156 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 557723005157 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 557723005158 S-adenosylmethionine binding site [chemical binding]; other site 557723005159 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 557723005160 Peptidase family M23; Region: Peptidase_M23; pfam01551 557723005161 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 557723005162 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557723005163 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 557723005164 HipA-like N-terminal domain; Region: HipA_N; pfam07805 557723005165 HipA-like C-terminal domain; Region: HipA_C; pfam07804 557723005166 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723005167 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 557723005168 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 557723005169 ATP binding site [chemical binding]; other site 557723005170 Mg++ binding site [ion binding]; other site 557723005171 motif III; other site 557723005172 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 557723005173 nucleotide binding region [chemical binding]; other site 557723005174 ATP-binding site [chemical binding]; other site 557723005175 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 557723005176 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 557723005177 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 557723005178 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 557723005179 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 557723005180 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 557723005181 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 557723005182 quinone interaction residues [chemical binding]; other site 557723005183 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 557723005184 active site 557723005185 catalytic residues [active] 557723005186 FMN binding site [chemical binding]; other site 557723005187 substrate binding site [chemical binding]; other site 557723005188 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 557723005189 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 557723005190 ligand binding site [chemical binding]; other site 557723005191 flexible hinge region; other site 557723005192 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 557723005193 putative switch regulator; other site 557723005194 non-specific DNA interactions [nucleotide binding]; other site 557723005195 DNA binding site [nucleotide binding] 557723005196 sequence specific DNA binding site [nucleotide binding]; other site 557723005197 putative cAMP binding site [chemical binding]; other site 557723005198 Uncharacterised protein family (UPF0270); Region: UPF0270; cl01180 557723005199 division inhibitor protein; Provisional; Region: slmA; PRK09480 557723005200 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723005201 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 557723005202 trimer interface [polypeptide binding]; other site 557723005203 active site 557723005204 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of...; Region: SH3; cl15350 557723005205 phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase, prokaryotic; Region: coaBC_dfp; TIGR00521 557723005206 Flavoprotein; Region: Flavoprotein; cl08021 557723005207 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 557723005208 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 557723005209 MPN+ (JAMM) motif; other site 557723005210 Zinc-binding site [ion binding]; other site 557723005211 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 557723005212 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 557723005213 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 557723005214 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 557723005215 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557723005216 active site 557723005217 phosphorylation site [posttranslational modification] 557723005218 intermolecular recognition site; other site 557723005219 dimerization interface [polypeptide binding]; other site 557723005220 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 557723005221 DNA binding site [nucleotide binding] 557723005222 sensor protein QseC; Provisional; Region: PRK10337 557723005223 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 557723005224 dimer interface [polypeptide binding]; other site 557723005225 phosphorylation site [posttranslational modification] 557723005226 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723005227 ATP binding site [chemical binding]; other site 557723005228 Mg2+ binding site [ion binding]; other site 557723005229 G-X-G motif; other site 557723005230 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 557723005231 oligomerisation interface [polypeptide binding]; other site 557723005232 mobile loop; other site 557723005233 roof hairpin; other site 557723005234 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 557723005235 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 557723005236 ring oligomerisation interface [polypeptide binding]; other site 557723005237 ATP/Mg binding site [chemical binding]; other site 557723005238 stacking interactions; other site 557723005239 hinge regions; other site 557723005240 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 557723005241 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 557723005242 dimer interface [polypeptide binding]; other site 557723005243 active site 557723005244 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 557723005245 putative transposase OrfB; Reviewed; Region: PHA02517 557723005246 Integrase core domain; Region: rve; cl01316 557723005247 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557723005248 GTPase CgtA; Reviewed; Region: obgE; PRK12298 557723005249 GTP1/OBG; Region: GTP1_OBG; pfam01018 557723005250 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 557723005251 G1 box; other site 557723005252 GTP/Mg2+ binding site [chemical binding]; other site 557723005253 Switch I region; other site 557723005254 G2 box; other site 557723005255 G3 box; other site 557723005256 Switch II region; other site 557723005257 G4 box; other site 557723005258 G5 box; other site 557723005259 EamA-like transporter family; Region: EamA; cl01037 557723005260 EamA-like transporter family; Region: EamA; cl01037 557723005261 EamA-like transporter family; Region: EamA; cl01037 557723005262 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 557723005263 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 557723005264 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 557723005265 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 557723005266 active site 557723005267 dimer interface [polypeptide binding]; other site 557723005268 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 557723005269 active site 557723005270 trimer interface [polypeptide binding]; other site 557723005271 allosteric site; other site 557723005272 active site lid [active] 557723005273 hexamer (dimer of trimers) interface [polypeptide binding]; other site 557723005274 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 557723005275 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557723005276 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557723005277 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 557723005278 Sodium:solute symporter family; Region: SSF; cl00456 557723005279 Protein of unknown function (DUF997); Region: DUF997; cl01614 557723005280 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ...; Region: Met_repressor_MetJ; cd00490 557723005281 dimerization interface [polypeptide binding]; other site 557723005282 DNA binding site [nucleotide binding] 557723005283 corepressor binding sites; other site 557723005284 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 557723005285 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 557723005286 transcription-repair coupling factor; Provisional; Region: PRK10689 557723005287 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 557723005288 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 557723005289 ATP binding site [chemical binding]; other site 557723005290 putative Mg++ binding site [ion binding]; other site 557723005291 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 557723005292 nucleotide binding region [chemical binding]; other site 557723005293 ATP-binding site [chemical binding]; other site 557723005294 TRCF domain; Region: TRCF; cl04088 557723005295 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 557723005296 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557723005297 putative substrate translocation pore; other site 557723005298 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 557723005299 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 557723005300 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557723005301 catalytic residue [active] 557723005302 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 557723005303 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557723005304 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 557723005305 dimer interface [polypeptide binding]; other site 557723005306 catalytic triad [active] 557723005307 peroxidatic and resolving cysteines [active] 557723005308 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 557723005309 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 557723005310 putative acyl-acceptor binding pocket; other site 557723005311 Osmosensory transporter coiled coil; Region: Osmo_CC; pfam08946 557723005312 FtsI repressor; Provisional; Region: PRK10883 557723005313 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557723005314 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 557723005315 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 557723005316 Mor transcription activator family; Region: Mor; cl02360 557723005317 PTS system, glucose-specific IIBC component; Region: PTS-II-BC-glcB; TIGR02002 557723005318 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 557723005319 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 557723005320 active site turn [active] 557723005321 phosphorylation site [posttranslational modification] 557723005322 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723005323 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723005324 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723005325 cystine transporter subunit; Provisional; Region: PRK11260 557723005326 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 557723005327 substrate binding pocket [chemical binding]; other site 557723005328 membrane-bound complex binding site; other site 557723005329 hinge residues; other site 557723005330 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557723005331 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 557723005332 dimer interface [polypeptide binding]; other site 557723005333 conserved gate region; other site 557723005334 putative PBP binding loops; other site 557723005335 ABC-ATPase subunit interface; other site 557723005336 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557723005337 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557723005338 Walker A/P-loop; other site 557723005339 ATP binding site [chemical binding]; other site 557723005340 Q-loop/lid; other site 557723005341 ABC transporter signature motif; other site 557723005342 Walker B; other site 557723005343 D-loop; other site 557723005344 H-loop/switch region; other site 557723005345 Protein of unknown function DUF262; Region: DUF262; cl14890 557723005346 Protein of unknown function DUF262; Region: DUF262; cl14890 557723005347 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 557723005348 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723005349 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723005350 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 557723005351 active site 557723005352 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 557723005353 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 557723005354 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 557723005355 active site 557723005356 FMN binding site [chemical binding]; other site 557723005357 substrate binding site [chemical binding]; other site 557723005358 3Fe-4S cluster binding site [ion binding]; other site 557723005359 Glutamate synthase domain 3 [Amino acid transport and metabolism]; Region: GltB; COG0070 557723005360 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 557723005361 