-- dump date 20140619_091900 -- class Genbank::misc_feature -- table misc_feature_note -- id note 515619000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 515619000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 515619000003 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 515619000004 Walker A motif; other site 515619000005 ATP binding site [chemical binding]; other site 515619000006 Walker B motif; other site 515619000007 arginine finger; other site 515619000008 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 515619000009 DnaA box-binding interface [nucleotide binding]; other site 515619000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 515619000011 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 515619000012 putative DNA binding surface [nucleotide binding]; other site 515619000013 dimer interface [polypeptide binding]; other site 515619000014 beta-clamp/clamp loader binding surface; other site 515619000015 beta-clamp/translesion DNA polymerase binding surface; other site 515619000016 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 515619000017 RNA binding surface [nucleotide binding]; other site 515619000018 recombination protein F; Reviewed; Region: recF; PRK00064 515619000019 ATP-binding cassette domain of RecF; Region: ABC_RecF; cd03242 515619000020 Walker A/P-loop; other site 515619000021 ATP binding site [chemical binding]; other site 515619000022 Q-loop/lid; other site 515619000023 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619000024 ABC transporter signature motif; other site 515619000025 Walker B; other site 515619000026 D-loop; other site 515619000027 H-loop/switch region; other site 515619000028 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 515619000029 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 515619000030 Mg2+ binding site [ion binding]; other site 515619000031 G-X-G motif; other site 515619000032 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 515619000033 anchoring element; other site 515619000034 dimer interface [polypeptide binding]; other site 515619000035 ATP binding site [chemical binding]; other site 515619000036 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 515619000037 active site 515619000038 putative metal-binding site [ion binding]; other site 515619000039 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 515619000040 DNA gyrase subunit A; Validated; Region: PRK05560 515619000041 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 515619000042 CAP-like domain; other site 515619000043 active site 515619000044 primary dimer interface [polypeptide binding]; other site 515619000045 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 515619000046 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 515619000047 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 515619000048 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 515619000049 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 515619000050 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 515619000051 fumarate hydratase; Provisional; Region: PRK06246 515619000052 Fumarase C-terminus; Region: Fumerase_C; cl00795 515619000053 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 515619000054 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 515619000055 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 515619000056 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 515619000057 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 515619000058 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 515619000059 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 515619000060 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 515619000061 putative substrate binding site [chemical binding]; other site 515619000062 putative ATP binding site [chemical binding]; other site 515619000063 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 515619000064 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 515619000065 active site 515619000066 phosphorylation site [posttranslational modification] 515619000067 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 515619000068 active site 515619000069 P-loop; other site 515619000070 phosphorylation site [posttranslational modification] 515619000071 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; COG1299 515619000072 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 515619000073 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 515619000074 nucleotide binding site [chemical binding]; other site 515619000075 NEF interaction site [polypeptide binding]; other site 515619000076 SBD interface [polypeptide binding]; other site 515619000077 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619000078 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619000079 active site 515619000080 phosphorylation site [posttranslational modification] 515619000081 intermolecular recognition site; other site 515619000082 dimerization interface [polypeptide binding]; other site 515619000083 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 515619000084 DNA binding site [nucleotide binding] 515619000085 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619000086 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 515619000087 dimer interface [polypeptide binding]; other site 515619000088 phosphorylation site [posttranslational modification] 515619000089 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 515619000090 ATP binding site [chemical binding]; other site 515619000091 Mg2+ binding site [ion binding]; other site 515619000092 G-X-G motif; other site 515619000093 putative hydratase; Provisional; Region: PRK11413 515619000094 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 515619000095 substrate binding site [chemical binding]; other site 515619000096 ligand binding site [chemical binding]; other site 515619000097 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 515619000098 substrate binding site [chemical binding]; other site 515619000099 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 515619000100 Domain of unknown function DUF20; Region: UPF0118; pfam01594 515619000101 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 515619000102 binding surface 515619000103 Tetratricopeptide repeat; Region: TPR_16; pfam13432 515619000104 TPR motif; other site 515619000105 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 515619000106 stage V sporulation protein K; Region: spore_V_K; TIGR02881 515619000107 Walker A motif; other site 515619000108 ATP binding site [chemical binding]; other site 515619000109 Walker B motif; other site 515619000110 glycogen branching enzyme; Provisional; Region: PRK12313 515619000111 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 515619000112 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 515619000113 active site 515619000114 catalytic site [active] 515619000115 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 515619000116 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 515619000117 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 515619000118 active site 515619000119 metal binding site [ion binding]; metal-binding site 515619000120 Bacterial SH3 domain homologues; Region: SH3b; smart00287 515619000121 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 515619000122 active site 515619000123 Catalytic domain of Protein Kinases; Region: PKc; cd00180 515619000124 active site 515619000125 ATP binding site [chemical binding]; other site 515619000126 substrate binding site [chemical binding]; other site 515619000127 activation loop (A-loop); other site 515619000128 Negative regulator of genetic competence (MecA); Region: MecA; cl02022 515619000129 hybrid cluster protein-associated redox disulfide domain; Region: prismane_assoc; TIGR03980 515619000130 flagellin; Provisional; Region: PRK12806 515619000131 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 515619000132 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 515619000133 Flagellar protein FliS; Region: FliS; cl00654 515619000134 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 515619000135 AAA domain; Region: AAA_31; pfam13614 515619000136 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 515619000137 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 515619000138 ATP binding site [chemical binding]; other site 515619000139 Walker A motif; other site 515619000140 hexamer interface [polypeptide binding]; other site 515619000141 Walker B motif; other site 515619000142 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 515619000143 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 515619000144 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 515619000145 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 515619000146 phosphopeptide binding site; other site 515619000147 Rhomboid family; Region: Rhomboid; pfam01694 515619000148 SCP-2 sterol transfer family; Region: SCP2; pfam02036 515619000149 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 515619000150 HIT family signature motif; other site 515619000151 catalytic residue [active] 515619000152 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Reviewed; Region: PRK12446 515619000153 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 515619000154 active site 515619000155 homodimer interface [polypeptide binding]; other site 515619000156 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619000157 Bacterial SH3 domain; Region: SH3_3; cl17532 515619000158 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 515619000159 ornithine carbamoyltransferase; Validated; Region: PRK02102 515619000160 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 515619000161 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 515619000162 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 515619000163 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619000164 DNA-binding site [nucleotide binding]; DNA binding site 515619000165 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 515619000166 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 515619000167 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 515619000168 nucleotide binding site [chemical binding]; other site 515619000169 Type III pantothenate kinase; Region: Pan_kinase; cl17198 515619000170 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 515619000171 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 515619000172 FMN binding site [chemical binding]; other site 515619000173 active site 515619000174 catalytic residues [active] 515619000175 substrate binding site [chemical binding]; other site 515619000176 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 515619000177 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 515619000178 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 515619000179 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 515619000180 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 515619000181 dimer interface [polypeptide binding]; other site 515619000182 putative anticodon binding site; other site 515619000183 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 515619000184 motif 1; other site 515619000185 active site 515619000186 motif 2; other site 515619000187 motif 3; other site 515619000188 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 515619000189 Putative transposase; Region: Y2_Tnp; pfam04986 515619000190 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 515619000191 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 515619000192 active site 515619000193 DNA binding site [nucleotide binding] 515619000194 Int/Topo IB signature motif; other site 515619000195 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619000196 NlpC/P60 family; Region: NLPC_P60; cl17555 515619000197 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619000198 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 515619000199 non-specific DNA binding site [nucleotide binding]; other site 515619000200 salt bridge; other site 515619000201 sequence-specific DNA binding site [nucleotide binding]; other site 515619000202 Resolvase, N terminal domain; Region: Resolvase; smart00857 515619000203 catalytic residues [active] 515619000204 Transposase; Region: DEDD_Tnp_IS110; pfam01548 515619000205 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 515619000206 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 515619000207 DNA binding domain of tn916 integrase; Region: Integrase_DNA; pfam02920 515619000208 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 515619000209 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 515619000210 Int/Topo IB signature motif; other site 515619000211 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 515619000212 dimer interface [polypeptide binding]; other site 515619000213 putative tRNA-binding site [nucleotide binding]; other site 515619000214 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 515619000215 Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Region: HTH_MerR-like; cd00592 515619000216 DNA binding residues [nucleotide binding] 515619000217 dimer interface [polypeptide binding]; other site 515619000218 hypothetical protein; Validated; Region: PRK07668 515619000219 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619000220 ATP-binding cassette domain of the bacitracin-resistance transporter; Region: ABC_BcrA_bacitracin_resist; cd03268 515619000221 Walker A/P-loop; other site 515619000222 ATP binding site [chemical binding]; other site 515619000223 Q-loop/lid; other site 515619000224 ABC transporter signature motif; other site 515619000225 Walker B; other site 515619000226 D-loop; other site 515619000227 H-loop/switch region; other site 515619000228 lantibiotic protection ABC transporter permease subunit, MutE/EpiE family; Region: lanti_perm_MutE; TIGR03732 515619000229 