domain interface; other site 557723005362 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723005363 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723005364 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723005365 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 557723005366 homotrimer interaction site [polypeptide binding]; other site 557723005367 putative active site [active] 557723005368 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 557723005369 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 557723005370 homodimer interface [polypeptide binding]; other site 557723005371 substrate-cofactor binding pocket; other site 557723005372 catalytic residue [active] 557723005373 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557723005374 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723005375 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 557723005376 dimerization interface [polypeptide binding]; other site 557723005377 substrate binding pocket [chemical binding]; other site 557723005378 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 557723005379 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 557723005380 motif II; other site 557723005381 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 557723005382 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723005383 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 557723005384 substrate binding site [chemical binding]; other site 557723005385 dimerization interface [polypeptide binding]; other site 557723005386 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 557723005387 active site 557723005388 metal binding site [ion binding]; metal-binding site 557723005389 hexamer interface [polypeptide binding]; other site 557723005390 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 557723005391 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723005392 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 557723005393 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 557723005394 cofactor binding site; other site 557723005395 DNA binding site [nucleotide binding] 557723005396 substrate interaction site [chemical binding]; other site 557723005397 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 557723005398 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694; cl15446 557723005399 cytoskeletal protein RodZ; Provisional; Region: PRK10856 557723005400 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723005401 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 557723005402 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 557723005403 tandem repeat interface [polypeptide binding]; other site 557723005404 oligomer interface [polypeptide binding]; other site 557723005405 active site residues [active] 557723005406 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 557723005407 tandem repeat interface [polypeptide binding]; other site 557723005408 oligomer interface [polypeptide binding]; other site 557723005409 active site residues [active] 557723005410 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 557723005411 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557723005412 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 557723005413 Walker A/P-loop; other site 557723005414 ATP binding site [chemical binding]; other site 557723005415 Q-loop/lid; other site 557723005416 ABC transporter signature motif; other site 557723005417 Walker B; other site 557723005418 D-loop; other site 557723005419 H-loop/switch region; other site 557723005420 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 557723005421 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005422 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 557723005423 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 557723005424 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005425 Walker A/P-loop; other site 557723005426 ATP binding site [chemical binding]; other site 557723005427 Q-loop/lid; other site 557723005428 ABC transporter signature motif; other site 557723005429 Walker B; other site 557723005430 D-loop; other site 557723005431 H-loop/switch region; other site 557723005432 CcmB protein; Region: CcmB; cl01016 557723005433 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557723005434 Heme exporter protein D (CcmD); Region: CcmD; cl11475 557723005435 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 557723005436 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 557723005437 transmembrane helices; other site 557723005438 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 557723005439 hinge regions; other site 557723005440 ADP binding site [chemical binding]; other site 557723005441 catalytic site [active] 557723005442 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 557723005443 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 557723005444 active site 557723005445 intersubunit interface [polypeptide binding]; other site 557723005446 zinc binding site [ion binding]; other site 557723005447 Na+ binding site [ion binding]; other site 557723005448 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 557723005449 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723005450 Walker A/P-loop; other site 557723005451 ATP binding site [chemical binding]; other site 557723005452 Q-loop/lid; other site 557723005453 ABC transporter signature motif; other site 557723005454 Walker B; other site 557723005455 D-loop; other site 557723005456 H-loop/switch region; other site 557723005457 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723005458 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 557723005459 dimer interface [polypeptide binding]; other site 557723005460 FMN binding site [chemical binding]; other site 557723005461 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 557723005462 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723005463 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557723005464 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 557723005465 domain; Region: GreA_GreB_N; pfam03449 557723005466 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557723005467 KpsF/GutQ family protein; Region: kpsF; TIGR00393 557723005468 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 