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619000230 lantibiotic protection ABC transporter permease subunit, MutG family; Region: lanti_perm_MutG; TIGR03733 515619000231 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619000232 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619000233 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619000234 active site 515619000235 phosphorylation site [posttranslational modification] 515619000236 intermolecular recognition site; other site 515619000237 dimerization interface [polypeptide binding]; other site 515619000238 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 515619000239 DNA binding site [nucleotide binding] 515619000240 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619000241 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 515619000242 dimer interface [polypeptide binding]; other site 515619000243 phosphorylation site [posttranslational modification] 515619000244 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 515619000245 ATP binding site [chemical binding]; other site 515619000246 Mg2+ binding site [ion binding]; other site 515619000247 G-X-G motif; other site 515619000248 septum formation inhibitor; Reviewed; Region: minC; PRK00513 515619000249 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 515619000250 septum site-determining protein MinD; Region: minD_bact; TIGR01968 515619000251 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 515619000252 Switch I; other site 515619000253 Switch II; other site 515619000254 Septum formation topological specificity factor MinE; Region: MinE; cl00538 515619000255 hypothetical protein; Provisional; Region: PRK09609 515619000256 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 515619000257 acetylornithine aminotransferase; Provisional; Region: PRK02627 515619000258 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 515619000259 inhibitor-cofactor binding pocket; inhibition site 515619000260 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619000261 catalytic residue [active] 515619000262 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619000263 ethanolamine permease; Region: 2A0305; TIGR00908 515619000264 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 515619000265 iron-containing alcohol dehydrogenases (Fe-ADH)-like; Region: Fe-ADH; cd08551 515619000266 active site 515619000267 metal binding site [ion binding]; metal-binding site 515619000268 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 515619000269 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 515619000270 non-specific DNA binding site [nucleotide binding]; other site 515619000271 salt bridge; other site 515619000272 sequence-specific DNA binding site [nucleotide binding]; other site 515619000273 Cupin domain; Region: Cupin_2; pfam07883 515619000274 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619000275 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619000276 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619000277 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619000278 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 515619000279 Walker A/P-loop; other site 515619000280 ATP binding site [chemical binding]; other site 515619000281 Q-loop/lid; other site 515619000282 ABC transporter signature motif; other site 515619000283 Walker B; other site 515619000284 D-loop; other site 515619000285 H-loop/switch region; other site 515619000286 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cl17915 515619000287 active site 515619000288 motif I; other site 515619000289 motif II; other site 515619000290 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 515619000291 FlgN protein; Region: FlgN; pfam05130 515619000292 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 515619000293 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 515619000294 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 515619000295 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 515619000296 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 515619000297 FliW protein; Region: FliW; cl00740 515619000298 Global regulator protein family; Region: CsrA; pfam02599 515619000299 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg1; cd04764 515619000300 DNA binding residues [nucleotide binding] 515619000301 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 515619000302 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 515619000303 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 515619000304 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 515619000305 Low molecular weight phosphatase family; Region: LMWPc; cl00105 515619000306 active site 515619000307 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619000308 active site 515619000309 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 515619000310 catalytic motif [active] 515619000311 Zn binding site [ion binding]; other site 515619000312 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 515619000313 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 515619000314 F0F1 ATP synthase subunit C; Provisional; Region: PRK13469 515619000315 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 515619000316 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 515619000317 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 515619000318 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 515619000319 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 515619000320 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 515619000321 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 515619000322 beta subunit interaction interface [polypeptide binding]; other site 515619000323 Walker A motif; other site 515619000324 ATP binding site [chemical binding]; other site 515619000325 Walker B motif; other site 515619000326 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 515619000327 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 515619000328 core domain interface [polypeptide binding]; other site 515619000329 delta subunit interface [polypeptide binding]; other site 515619000330 epsilon subunit interface [polypeptide binding]; other site 515619000331 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 515619000332 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 515619000333 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 515619000334 alpha subunit interaction interface [polypeptide binding]; other site 515619000335 Walker A motif; other site 515619000336 ATP binding site [chemical binding]; other site 515619000337 Walker B motif; other site 515619000338 inhibitor binding site; inhibition site 515619000339 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 515619000340 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 515619000341 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 515619000342 gamma subunit interface [polypeptide binding]; other site 515619000343 epsilon subunit interface [polypeptide binding]; other site 515619000344 LBP interface [polypeptide binding]; other site 515619000345 Riboflavin kinase; Region: Flavokinase; cl03312 515619000346 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619000347 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 515619000348 DNA binding site [nucleotide binding] 515619000349 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619000350 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619000351 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK13450 515619000352 Cupin domain; Region: Cupin_2; cl17218 515619000353 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619000354 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619000355 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family; Region: bind_CPR_0540; TIGR03850 515619000356 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619000357 ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]; Region: UgpA; COG1175 515619000358 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619000359 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619000360 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 515619000361 dimer interface [polypeptide binding]; other site 515619000362 conserved gate region; other site 515619000363 putative PBP binding loops; other site 515619000364 ABC-ATPase subunit interface; other site 515619000365 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase; Region: TIGR02336 515619000366 Lacto-N-biose phosphorylase; Region: Lact_bio_phlase; pfam09508 515619000367 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 515619000368 active site 515619000369 Phosphotransferase enzyme family; Region: APH; pfam01636 515619000370 3H domain; Region: 3H; pfam02829 515619000371 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 515619000372 active site 515619000373 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 515619000374 dimer interface [polypeptide binding]; other site 515619000375 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 515619000376 Ligand Binding Site [chemical binding]; other site 515619000377 Molecular Tunnel; other site 515619000378 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619000379 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619000380 Walker A/P-loop; other site 515619000381 ATP binding site [chemical binding]; other site 515619000382 Q-loop/lid; other site 515619000383 ABC transporter signature motif; other site 515619000384 Walker B; other site 515619000385 D-loop; other site 515619000386 H-loop/switch region; other site 515619000387 FtsX-like permease family; Region: FtsX; pfam02687 515619000388 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 515619000389 FtsX-like permease family; Region: FtsX; pfam02687 515619000390 HAMP domain; Region: HAMP; pfam00672 515619000391 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619000392 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619000393 dimer interface [polypeptide binding]; other site 515619000394 putative CheW interface [polypeptide binding]; other site 515619000395 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 515619000396 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619000397 Coenzyme A binding pocket [chemical binding]; other site 515619000398 Z1 domain; Region: Z1; pfam10593 515619000399 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 515619000400 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 515619000401 cofactor binding site; other site 515619000402 DNA binding site [nucleotide binding] 515619000403 substrate interaction site [chemical binding]; other site 515619000404 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 515619000405 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 515619000406 Domain of unknown function (DUF4420); Region: DUF4420; pfam14390 515619000407 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 515619000408 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 515619000409 cofactor binding site; other site 515619000410 DNA binding site [nucleotide binding] 515619000411 substrate interaction site [chemical binding]; other site 515619000412 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 515619000413 active site 515619000414 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 515619000415 non-specific DNA binding site [nucleotide binding]; other site 515619000416 salt bridge; other site 515619000417 sequence-specific DNA binding site [nucleotide binding]; other site 515619000418 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 515619000419 additional DNA contacts [nucleotide binding]; other site 515619000420 mismatch recognition site; other site 515619000421 active site 515619000422 zinc binding site [ion binding]; other site 515619000423 DNA intercalation site [nucleotide binding]; other site 515619000424 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 515619000425 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 515619000426 cofactor binding site; other site 515619000427 DNA binding site [nucleotide binding] 515619000428 substrate interaction site [chemical binding]; other site 515619000429 DNA binding domains of BfiI, EcoRII and plant B3 proteins; Region: BfiI_C_EcoRII_N_B3; cl15242 515619000430 DNA binding site [nucleotide binding] 515619000431 EcoRII C terminal; Region: EcoRII-C; pfam09019 515619000432 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619000433 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 515619000434 catalytic residues [active] 515619000435 catalytic nucleophile [active] 515619000436 Recombinase; Region: Recombinase; pfam07508 515619000437 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619000438 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 515619000439 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 515619000440 putative Mg++ binding site [ion binding]; other site 515619000441 nucleotide binding region [chemical binding]; other site 515619000442 Helicase conserved C-terminal domain; Region: Helicase_C; pfam00271 515619000443 ATP-binding site [chemical binding]; other site 515619000444 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 515619000445 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 515619000446 active site 515619000447 8-oxo-dGMP binding site [chemical binding]; other site 515619000448 nudix motif; other site 515619000449 metal binding site [ion binding]; metal-binding site 515619000450 Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from...; Region: ArsC_family; cd02977 515619000451 ArsC family; Region: ArsC; pfam03960 515619000452 catalytic residue [active] 515619000453 TIGR02300 family protein; Region: FYDLN_acid 515619000454 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 515619000455 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 515619000456 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 515619000457 