557723005469 putative active site [active] 557723005470 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 557723005471 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 557723005472 binding surface 557723005473 TPR motif; other site 557723005474 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 557723005475 Transposase; Region: DEDD_Tnp_IS110; pfam01548 557723005476 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 557723005477 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 557723005478 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 557723005479 FeS/SAM binding site; other site 557723005480 Predicted transcriptional regulator [Transcription]; Region: COG2944 557723005481 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 557723005482 non-specific DNA binding site [nucleotide binding]; other site 557723005483 salt bridge; other site 557723005484 sequence-specific DNA binding site [nucleotide binding]; other site 557723005485 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 557723005486 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 557723005487 HIGH motif; other site 557723005488 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 557723005489 active site 557723005490 KMSKS motif; other site 557723005491 copper exporting ATPase; Provisional; Region: copA; PRK10671 557723005492 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557723005493 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557723005494 Cytochrome b562; Region: Cytochrom_B562; cl01546 557723005495 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 557723005496 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 557723005497 dimer interface [polypeptide binding]; other site 557723005498 active site 557723005499 Restriction endonuclease [Defense mechanisms]; Region: COG3587 557723005500 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005501 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 557723005502 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723005503 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 557723005504 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 557723005505 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 557723005506 GDP-binding site [chemical binding]; other site 557723005507 ACT binding site; other site 557723005508 IMP binding site; other site 557723005509 FtsH protease regulator HflC; Provisional; Region: PRK11029 557723005510 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 557723005511 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 557723005512 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 557723005513 HflK protein; Region: hflK; TIGR01933 557723005514 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 557723005515 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557723005516 Coenzyme A binding pocket [chemical binding]; other site 557723005517 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 557723005518 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 557723005519 inhibitor-cofactor binding pocket; inhibition site 557723005520 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723005521 catalytic residue [active] 557723005522 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 557723005523 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005524 Walker A/P-loop; other site 557723005525 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 557723005526 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 557723005527 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 557723005528 active site 557723005529 catalytic site [active] 557723005530 substrate binding site [chemical binding]; other site 557723005531 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557723005532 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 557723005533 dimer interface [polypeptide binding]; other site 557723005534 active site 557723005535 metal binding site [ion binding]; metal-binding site 557723005536 glutathione binding site [chemical binding]; other site 557723005537 Dicarboxylate transport; Region: DctA-YdbH; cl14674 557723005538 Predicted transcriptional regulator [Transcription]; Region: COG2944 557723005539 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 557723005540 non-specific DNA binding site [nucleotide binding]; other site 557723005541 salt bridge; other site 557723005542 sequence-specific DNA binding site [nucleotide binding]; other site 557723005543 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 557723005544 Malic enzyme, N-terminal domain; Region: malic; pfam00390 557723005545 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 557723005546 putative NAD(P) binding site [chemical binding]; other site 557723005547 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 557723005548 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 557723005549 putative GSH binding site [chemical binding]; other site 557723005550 catalytic residues [active] 557723005551 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 557723005552 Putative ATPase (DUF699); Region: DUF699; pfam05127 557723005553 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557723005554 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 557723005555 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 557723005556 N-terminal plug; other site 557723005557 ligand-binding site [chemical binding]; other site 557723005558 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 557723005559 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557723005560 Surface antigen; Region: Bac_surface_Ag; cl03097 557723005561 haemagglutination activity domain; Region: Haemagg_act; cl05436 557723005562 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557723005563 pyruvate kinase; Provisional; Region: PRK05826 557723005564 domain interfaces; other site 557723005565 active site 557723005566 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 557723005567 catalytic core [active] 557723005568 sugar phosphate antiporter; Reviewed; Region: uhpT; PRK09556 557723005569 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 557723005570 putative substrate translocation pore; other site 557723005571 sensory histidine kinase UhpB; Provisional; Region: PRK11644 557723005572 MASE1; Region: MASE1; pfam05231 557723005573 Histidine kinase; Region: HisKA_3; pfam07730 557723005574 6-phosphofructokinase; Provisional; Region: PRK03202 557723005575 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 557723005576 active site 557723005577 ADP/pyrophosphate binding site [chemical binding]; other site 557723005578 dimerization interface [polypeptide binding]; other site 557723005579 allosteric effector site; other site 557723005580 fructose-1,6-bisphosphate binding site; other site 557723005581 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 557723005582 Aminotransferase class-V; Region: Aminotran_5; pfam00266 557723005583 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557723005584 catalytic residue [active] 557723005585 Staphylococcal nuclease homologues; Region: SNc; smart00318 557723005586 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 557723005587 Catalytic site; other site 557723005588 Excalibur calcium-binding domain; Region: Excalibur; cl05460 557723005589 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557723005590 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 557723005591 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 557723005592 putative dimerization interface [polypeptide binding]; other site 557723005593 proline dipeptidase; Provisional; Region: PRK13607 557723005594 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 557723005595 active site 557723005596 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 557723005597 CPxP motif; other site 557723005598 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 557723005599 S-adenosylmethionine binding site [chemical binding]; other site 557723005600 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 557723005601 RNase E inhibitor protein; Provisional; Region: PRK11191 557723005602 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 557723005603 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 557723005604 G1 box; other site 557723005605 GTP/Mg2+ binding site [chemical binding]; other site 557723005606 Switch I region; other site 557723005607 G2 box; other site 557723005608 G3 box; other site 557723005609 Switch II region; other site 557723005610 G4 box; other site 557723005611 G5 box; other site 557723005612 Protein of unknown function (DUF805); Region: DUF805; cl01224 557723005613 aminopeptidase N; Provisional; Region: pepN; PRK14015 557723005614 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 557723005615 active site 557723005616 Zn binding site [ion binding]; other site 557723005617 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 557723005618 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557723005619 catalytic residue [active] 557723005620 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 557723005621 active site 557723005622 motif I; other site 557723005623 motif II; other site 557723005624 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 557723005625 putative active site [active] 557723005626 putative substrate binding site [chemical binding]; other site 557723005627 dimer interface [polypeptide binding]; other site 557723005628 catalytic site [active] 557723005629 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 557723005630 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 557723005631 active site 557723005632 metal binding site [ion binding]; metal-binding site 557723005633 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557723005634 putative peptidoglycan binding site; other site 557723005635 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 557723005636 putative active site [active] 557723005637 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 557723005638 ligand binding site; other site 557723005639 tetramer interface; other site 557723005640 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 557723005641 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 557723005642 active site 557723005643 GT2_AmsE_like is involved in exopolysaccharide amylovora biosynthesis; Region: GT2_AmsE_like; cd04195 557723005644 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557723005645 CcmE; Region: CcmE; cl00994 557723005646 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 557723005647 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 557723005648 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 557723005649 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 557723005650 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723005651 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 557723005652 rod shape-determining protein MreB; Provisional; Region: PRK13927 557723005653 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 557723005654 ATP binding site [chemical binding]; other site 557723005655 profilin binding site; other site 557723005656 rod shape-determining protein MreC; Provisional; Region: PRK14872 557723005657 rod shape-determining protein MreC; Region: MreC; pfam04085 557723005658 rod shape-determining protein MreD; Region: MreD; cl01087 557723005659 recombination factor protein RarA; Reviewed; Region: PRK13342 557723005660 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 557723005661 Walker A motif; other site 557723005662 ATP binding site [chemical binding]; other site 557723005663 Walker B motif; other site 557723005664 arginine finger; other site 557723005665 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 557723005666 Protein of unknown function (DUF560); Region: DUF560; pfam04575 557723005667 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557723005668 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557723005669 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557723005670 Transferrin binding protein-like solute binding protein; Region: Lipoprotein_5; pfam01298 557723005671 TonB-dependent lactoferrin and transferrin receptors; Region: TonB-tbp-lbp; TIGR01776 557723005672 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 557723005673 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 557723005674 ligand-binding site [chemical binding]; other site 557723005675 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 557723005676 30S subunit binding site; other site 557723005677 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 