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the...; Region: MTH1; cd03427 515619000458 putative active site [active] 515619000459 nucleotide binding site [chemical binding]; other site 515619000460 nudix motif; other site 515619000461 putative metal binding site [ion binding]; other site 515619000462 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 515619000463 Purine catabolism regulatory protein-like family; Region: PucR; pfam07905 515619000464 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 515619000465 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 515619000466 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 515619000467 substrate binding pocket [chemical binding]; other site 515619000468 membrane-bound complex binding site; other site 515619000469 hinge residues; other site 515619000470 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 515619000471 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 515619000472 dimer interface [polypeptide binding]; other site 515619000473 conserved gate region; other site 515619000474 putative PBP binding loops; other site 515619000475 ABC-ATPase subunit interface; other site 515619000476 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 515619000477 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 515619000478 Walker A/P-loop; other site 515619000479 ATP binding site [chemical binding]; other site 515619000480 Q-loop/lid; other site 515619000481 ABC transporter signature motif; other site 515619000482 Walker B; other site 515619000483 D-loop; other site 515619000484 H-loop/switch region; other site 515619000485 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619000486 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 515619000487 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619000488 Walker A/P-loop; other site 515619000489 ATP binding site [chemical binding]; other site 515619000490 Q-loop/lid; other site 515619000491 ABC transporter signature motif; other site 515619000492 Walker B; other site 515619000493 D-loop; other site 515619000494 H-loop/switch region; other site 515619000495 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 515619000496 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 515619000497 TM-ABC transporter signature motif; other site 515619000498 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 515619000499 zinc binding site [ion binding]; other site 515619000500 putative ligand binding site [chemical binding]; other site 515619000501 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 515619000502 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 515619000503 active site 515619000504 HIGH motif; other site 515619000505 dimer interface [polypeptide binding]; other site 515619000506 KMSKS motif; other site 515619000507 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 515619000508 RNA binding surface [nucleotide binding]; other site 515619000509 EUBREC_0194; RF00230 T-box leader; T-box leader 515619000510 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 515619000511 Sodium Bile acid symporter family; Region: SBF; pfam01758 515619000512 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 515619000513 Carbon starvation protein CstA; Region: CstA; pfam02554 515619000514 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 515619000515 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619000516 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 515619000517 endonuclease IV; Provisional; Region: PRK01060 515619000518 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 515619000519 AP (apurinic/apyrimidinic) site pocket; other site 515619000520 DNA interaction; other site 515619000521 Metal-binding active site; metal-binding site 515619000522 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 515619000523 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 515619000524 Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_1; cd09154 515619000525 putative active site [active] 515619000526 catalytic site [active] 515619000527 Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_2; cd09160 515619000528 putative active site [active] 515619000529 catalytic site [active] 515619000530 Acylphosphatase; Region: Acylphosphatase; pfam00708 515619000531 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 515619000532 PIN domain; Region: PIN_3; pfam13470 515619000533 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 515619000534 Domain of unknown function (DUF3783); Region: DUF3783; pfam12646 515619000535 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619000536 active site 515619000537 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619000538 phosphorylation site [posttranslational modification] 515619000539 intermolecular recognition site; other site 515619000540 dimerization interface [polypeptide binding]; other site 515619000541 LytTr DNA-binding domain; Region: LytTR; smart00850 515619000542 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 515619000543 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619000544 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619000545 Walker A/P-loop; other site 515619000546 ATP binding site [chemical binding]; other site 515619000547 Q-loop/lid; other site 515619000548 ABC transporter signature motif; other site 515619000549 Walker B; other site 515619000550 D-loop; other site 515619000551 H-loop/switch region; other site 515619000552 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619000553 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 515619000554 Cupin domain; Region: Cupin_2; pfam07883 515619000555 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619000556 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619000557 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 515619000558 zinc binding site [ion binding]; other site 515619000559 putative ligand binding site [chemical binding]; other site 515619000560 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 515619000561 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 515619000562 TM-ABC transporter signature motif; other site 515619000563 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 515619000564 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619000565 Walker A/P-loop; other site 515619000566 ATP binding site [chemical binding]; other site 515619000567 Q-loop/lid; other site 515619000568 ABC transporter signature motif; other site 515619000569 Walker B; other site 515619000570 D-loop; other site 515619000571 H-loop/switch region; other site 515619000572 Protein of unknown function (DUF3990); Region: DUF3990; pfam13151 515619000573 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 515619000574 non-specific DNA binding site [nucleotide binding]; other site 515619000575 salt bridge; other site 515619000576 sequence-specific DNA binding site [nucleotide binding]; other site 515619000577 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 515619000578 thiamine phosphate binding site [chemical binding]; other site 515619000579 active site 515619000580 pyrophosphate binding site [ion binding]; other site 515619000581 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 515619000582 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; cl15377 515619000583 FeS/SAM binding site; other site 515619000584 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 515619000585 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 515619000586 ThiS interaction site; other site 515619000587 putative active site [active] 515619000588 tetramer interface [polypeptide binding]; other site 515619000589 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 515619000590 thiS-thiF/thiG interaction site; other site 515619000591 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14095 515619000592 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 515619000593 active site 515619000594 dimer interface [polypeptide binding]; other site 515619000595 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 515619000596 dimer interface [polypeptide binding]; other site 515619000597 active site 515619000598 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 515619000599 [FeFe] hydrogenase H-cluster radical SAM maturase HydE; Region: rSAM_HydE; TIGR03956 515619000600 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 515619000601 FeS/SAM binding site; other site 515619000602 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 515619000603 [FeFe] hydrogenase H-cluster radical SAM maturase HydG; Region: rSAM_HydG; TIGR03955 515619000604 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 515619000605 FeS/SAM binding site; other site 515619000606 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 515619000607 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 515619000608 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 515619000609 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 515619000610 G1 box; other site 515619000611 GTP/Mg2+ binding site [chemical binding]; other site 515619000612 Switch I region; other site 515619000613 G2 box; other site 515619000614 Switch II region; other site 515619000615 G3 box; other site 515619000616 G4 box; other site 515619000617 G5 box; other site 515619000618 Domain of unknown function, E. rectale Gene description (DUF3877); Region: DUF3877; pfam12993 515619000619 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 515619000620 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 515619000621 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 515619000622 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 515619000623 FeS/SAM binding site; other site 515619000624 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 515619000625 active site 515619000626 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 515619000627 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 515619000628 S-adenosylmethionine binding site [chemical binding]; other site 515619000629 Peptidase family M23; Region: Peptidase_M23; pfam01551 515619000630 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619000631 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619000632 metal binding site [ion binding]; metal-binding site 515619000633 active site 515619000634 I-site; other site 515619000635 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 515619000636 GIY-YIG motif/motif A; other site 515619000637 putative active site [active] 515619000638 putative metal binding site [ion binding]; other site 515619000639 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 515619000640 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 515619000641 dimer interface [polypeptide binding]; other site 515619000642 conserved gate region; other site 515619000643 putative PBP binding loops; other site 515619000644 ABC-ATPase subunit interface; other site 515619000645 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619000646 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 515619000647 dimer interface [polypeptide binding]; other site 515619000648 conserved gate region; other site 515619000649 putative PBP binding loops; other site 515619000650 ABC-ATPase subunit interface; other site 515619000651 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619000652 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619000653 DNA binding site [nucleotide binding] 515619000654 domain linker motif; other site 515619000655 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619000656 ligand binding site [chemical binding]; other site 515619000657 dimerization interface [polypeptide binding]; other site 515619000658 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 515619000659 Domain of unknown function DUF20; Region: UPF0118; pfam01594 515619000660 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619000661 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619000662 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619000663 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619000664 DNA binding site [nucleotide binding] 515619000665 domain linker motif; other site 515619000666 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 515619000667 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619000668 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 515619000669 dimer interface [polypeptide binding]; other site 515619000670 conserved gate region; other site 515619000671 putative PBP binding loops; other site 515619000672 ABC-ATPase subunit interface; other site 515619000673 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619000674 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 515619000675 dimer interface [polypeptide binding]; other site 515619000676 conserved gate region; other site 515619000677 putative PBP binding loops; other site 515619000678 ABC-ATPase subunit interface; other site 515619000679 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619000680 Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]; Region: SacC; COG1621 515619000681 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 515619000682 substrate binding [chemical binding]; other site 515619000683 active site 515619000684 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 515619000685 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 515619000686 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 515619000687 putative substrate binding site [chemical binding]; other site 515619000688 putative ATP binding site [chemical binding]; other site 515619000689 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619000690 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619000691 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 515619000692 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 515619000693 Sulfate transporter family; Region: Sulfate_transp; pfam00916 515619000694 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 515619000695 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 515619000696 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 515619000697 ATP binding site [chemical binding]; other site 515619000698 putative Mg++ binding site [ion binding]; other site 515619000699 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 515619000700 nucleotide binding region [chemical binding]; other site 515619000701 ATP-binding site [chemical binding]; other site 515619000702 HRDC domain; Region: HRDC; pfam00570 515619000703 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; pfam07155 515619000704 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 515619000705 active site 515619000706 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 515619000707 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 515619000708 putative oligomer interface [polypeptide binding]; other site 515619000709 putative active site [active] 515619000710 metal binding site [ion binding]; metal-binding site 515619000711 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_1; cd08352 515619000712 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 515619000713 putative metal binding site [ion binding]; other site 515619000714 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 515619000715 CBD_II domain; Region: CBD_II; smart00637 515619000716 Cellulose binding domain; Region: CBM_2; pfam00553 515619000717 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 515619000718 metal ion-dependent adhesion site (MIDAS); other site 515619000719 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 515619000720 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 515619000721 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 515619000722 trimer interface [polypeptide binding]; other site 515619000723 putative Zn binding site [ion binding]; other site 515619000724 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 515619000725 Domain of unknown function (DUF1287); Region: DUF1287; cl01519 515619000726 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 515619000727 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619000728 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619000729 DNA binding site [nucleotide binding] 515619000730 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 515619000731 Glycosyl hydrolase family 32; Region: GH32_Aec43_like; cd08995 515619000732 active site 515619000733 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619000734 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619000735 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619000736 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 515619000737 putative PBP binding loops; other site 515619000738 dimer interface [polypeptide binding]; other site 515619000739 ABC-ATPase subunit interface; other site 515619000740 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619000741 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 515619000742 dimer interface [polypeptide binding]; other site 515619000743 conserved gate region; other site 515619000744 putative PBP binding loops; other site 515619000745 ABC-ATPase subunit interface; other site 515619000746 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 515619000747 Rubredoxin [Energy production and conversion]; Region: COG1773 515619000748 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 515619000749 iron binding site [ion binding]; other site 515619000750 Rubrerythrin [Energy production and conversion]; Region: COG1592 515619000751 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 515619000752 diiron binding motif [ion binding]; other site 515619000753 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 515619000754 metal binding site 2 [ion binding]; metal-binding site 515619000755 putative DNA binding helix; other site 515619000756 metal binding site 1 [ion binding]; metal-binding site 515619000757 dimer interface [polypeptide binding]; other site 515619000758 structural Zn2+ binding site [ion binding]; other site 515619000759 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 515619000760 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 515619000761 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 515619000762 intersubunit interface [polypeptide binding]; other site 515619000763 active site 515619000764 catalytic residue [active] 515619000765 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 515619000766 active site 515619000767 catalytic motif [active] 515619000768 Zn binding site [ion binding]; other site 515619000769 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 515619000770 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 515619000771 active site 515619000772 phosphopentomutase; Provisional; Region: PRK05362 515619000773 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 515619000774 purine nucleoside phosphorylase; Provisional; Region: PRK08202 515619000775 AAA domain; Region: AAA_22; pfam13401 515619000776 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 515619000777 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 515619000778 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 515619000779 nucleoside/Zn binding site; other site 515619000780 dimer interface [polypeptide binding]; other site 515619000781 catalytic motif [active] 515619000782 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 515619000783 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619000784 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 515619000785 DNA binding residues [nucleotide binding] 515619000786 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 515619000787 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 515619000788 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 515619000789 putative NADH binding site [chemical binding]; other site 515619000790 putative active site [active] 515619000791 nudix motif; other site 515619000792 putative metal binding site [ion binding]; other site 515619000793 Transcriptional regulator; Region: Rrf2; cl17282 515619000794 Rrf2 family protein; Region: rrf2_super; TIGR00738 515619000795 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 515619000796 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 515619000797 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619000798 catalytic residue [active] 515619000799 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 515619000800 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 515619000801 trimerization site [polypeptide binding]; other site 515619000802 active site 515619000803 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 515619000804 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 515619000805 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 515619000806 salt bridge; other site 515619000807 non-specific DNA binding site [nucleotide binding]; other site 515619000808 sequence-specific DNA binding site [nucleotide binding]; other site 515619000809 Protein of unknown function DUF86; Region: DUF86; cl01031 515619000810 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 515619000811 non-specific DNA binding site [nucleotide binding]; other site 515619000812 salt bridge; other site 515619000813 sequence-specific DNA binding site [nucleotide binding]; other site 515619000814 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 515619000815 active site 515619000816 NTP binding site [chemical binding]; other site 515619000817 metal binding triad [ion binding]; metal-binding site 515619000818 antibiotic binding site [chemical binding]; other site 515619000819 Archaeal ATPase; Region: Arch_ATPase; pfam01637 515619000820 AAA ATPase domain; Region: AAA_16; pfam13191 515619000821 Antitoxin of toxin-antitoxin stability system N-terminal; Region: RelB_N; pfam12910 515619000822 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 515619000823 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 515619000824 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 515619000825 dimer interface [polypeptide binding]; other site 515619000826 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619000827 catalytic residue [active] 515619000828 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 515619000829 non-specific DNA binding site [nucleotide binding]; other site 515619000830 salt bridge; other site 515619000831 sequence-specific DNA binding site [nucleotide binding]; other site 515619000832 HipA N-terminal domain; Region: Couple_hipA; cl11853 515619000833 HipA-like C-terminal domain; Region: HipA_C; pfam07804 515619000834 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 515619000835 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 515619000836 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 515619000837 FeS/SAM binding site; other site 515619000838 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl17272 515619000839 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 515619000840 dimer interface [polypeptide binding]; other site 515619000841 pyridoxal binding site [chemical binding]; other site 515619000842 ATP binding site [chemical binding]; other site 515619000843 Protein of unknown function, DUF624; Region: DUF624; pfam04854 515619000844 6-phosphofructokinase; Provisional; Region: PRK03202 515619000845 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 515619000846 active site 515619000847 ADP/pyrophosphate binding site [chemical binding]; other site 515619000848 dimerization interface [polypeptide binding]; other site 515619000849 allosteric effector site; other site 515619000850 fructose-1,6-bisphosphate binding site; other site 515619000851 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 515619000852 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 515619000853 Walker A motif; other site 515619000854 ATP binding site [chemical binding]; other site 515619000855 Walker B motif; other site 515619000856 arginine finger; other site 515619000857 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 515619000858 hypothetical protein; Validated; Region: PRK00153 515619000859 recombination protein RecR; Reviewed; Region: recR; PRK00076 515619000860 RecR protein; Region: RecR; pfam02132 515619000861 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 515619000862 putative active site [active] 515619000863 putative metal-binding site [ion binding]; other site 515619000864 tetramer interface [polypeptide binding]; other site 515619000865 transketolase; Reviewed; Region: PRK05899 515619000866 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 515619000867 TPP-binding site [chemical binding]; other site 515619000868 dimer interface [polypeptide binding]; other site 515619000869 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 515619000870 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 515619000871 PYR/PP interface [polypeptide binding]; other site 515619000872 dimer interface [polypeptide binding]; other site 515619000873 TPP binding site [chemical binding]; other site 515619000874 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 515619000875 Colicin V production protein; Region: Colicin_V; pfam02674 515619000876 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 515619000877 active site 515619000878 catalytic residues [active] 515619000879 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 515619000880 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 515619000881 putative ligand binding site [chemical binding]; other site 515619000882 putative NAD binding site [chemical binding]; other site 515619000883 catalytic site [active] 515619000884 Sulfatase; Region: Sulfatase; cl17466 515619000885 DHH family; Region: DHH; pfam01368 515619000886 phosphoglycolate phosphatase; Provisional; Region: PRK13222 515619000887 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 515619000888 motif II; other site 515619000889 Transcriptional antiterminator [Transcription]; Region: BglG; COG3711 515619000890 PRD domain; Region: PRD; pfam00874 515619000891 PRD domain; Region: PRD; pfam00874 515619000892 PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved...; Region: PTS_IIB_bgl_like; cd05568 515619000893 active site 515619000894 P-loop; other site 515619000895 phosphorylation site [posttranslational modification] 515619000896 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 515619000897 active site 515619000898 phosphorylation site [posttranslational modification] 515619000899 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 515619000900 dimerization domain swap beta strand [polypeptide binding]; other site 515619000901 regulatory protein interface [polypeptide binding]; other site 515619000902 active site 515619000903 regulatory phosphorylation site [posttranslational modification]; other site 515619000904 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 515619000905 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 515619000906 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 515619000907 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 515619000908 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1672 515619000909 AAA domain; Region: AAA_14; pfam13173 515619000910 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 515619000911 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 515619000912 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619000913 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619000914 Walker A/P-loop; other site 515619000915 ATP binding site [chemical binding]; other site 515619000916 Q-loop/lid; other site 515619000917 ABC transporter signature motif; other site 515619000918 Walker B; other site 515619000919 D-loop; other site 515619000920 H-loop/switch region; other site 515619000921 FtsX-like permease family; Region: FtsX; pfam02687 515619000922 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619000923 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619000924 active site 515619000925 phosphorylation site [posttranslational modification] 515619000926 intermolecular recognition site; other site 515619000927 dimerization interface [polypeptide binding]; other site 515619000928 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 515619000929 DNA binding site [nucleotide binding] 515619000930 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619000931 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 515619000932 dimer interface [polypeptide binding]; other site 515619000933 phosphorylation site [posttranslational modification] 515619000934 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619000935 ATP binding site [chemical binding]; other site 515619000936 Mg2+ binding site [ion binding]; other site 515619000937 G-X-G motif; other site 515619000938 flagellar capping protein; Validated; Region: fliD; PRK07737 515619000939 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 515619000940 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 515619000941 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 515619000942 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 515619000943 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 515619000944 putative homodimer interface [polypeptide binding]; other site 515619000945 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 515619000946 heterodimer interface [polypeptide binding]; other site 515619000947 homodimer interface [polypeptide binding]; other site 515619000948 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 515619000949 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 515619000950 23S rRNA interface [nucleotide binding]; other site 515619000951 L7/L12 interface [polypeptide binding]; other site 515619000952 putative thiostrepton binding site; other site 515619000953 L25 interface [polypeptide binding]; other site 515619000954 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 515619000955 mRNA/rRNA interface [nucleotide binding]; other site 515619000956 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 515619000957 23S rRNA interface [nucleotide binding]; other site 515619000958 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 515619000959 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 515619000960 core dimer interface [polypeptide binding]; other site 515619000961 peripheral dimer interface [polypeptide binding]; other site 515619000962 L10 interface [polypeptide binding]; other site 515619000963 L11 interface [polypeptide binding]; other site 515619000964 putative EF-Tu interaction site [polypeptide binding]; other site 515619000965 putative EF-G interaction site [polypeptide binding]; other site 515619000966 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 515619000967 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 515619000968 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 515619000969 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 515619000970 RPB1 interaction site [polypeptide binding]; other site 515619000971 RPB10 interaction site [polypeptide binding]; other site 515619000972 RPB11 interaction site [polypeptide binding]; other site 515619000973 RPB3 interaction site [polypeptide binding]; other site 515619000974 RPB12 interaction site [polypeptide binding]; other site 515619000975 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 515619000976 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 515619000977 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 515619000978 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 515619000979 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 515619000980 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 515619000981 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 515619000982 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 515619000983 G-loop; other site 515619000984 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 515619000985 DNA binding site [nucleotide binding] 515619000986 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 515619000987 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 515619000988 S17 interaction site [polypeptide binding]; other site 515619000989 S8 interaction site; other site 515619000990 16S rRNA interaction site [nucleotide binding]; other site 515619000991 streptomycin interaction site [chemical binding]; other site 515619000992 23S rRNA interaction site [nucleotide binding]; other site 515619000993 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 515619000994 30S ribosomal protein S7; Validated; Region: PRK05302 515619000995 elongation factor G; Reviewed; Region: PRK00007 515619000996 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 515619000997 G1 box; other site 515619000998 putative GEF interaction site [polypeptide binding]; other site 515619000999 GTP/Mg2+ binding site [chemical binding]; other site 515619001000 Switch I region; other site 515619001001 G2 box; other site 515619001002 G3 box; other site 515619001003 Switch II region; other site 515619001004 G4 box; other site 515619001005 G5 box; other site 515619001006 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 515619001007 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 515619001008 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 515619001009 elongation factor Tu; Reviewed; Region: PRK00049 515619001010 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 515619001011 G1 box; other site 515619001012 GEF interaction site [polypeptide binding]; other site 515619001013 GTP/Mg2+ binding site [chemical binding]; other site 515619001014 Switch I region; other site 515619001015 G2 box; other site 515619001016 G3 box; other site 515619001017 Switch II region; other site 515619001018 G4 box; other site 515619001019 G5 box; other site 515619001020 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 515619001021 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 515619001022 Antibiotic Binding Site [chemical binding]; other site 515619001023 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 515619001024 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 515619001025 P-loop; other site 515619001026 Magnesium ion binding site [ion binding]; other site 515619001027 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619001028 PemK-like protein; Region: PemK; pfam02452 515619001029 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 515619001030 non-specific DNA binding site [nucleotide binding]; other site 515619001031 salt bridge; other site 515619001032 sequence-specific DNA binding site [nucleotide binding]; other site 515619001033 Helix-turn-helix domain; Region: HTH_17; pfam12728 515619001034 integrase; Provisional; Region: int; PHA02601 515619001035 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 515619001036 Int/Topo IB signature motif; other site 515619001037 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619001038 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 515619001039 Walker A motif; other site 515619001040 ATP binding site [chemical binding]; other site 515619001041 Walker B motif; other site 515619001042 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 515619001043 adenosine deaminase; Provisional; Region: PRK09358 515619001044 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 515619001045 active site 515619001046 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 515619001047 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 515619001048 FeS/SAM binding site; other site 515619001049 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 515619001050 H+ Antiporter protein; Region: 2A0121; TIGR00900 515619001051 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 515619001052 putative substrate translocation pore; other site 515619001053 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 515619001054 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619001055 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 515619001056 Coenzyme A binding pocket [chemical binding]; other site 515619001057 Stress responsive A/B Barrel Domain; Region: Dabb; smart00886 515619001058 HAMP domain; Region: HAMP; pfam00672 515619001059 dimerization interface [polypeptide binding]; other site 515619001060 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619001061 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619001062 dimer interface [polypeptide binding]; other site 515619001063 putative CheW interface [polypeptide binding]; other site 515619001064 two-component sensor protein; Provisional; Region: cpxA; PRK09470 515619001065 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 515619001066 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 515619001067 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 515619001068 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 515619001069 ACS interaction site; other site 515619001070 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 515619001071 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 515619001072 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 515619001073 trimer interface [polypeptide binding]; other site 515619001074 putative metal binding site [ion binding]; other site 515619001075 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 515619001076 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 515619001077 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 515619001078 Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins; Region: GDPD_TtGDE_like; cd08563 515619001079 active site 515619001080 catalytic site [active] 515619001081 metal binding site [ion binding]; metal-binding site 515619001082 dimer interface [polypeptide binding]; other site 515619001083 polyphosphate kinase; Provisional; Region: PRK05443 515619001084 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 515619001085 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 515619001086 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 515619001087 putative active site [active] 515619001088 catalytic site [active] 515619001089 Catalytic C-terminal domain, second repeat, of uncharacterized prokaryotic polyphosphate kinases; Region: PLDc_PPK1_C2_unchar; cd09169 515619001090 putative domain interface [polypeptide binding]; other site 515619001091 putative active site [active] 515619001092 catalytic site [active] 515619001093 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 515619001094 putative deacylase active site [active] 515619001095 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 515619001096 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 515619001097 active site 515619001098 HIGH motif; other site 515619001099 dimer interface [polypeptide binding]; other site 515619001100 KMSKS motif; other site 515619001101 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 515619001102 uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family; Region: EcCorA_ZntB-like_u2; cd12827 515619001103 Cl binding site [ion binding]; other site 515619001104 oligomer interface [polypeptide binding]; other site 515619001105 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 515619001106 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 515619001107 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 515619001108 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 515619001109 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 515619001110 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 515619001111 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 515619001112 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 515619001113 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 515619001114 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 515619001115 protein-rRNA interface [nucleotide binding]; other site 515619001116 putative translocon binding site; other site 515619001117 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 515619001118 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 515619001119 G-X-X-G motif; other site 515619001120 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 515619001121 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 515619001122 23S rRNA interface [nucleotide binding]; other site 515619001123 5S rRNA interface [nucleotide binding]; other site 515619001124 putative antibiotic binding site [chemical binding]; other site 515619001125 L25 interface [polypeptide binding]; other site 515619001126 L27 interface [polypeptide binding]; other site 515619001127 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 515619001128 23S rRNA interface [nucleotide binding]; other site 515619001129 putative translocon interaction site; other site 515619001130 signal recognition particle (SRP54) interaction site; other site 515619001131 L23 interface [polypeptide binding]; other site 515619001132 trigger factor interaction site; other site 515619001133 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 515619001134 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 515619001135 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 515619001136 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 515619001137 RNA binding site [nucleotide binding]; other site 515619001138 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 515619001139 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 515619001140 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 515619001141 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 515619001142 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 515619001143 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 515619001144 