557723005678 putative acyl-acceptor binding pocket; other site 557723005679 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 557723005680 dimerization interface [polypeptide binding]; other site 557723005681 active site 557723005682 Domain of unknown function (DUF74); Region: DUF74; cl00426 557723005683 Flagellin N-methylase; Region: FliB; cl00497 557723005684 excinuclease ABC subunit B; Provisional; Region: PRK05298 557723005685 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 557723005686 ATP binding site [chemical binding]; other site 557723005687 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 557723005688 nucleotide binding region [chemical binding]; other site 557723005689 ATP-binding site [chemical binding]; other site 557723005690 Ultra-violet resistance protein B; Region: UvrB; pfam12344 557723005691 UvrB/uvrC motif; Region: UVR; pfam02151 557723005692 PII uridylyl-transferase; Provisional; Region: glnD; PRK01759 557723005693 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557723005694 metal binding triad; other site 557723005695 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557723005696 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557723005697 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 557723005698 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 557723005699 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 557723005700 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 557723005701 putative PBP binding loops; other site 557723005702 dimer interface [polypeptide binding]; other site 557723005703 ABC-ATPase subunit interface; other site 557723005704 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 557723005705 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557723005706 Walker A/P-loop; other site 557723005707 ATP binding site [chemical binding]; other site 557723005708 Q-loop/lid; other site 557723005709 ABC transporter signature motif; other site 557723005710 Walker B; other site 557723005711 D-loop; other site 557723005712 H-loop/switch region; other site 557723005713 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557723005714 enolase; Provisional; Region: eno; PRK00077 557723005715 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 557723005716 dimer interface [polypeptide binding]; other site 557723005717 metal binding site [ion binding]; metal-binding site 557723005718 substrate binding pocket [chemical binding]; other site 557723005719 Protein of unknown function (DUF520); Region: DUF520; cl00723 557723005720 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 557723005721 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557723005722 ATP binding site [chemical binding]; other site 557723005723 Mg2+ binding site [ion binding]; other site 557723005724 G-X-G motif; other site 557723005725 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 557723005726 anchoring element; other site 557723005727 dimer interface [polypeptide binding]; other site 557723005728 ATP binding site [chemical binding]; other site 557723005729 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 557723005730 active site 557723005731 putative metal-binding site [ion binding]; other site 557723005732 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 557723005733 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 557723005734 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 557723005735 tetramer interface [polypeptide binding]; other site 557723005736 heme binding pocket [chemical binding]; other site 557723005737 NADPH binding site [chemical binding]; other site 557723005738 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 557723005739 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557723005740 putative active site [active] 557723005741 putative metal binding site [ion binding]; other site 557723005742 Organiser of macrodomain of Terminus of chromosome; Region: MatP; cl11476 557723005743 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 557723005744 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 557723005745 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557723005746 active site 2 [active] 557723005747 active site 1 [active] 557723005748 hypothetical protein; Provisional; Region: PRK10506 557723005749 hypothetical protein; Provisional; Region: PRK10557 557723005750 multidrug efflux protein; Reviewed; Region: PRK01766 557723005751 MatE; Region: MatE; cl10513 557723005752 MatE; Region: MatE; cl10513 557723005753 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 557723005754 active site 557723005755 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 557723005756 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 557723005757 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 557723005758 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 557723005759 Walker A/P-loop; other site 557723005760 ATP binding site [chemical binding]; other site 557723005761 Q-loop/lid; other site 557723005762 ABC transporter signature motif; other site 557723005763 Walker B; other site 557723005764 D-loop; other site 557723005765 H-loop/switch region; other site 557723005766 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 557723005767 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 557723005768 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 557723005769 putative metal binding site [ion binding]; other site 557723005770 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 557723005771 putative active site [active] 557723005772 Ap4A binding site [chemical binding]; other site 557723005773 nudix motif; other site 557723005774 putative metal binding site [ion binding]; other site 557723005775 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557723005776 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557723005777 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 557723005778 LexA regulated protein; Provisional; Region: PRK11675 557723005779 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557723005780 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 557723005781 metal binding site 2 [ion binding]; metal-binding site 557723005782 putative DNA binding helix; other site 557723005783 metal binding site 1 [ion binding]; metal-binding