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 515619001145 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 515619001146 5S rRNA interface [nucleotide binding]; other site 515619001147 L27 interface [polypeptide binding]; other site 515619001148 23S rRNA interface [nucleotide binding]; other site 515619001149 L5 interface [polypeptide binding]; other site 515619001150 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 515619001151 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 515619001152 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 515619001153 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 515619001154 23S rRNA binding site [nucleotide binding]; other site 515619001155 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 515619001156 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 515619001157 SecY translocase; Region: SecY; pfam00344 515619001158 adenylate kinase; Reviewed; Region: adk; PRK00279 515619001159 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 515619001160 AMP-binding site [chemical binding]; other site 515619001161 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 515619001162 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 515619001163 active site 515619001164 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 515619001165 rRNA binding site [nucleotide binding]; other site 515619001166 predicted 30S ribosome binding site; other site 515619001167 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 515619001168 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 515619001169 30S ribosomal protein S13; Region: bact_S13; TIGR03631 515619001170 30S ribosomal protein S11; Validated; Region: PRK05309 515619001171 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 515619001172 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 515619001173 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 515619001174 RNA binding surface [nucleotide binding]; other site 515619001175 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 515619001176 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 515619001177 alphaNTD homodimer interface [polypeptide binding]; other site 515619001178 alphaNTD - beta interaction site [polypeptide binding]; other site 515619001179 alphaNTD - beta' interaction site [polypeptide binding]; other site 515619001180 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 515619001181 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 515619001182 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK06827 515619001183 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 515619001184 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619001185 active site 515619001186 DNA replication protein DnaC; Validated; Region: PRK06835 515619001187 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 515619001188 Walker A motif; other site 515619001189 ATP binding site [chemical binding]; other site 515619001190 Putative primosome component and related proteins [DNA replication, recombination, and repair]; Region: DnaD; COG3935 515619001191 Replication initiation and membrane attachment; Region: DnaB_2; pfam07261 515619001192 Replication initiation and membrane attachment; Region: DnaB_2; cl12121 515619001193 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 515619001194 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 515619001195 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 515619001196 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 515619001197 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 515619001198 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 515619001199 ligand binding site; other site 515619001200 oligomer interface; other site 515619001201 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 515619001202 dimer interface [polypeptide binding]; other site 515619001203 N-terminal domain interface [polypeptide binding]; other site 515619001204 sulfate 1 binding site; other site 515619001205 ADP-glucose pyrophosphorylase [Carbohydrate transport and metabolism]; Region: GlgC; COG0448 515619001206 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 515619001207 ligand binding site; other site 515619001208 oligomer interface; other site 515619001209 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 515619001210 dimer interface [polypeptide binding]; other site 515619001211 N-terminal domain interface [polypeptide binding]; other site 515619001212 sulfate 1 binding site; other site 515619001213 regulatory protein SpoVG; Reviewed; Region: PRK13259 515619001214 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 515619001215 8-oxoguanine DNA glycosylase, N-terminal domain; Region: OGG_N; pfam07934 515619001216 8-oxoguanine DNA-glycosylase (ogg); Region: ogg; TIGR00588 515619001217 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 515619001218 minor groove reading motif; other site 515619001219 helix-hairpin-helix signature motif; other site 515619001220 active site 515619001221 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 515619001222 putative active site [active] 515619001223 catalytic residue [active] 515619001224 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 515619001225 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 515619001226 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 515619001227 ATP binding site [chemical binding]; other site 515619001228 putative Mg++ binding site [ion binding]; other site 515619001229 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 515619001230 nucleotide binding region [chemical binding]; other site 515619001231 ATP-binding site [chemical binding]; other site 515619001232 TRCF domain; Region: TRCF; pfam03461 515619001233 shikimate kinase; Reviewed; Region: aroK; PRK00131 515619001234 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 515619001235 ADP binding site [chemical binding]; other site 515619001236 magnesium binding site [ion binding]; other site 515619001237 putative shikimate binding site; other site 515619001238 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 515619001239 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 515619001240 hinge; other site 515619001241 active site 515619001242 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 515619001243 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619001244 Zn2+ binding site [ion binding]; other site 515619001245 Mg2+ binding site [ion binding]; other site 515619001246 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 515619001247 S-adenosylmethionine synthetase; Validated; Region: PRK05250 515619001248 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 515619001249 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 515619001250 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619001251 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619001252 active site 515619001253 phosphorylation site [posttranslational modification] 515619001254 intermolecular recognition site; other site 515619001255 dimerization interface [polypeptide binding]; other site 515619001256 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 515619001257 DNA binding site [nucleotide binding] 515619001258 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619001259 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 515619001260 dimerization interface [polypeptide binding]; other site 515619001261 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 515619001262 dimer interface [polypeptide binding]; other site 515619001263 phosphorylation site [posttranslational modification] 515619001264 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 515619001265 ATP binding site [chemical binding]; other site 515619001266 Mg2+ binding site [ion binding]; other site 515619001267 G-X-G motif; other site 515619001268 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619001269 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 515619001270 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 515619001271 MraW methylase family; Region: Methyltransf_5; cl17771 515619001272 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 515619001273 Pyruvate formate lyase 1; Region: PFL1; cd01678 515619001274 coenzyme A binding site [chemical binding]; other site 515619001275 active site 515619001276 catalytic residues [active] 515619001277 glycine loop; other site 515619001278 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 515619001279 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 515619001280 FeS/SAM binding site; other site 515619001281 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 515619001282 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 515619001283 active site 515619001284 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619001285 DNA-binding site [nucleotide binding]; DNA binding site 515619001286 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 515619001287 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 515619001288 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619001289 Walker A/P-loop; other site 515619001290 ATP binding site [chemical binding]; other site 515619001291 Q-loop/lid; other site 515619001292 ABC transporter signature motif; other site 515619001293 Walker B; other site 515619001294 D-loop; other site 515619001295 H-loop/switch region; other site 515619001296 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 515619001297 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 515619001298 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 515619001299 TM-ABC transporter signature motif; other site 515619001300 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619001301 active site 515619001302 phosphorylation site [posttranslational modification] 515619001303 intermolecular recognition site; other site 515619001304 dimerization interface [polypeptide binding]; other site 515619001305 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619001306 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619001307 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 515619001308 Histidine kinase; Region: His_kinase; pfam06580 515619001309 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 515619001310 ATP binding site [chemical binding]; other site 515619001311 Mg2+ binding site [ion binding]; other site 515619001312 G-X-G motif; other site 515619001313 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 515619001314 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 515619001315 ligand binding site [chemical binding]; other site 515619001316 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional; Region: PRK15395 515619001317 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 515619001318 ligand binding site [chemical binding]; other site 515619001319 calcium binding site [ion binding]; other site 515619001320 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619001321 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619001322 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619001323 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619001324 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619001325 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619001326 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 515619001327 dimer interface [polypeptide binding]; other site 515619001328 conserved gate region; other site 515619001329 putative PBP binding loops; other site 515619001330 ABC-ATPase subunit interface; other site 515619001331 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619001332 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 515619001333 dimer interface [polypeptide binding]; other site 515619001334 conserved gate region; other site 515619001335 putative PBP binding loops; other site 515619001336 ABC-ATPase subunit interface; other site 515619001337 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 515619001338 Melibiase; Region: Melibiase; pfam02065 515619001339 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 515619001340 active site 515619001341 sucrose phosphorylase; Region: sucrose_gtfA; TIGR03852 515619001342 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 515619001343 active site 515619001344 catalytic site [active] 515619001345 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 515619001346 AAA domain; Region: AAA_14; pfam13173 515619001347 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 515619001348 putative active site [active] 515619001349 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619001350 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 515619001351 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619001352 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619001353 DNA binding site [nucleotide binding] 515619001354 domain linker motif; other site 515619001355 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619001356 dimerization interface [polypeptide binding]; other site 515619001357 ligand binding site [chemical binding]; other site 515619001358 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619001359 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619001360 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 515619001361 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 515619001362 dimer interface [polypeptide binding]; other site 515619001363 conserved gate region; other site 515619001364 putative PBP binding loops; other site 515619001365 ABC-ATPase subunit interface; other site 515619001366 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619001367 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 515619001368 dimer interface [polypeptide binding]; other site 515619001369 conserved gate region; other site 515619001370 putative PBP binding loops; other site 515619001371 ABC-ATPase subunit interface; other site 515619001372 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 515619001373 This family represents an uncharacterized glycosyl hydrolase family 31 (GH31) enzyme found in bacteria and eukaryotes that is related to the XylS xylosidase of Sulfolobus solfataricus. Alpha-xylosidases catalyze the release of an alpha-xylose residue...; Region: GH31_xylosidase_XylS-like; cd06595 515619001374 putative active site [active] 515619001375 putative catalytic site [active] 515619001376 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 515619001377 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 515619001378 Alpha-glucosidase II (alpha-D-glucoside glucohydrolase) is a glycosyl hydrolase family 31 (GH31) enzyme, found in bacteria and plants, which has exo-alpha-1,4-glucosidase and oligo-1,6-glucosidase activities. Alpha-glucosidase II has been characterized...; Region: GH31_glucosidase_II_MalA; cd06604 515619001379 trimer interface [polypeptide binding]; other site 515619001380 active site 515619001381 homohexamer (dimer of homotrimer) interface [polypeptide binding]; other site 515619001382 catalytic site [active] 515619001383 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 515619001384 active site 515619001385 putative catalytic site [active] 515619001386 DNA binding site [nucleotide binding] 515619001387 putative phosphate binding site [ion binding]; other site 515619001388 metal binding site A [ion binding]; metal-binding site 515619001389 AP binding site [nucleotide binding]; other site 515619001390 metal binding site B [ion binding]; metal-binding site 515619001391 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 515619001392 AAA domain; Region: AAA_14; pfam13173 515619001393 Nuclease-related domain; Region: NERD; pfam08378 515619001394 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_4; cd13144 515619001395 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619001396 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 515619001397 MarR family; Region: MarR_2; pfam12802 515619001398 MarR family; Region: MarR_2; cl17246 515619001399 Predicted permeases [General function prediction only]; Region: COG0730 515619001400 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 515619001401 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 515619001402 dimerization interface [polypeptide binding]; other site 515619001403 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619001404 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619001405 dimer interface [polypeptide binding]; other site 515619001406 putative CheW interface [polypeptide binding]; other site 515619001407 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619001408 active site 515619001409 I-site; other site 515619001410 metal binding site [ion binding]; metal-binding site 515619001411 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619001412 Predicted transcriptional regulators [Transcription]; Region: COG1725 515619001413 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619001414 DNA-binding site [nucleotide binding]; DNA binding site 515619001415 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 515619001416 Hemerythrin; Region: Hemerythrin; cd12107 515619001417 Fe binding site [ion binding]; other site 515619001418 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619001419 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619001420 metal binding site [ion binding]; metal-binding site 515619001421 active site 515619001422 I-site; other site 515619001423 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 515619001424 AzlC protein; Region: AzlC; cl00570 515619001425 NAD(P)H-quinone oxidoreductase subunit F; Validated; Region: PRK07376 515619001426 glycerate kinase; Region: TIGR00045 515619001427 prolyl-tRNA synthetase; Provisional; Region: PRK08661 515619001428 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_arch_euk; cd00778 515619001429 dimer interface [polypeptide binding]; other site 515619001430 motif 1; other site 515619001431 active site 515619001432 motif 2; other site 515619001433 motif 3; other site 515619001434 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in...; Region: ProRS_anticodon_zinc; cd00862 515619001435 anticodon binding site; other site 515619001436 zinc-binding site [ion binding]; other site 515619001437 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 515619001438 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 515619001439 active site 515619001440 NTP binding site [chemical binding]; other site 515619001441 metal binding triad [ion binding]; metal-binding site 515619001442 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 515619001443 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619001444 Zn2+ binding site [ion binding]; other site 515619001445 Mg2+ binding site [ion binding]; other site 515619001446 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 515619001447 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 515619001448 spore coat protein YsxE; Region: spore_ysxE; TIGR02904 515619001449 PEGA domain; Region: PEGA; pfam08308 515619001450 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 515619001451 IHF dimer interface [polypeptide binding]; other site 515619001452 IHF - DNA interface [nucleotide binding]; other site 515619001453 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 515619001454 RNA binding surface [nucleotide binding]; other site 515619001455 YabP family; Region: YabP; cl06766 515619001456 Septum formation initiator; Region: DivIC; cl17659 515619001457 stage II sporulation protein E; Region: spore_II_E; TIGR02865 515619001458 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 515619001459 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 515619001460 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 515619001461 Ligand Binding Site [chemical binding]; other site 515619001462 TilS substrate C-terminal domain; Region: TilS_C; smart00977 515619001463 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619001464 active site 515619001465 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 515619001466 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 515619001467 Walker A motif; other site 515619001468 ATP binding site [chemical binding]; other site 515619001469 Walker B motif; other site 515619001470 arginine finger; other site 515619001471 Peptidase family M41; Region: Peptidase_M41; pfam01434 515619001472 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619001473 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619001474 DNA binding site [nucleotide binding] 515619001475 domain linker motif; other site 515619001476 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619001477 dimerization interface [polypeptide binding]; other site 515619001478 ligand binding site [chemical binding]; other site 515619001479 potential frameshift: common BLAST hit: gi|18311320|ref|NP_563254.1| 4-alpha-glucanotransferase 515619001480 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 515619001481 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 515619001482 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 515619001483 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619001484 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619001485 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 515619001486 dimer interface [polypeptide binding]; other site 515619001487 conserved gate region; other site 515619001488 putative PBP binding loops; other site 515619001489 ABC-ATPase subunit interface; other site 515619001490 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619001491 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 515619001492 dimer interface [polypeptide binding]; other site 515619001493 conserved gate region; other site 515619001494 putative PBP binding loops; other site 515619001495 ABC-ATPase subunit interface; other site 515619001496 Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac2_AmyA; cd11316 515619001497 Ca binding site [ion binding]; other site 515619001498 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 515619001499 active site 515619001500 catalytic site [active] 515619001501 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 515619001502 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 515619001503 putative acyl-acceptor binding pocket; other site 515619001504 PrcB C-terminal; Region: PrcB_C; pfam14343 515619001505 Protein of unknown function (DUF1021); Region: DUF1021; cl01852 515619001506 Domain of unknown function (DUF3794); Region: DUF3794; pfam12673 515619001507 Domain of unknown function (DUF3794); Region: DUF3794; pfam12673 515619001508 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 515619001509 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 515619001510 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619001511 NlpC/P60 family; Region: NLPC_P60; pfam00877 515619001512 Yqey-like protein; Region: YqeY; cl17540 515619001513 methionine aminopeptidase; Provisional; Region: PRK12318 515619001514 SEC-C motif; Region: SEC-C; pfam02810 515619001515 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 515619001516 active site 515619001517 Domain of unknown function (DUF4317); Region: DUF4317; pfam14199 515619001518 Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]; Region: FusA; COG0480 515619001519 Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline resistant proteins; Region: TetM_like; cd04168 515619001520 G1 box; other site 515619001521 putative GEF interaction site [polypeptide binding]; other site 515619001522 GTP/Mg2+ binding site [chemical binding]; other site 515619001523 Switch I region; other site 515619001524 G2 box; other site 515619001525 G3 box; other site 515619001526 Switch II region; other site 515619001527 G4 box; other site 515619001528 G5 box; other site 515619001529 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 515619001530 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cl02789 515619001531 Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a...; Region: Tet_C; cd03711 515619001532 YacP-like NYN domain; Region: NYN_YacP; pfam05991 515619001533 aspartate aminotransferase; Provisional; Region: PRK06836 515619001534 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 515619001535 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619001536 homodimer interface [polypeptide binding]; other site 515619001537 catalytic residue [active] 515619001538 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 515619001539 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619001540 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 515619001541 Protein phosphatase 2C; Region: PP2C; pfam00481 515619001542 active site 515619001543 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 515619001544 Catalytic domain of Protein Kinases; Region: PKc; cd00180 515619001545 active site 515619001546 ATP binding site [chemical binding]; other site 515619001547 substrate binding site [chemical binding]; other site 515619001548 activation loop (A-loop); other site 515619001549 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 515619001550 phosphopeptide binding site; other site 515619001551 WXG100 family type VII secretion target; Region: WXG100_ESAT6; TIGR03930 515619001552 Proteins of 100 residues with WXG; Region: WXG100; cl02005 515619001553 Protein of unknown function (DUF4237); Region: DUF4237; pfam14021 515619001554 WXG100 family type VII secretion target; Region: WXG100_ESAT6; TIGR03930 515619001555 Protein of unknown function (DUF4237); Region: DUF4237; pfam14021 515619001556 WXG100 protein secretion system (Wss), protein YukD; Region: YukD; pfam08817 515619001557 type VII secretion protein EssC, C-terminal domain; Region: T7_EssCb_Firm; TIGR03928 515619001558 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 515619001559 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 515619001560 C-terminal domain of Faecalibacterium prausnitzii A2-165 FrmR , and related domains; this domain family was previously known as part of DUF156; Region: FpFrmR-Cterm-like_DUF156; cd10156 515619001561 putative homodimer interface [polypeptide binding]; other site 515619001562 putative homotetramer interface [polypeptide binding]; other site 515619001563 putative allosteric switch controlling residues; other site 515619001564 putative metal binding site [ion binding]; other site 515619001565 putative homodimer-homodimer interface [polypeptide binding]; other site 515619001566 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 515619001567 metal-binding site [ion binding] 515619001568 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 515619001569 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 515619001570 metal-binding site [ion binding] 515619001571 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 515619001572 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 515619001573 motif II; other site 515619001574 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 515619001575 metal-binding site [ion binding] 515619001576 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 515619001577 Stage III sporulation protein D; Region: SpoIIID; pfam12116 515619001578 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619001579 GMP synthase; Reviewed; Region: guaA; PRK00074 515619001580 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 515619001581 AMP/PPi binding site [chemical binding]; other site 515619001582 candidate oxyanion hole; other site 515619001583 catalytic triad [active] 515619001584 potential glutamine specificity residues [chemical binding]; other site 515619001585 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 515619001586 ATP Binding subdomain [chemical binding]; other site 515619001587 Ligand Binding sites [chemical binding]; other site 515619001588 Dimerization