site 557723005784 dimer interface [polypeptide binding]; other site 557723005785 structural Zn2+ binding site [ion binding]; other site 557723005786 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 557723005787 mce related protein; Region: MCE; cl15431 557723005788 mce related protein; Region: MCE; cl15431 557723005789 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 557723005790 mce related protein; Region: MCE; cl15431 557723005791 mce related protein; Region: MCE; cl15431 557723005792 mce related protein; Region: MCE; cl15431 557723005793 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 557723005794 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 557723005795 carboxy-terminal protease; Provisional; Region: PRK11186 557723005796 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 557723005797 protein binding site [polypeptide binding]; other site 557723005798 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 557723005799 Catalytic dyad [active] 557723005800 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 557723005801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 557723005802 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 557723005803 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 557723005804 Peptidase M15; Region: Peptidase_M15_3; cl01194 557723005805 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557723005806 VacJ like lipoprotein; Region: VacJ; cl01073 557723005807 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 557723005808 cystathionine gamma-synthase; Reviewed; Region: PRK08247 557723005809 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 557723005810 homodimer interface [polypeptide binding]; other site 557723005811 substrate-cofactor binding pocket; other site 557723005812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557723005813 catalytic residue [active] 557723005814 dihydrodipicolinate reductase; Provisional; Region: PRK00048 557723005815 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557723005816 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 557723005817 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 557723005818 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 557723005819 FAD binding site [chemical binding]; other site 557723005820 isocitrate dehydrogenase; Validated; Region: PRK07362 557723005821 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 557723005822 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 557723005823 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 557723005824 substrate binding site [chemical binding]; other site 557723005825 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 557723005826 substrate binding site [chemical binding]; other site 557723005827 ligand binding site [chemical binding]; other site 557723005828 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 557723005829 dimer interface [polypeptide binding]; other site 557723005830 Citrate synthase; Region: Citrate_synt; pfam00285 557723005831 active site 557723005832 citrylCoA binding site [chemical binding]; other site 557723005833 NADH binding [chemical binding]; other site 557723005834 cationic pore residues; other site 557723005835 oxalacetate/citrate binding site [chemical binding]; other site 557723005836 coenzyme A binding site [chemical binding]; other site 557723005837 catalytic triad [active] 557723005838 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 557723005839 Adenylate kinase; Region: ADK; pfam00406 557723005840 AMP-binding site [chemical binding]; other site 557723005841 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 557723005842 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 557723005843 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 557723005844 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 557723005845 active site 557723005846 dimer interface [polypeptide binding]; other site 557723005847 metal binding site [ion binding]; metal-binding site 557723005848 shikimate kinase; Reviewed; Region: aroK; PRK00131 557723005849 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 557723005850 ADP binding site [chemical binding]; other site 557723005851 magnesium binding site [ion binding]; other site 557723005852 putative shikimate binding site; other site 557723005853 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 557723005854 Transglycosylase; Region: Transgly; cl07896 557723005855 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557723005856 Cell division protein FtsA; Region: FtsA; cl11496 557723005857 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 557723005858 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557723005859 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557723005860 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 557723005861 putative RNA binding site [nucleotide binding]; other site 557723005862 thiamine monophosphate kinase; Provisional; Region: PRK05731 557723005863 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 557723005864 ATP binding site [chemical binding]; other site 557723005865 dimerization interface [polypeptide binding]; other site 557723005866 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 557723005867 tetramer interfaces [polypeptide binding]; other site 557723005868 binuclear metal-binding site [ion binding]; other site 557723005869 LysE type translocator; Region: LysE; cl00565 557723005870 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 557723005871 catalytic residues [active] 557723005872 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557723005873 CoenzymeA binding site [chemical binding]; other site 557723005874 subunit interaction site [polypeptide binding]; other site 557723005875 PHB binding site; other site 557723005876 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557723005877 FAD binding domain; Region: FAD_binding_4; pfam01565 557723005878 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 557723005879 outer membrane protein A; Reviewed; Region: PRK10808 557723005880 Surface antigen; Region: Surface_Ag_2; cl01155 557723005881 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557723005882 ligand binding site [chemical binding]; other site 557723005883 SelR domain; Region: SelR; cl00369