subdomain; other site 515619001589 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619001590 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 515619001591 non-specific DNA binding site [nucleotide binding]; other site 515619001592 salt bridge; other site 515619001593 sequence-specific DNA binding site [nucleotide binding]; other site 515619001594 integrase; Provisional; Region: int; PHA02601 515619001595 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 515619001596 Int/Topo IB signature motif; other site 515619001597 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 515619001598 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 515619001599 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 515619001600 cofactor binding site; other site 515619001601 DNA binding site [nucleotide binding] 515619001602 substrate interaction site [chemical binding]; other site 515619001603 HaeIII restriction endonuclease; Region: RE_HaeIII; pfam09556 515619001604 Uncharacterized conserved protein [Function unknown]; Region: COG4933 515619001605 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; pfam03372 515619001606 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 515619001607 putative catalytic site [active] 515619001608 putative phosphate binding site [ion binding]; other site 515619001609 putative metal binding site [ion binding]; other site 515619001610 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 515619001611 nudix motif; other site 515619001612 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 515619001613 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 515619001614 motif II; other site 515619001615 Predicted amidohydrolase [General function prediction only]; Region: COG0388 515619001616 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 515619001617 active site 515619001618 catalytic triad [active] 515619001619 dimer interface [polypeptide binding]; other site 515619001620 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619001621 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619001622 Coenzyme A binding pocket [chemical binding]; other site 515619001623 Helix-turn-helix domain; Region: HTH_38; pfam13936 515619001624 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 515619001625 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619001626 Coenzyme A binding pocket [chemical binding]; other site 515619001627 AAA domain; Region: AAA_21; pfam13304 515619001628 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619001629 ABC transporter signature motif; other site 515619001630 Walker B; other site 515619001631 D-loop; other site 515619001632 H-loop/switch region; other site 515619001633 RloB-like protein; Region: RloB; pfam13707 515619001634 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 515619001635 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 515619001636 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 515619001637 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 515619001638 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619001639 Coenzyme A binding pocket [chemical binding]; other site 515619001640 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 515619001641 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619001642 Coenzyme A binding pocket [chemical binding]; other site 515619001643 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 515619001644 catalytic core [active] 515619001645 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 515619001646 Part of AAA domain; Region: AAA_19; pfam13245 515619001647 AAA domain; Region: AAA_12; pfam13087 515619001648 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 515619001649 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 515619001650 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 515619001651 nudix motif; other site 515619001652 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 515619001653 Divergent AAA domain; Region: AAA_4; pfam04326 515619001654 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 515619001655 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 515619001656 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 515619001657 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 515619001658 ATP binding site [chemical binding]; other site 515619001659 putative Mg++ binding site [ion binding]; other site 515619001660 helicase superfamily c-terminal domain; Region: HELICc; smart00490 515619001661 C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family nucleases fused to DEAD/DEAH box helicases; Region: PLDc_C_DEXD_like; cd09126 515619001662 PLD-like domain; Region: PLDc_2; pfam13091 515619001663 Virulence protein [General function prediction only]; Region: COG3943 515619001664 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 515619001665 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 515619001666 non-specific DNA binding site [nucleotide binding]; other site 515619001667 salt bridge; other site 515619001668 sequence-specific DNA binding site [nucleotide binding]; other site 515619001669 RNA ligase; Region: RNA_ligase; pfam09414 515619001670 Domain of unknown function DUF128; Region: DUF128; pfam01995 515619001671 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_M15_4; pfam13539 515619001672 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 515619001673 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 515619001674 active site 515619001675 catalytic tetrad [active] 515619001676 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619001677 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 515619001678 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 515619001679 Uncharacterized conserved protein [Function unknown]; Region: COG3937 515619001680 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 515619001681 ABC1 family; Region: ABC1; cl17513 515619001682 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 515619001683 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 515619001684 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 515619001685 PhoU domain; Region: PhoU; pfam01895 515619001686 PhoU domain; Region: PhoU; pfam01895 515619001687 L-ribulokinase-like proteins; a subfamily of the FGGY family of carbohydrate kinases; Region: FGGY_L-RBK_like; cd07778 515619001688 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 515619001689 putative N- and C-terminal domain interface [polypeptide binding]; other site 515619001690 putative active site [active] 515619001691 MgATP binding site [chemical binding]; other site 515619001692 catalytic site [active] 515619001693 metal binding site [ion binding]; metal-binding site 515619001694 putative carbohydrate binding site [chemical binding]; other site 515619001695 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 515619001696 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 515619001697 intersubunit interface [polypeptide binding]; other site 515619001698 active site 515619001699 Zn2+ binding site [ion binding]; other site 515619001700 Beta-lactamase; Region: Beta-lactamase; pfam00144 515619001701 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 515619001702 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619001703 EamA-like transporter family; Region: EamA; cl17759 515619001704 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 515619001705 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 515619001706 active site 515619001707 regulatory protein interface [polypeptide binding]; other site 515619001708 regulatory phosphorylation site [posttranslational modification]; other site 515619001709 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 515619001710 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 515619001711 FMN binding site [chemical binding]; other site 515619001712 substrate binding site [chemical binding]; other site 515619001713 putative catalytic residue [active] 515619001714 Glycogen debranching enzyme N terminal; Region: GDE_N; pfam12439 515619001715 glycogen debranching enzyme, archaeal type, putative; Region: gde_arch; TIGR01561 515619001716 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 515619001717 flagellar operon protein TIGR03826; Region: YvyF 515619001718 glutamate racemase; Provisional; Region: PRK00865 515619001719 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 515619001720 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 515619001721 minor groove reading motif; other site 515619001722 helix-hairpin-helix signature motif; other site 515619001723 substrate binding pocket [chemical binding]; other site 515619001724 active site 515619001725 Protein of unknown function DUF45; Region: DUF45; pfam01863 515619001726 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 515619001727 nudix motif; other site 515619001728 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 515619001729 CTP synthetase; Validated; Region: pyrG; PRK05380 515619001730 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 515619001731 Catalytic site [active] 515619001732 active site 515619001733 UTP binding site [chemical binding]; other site 515619001734 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 515619001735 active site 515619001736 putative oxyanion hole; other site 515619001737 catalytic triad [active] 515619001738 FtsH Extracellular; Region: FtsH_ext; pfam06480 515619001739 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 515619001740 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 515619001741 Walker A motif; other site 515619001742 ATP binding site [chemical binding]; other site 515619001743 Walker B motif; other site 515619001744 arginine finger; other site 515619001745 Peptidase family M41; Region: Peptidase_M41; pfam01434 515619001746 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 515619001747 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 515619001748 GIY-YIG motif/motif A; other site 515619001749 active site 515619001750 catalytic site [active] 515619001751 putative DNA binding site [nucleotide binding]; other site 515619001752 metal binding site [ion binding]; metal-binding site 515619001753 UvrB/uvrC motif; Region: UVR; pfam02151 515619001754 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 515619001755 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 515619001756 Hpr(Ser) kinase/phosphatase; Region: hpr-ser; TIGR00679 515619001757 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 515619001758 Hpr binding site; other site 515619001759 active site 515619001760 homohexamer subunit interaction site [polypeptide binding]; other site 515619001761 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 515619001762 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 515619001763 oligomer interface [polypeptide binding]; other site 515619001764 putative active site [active] 515619001765 metal binding site [ion binding]; metal-binding site 515619001766 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 515619001767 FAD binding domain; Region: FAD_binding_4; pfam01565 515619001768 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 515619001769 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 515619001770 shikimate kinase; Provisional; Region: PRK13947 515619001771 Sporulation Regulator WhiA C terminal domain; Region: HTH_WhiA; pfam02650 515619001772 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 515619001773 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 515619001774 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 515619001775 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 515619001776 intersubunit interface [polypeptide binding]; other site 515619001777 active site 515619001778 zinc binding site [ion binding]; other site 515619001779 Na+ binding site [ion binding]; other site 515619001780 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 515619001781 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 515619001782 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 515619001783 ammonium transporter; Region: amt; TIGR00836 515619001784 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 515619001785 Nitrogen regulatory protein P-II; Region: P-II; smart00938 515619001786 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 515619001787 Transglycosylase; Region: Transgly; pfam00912 515619001788 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 515619001789 Uncharacterized conserved protein [Function unknown]; Region: COG1739 515619001790 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 515619001791 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 515619001792 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 515619001793 active site 515619001794 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 515619001795 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 515619001796 S1 domain; Region: S1_2; pfam13509 515619001797 S1 domain; Region: S1_2; pfam13509 515619001798 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 515619001799 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 515619001800 homotrimer interaction site [polypeptide binding]; other site 515619001801 putative active site [active] 515619001802 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619001803 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619001804 NlpC/P60 family; Region: NLPC_P60; pfam00877 515619001805 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; cl04270 515619001806 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 515619001807 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 515619001808 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 515619001809 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619001810 Walker A/P-loop; other site 515619001811 ATP binding site [chemical binding]; other site 515619001812 Q-loop/lid; other site 515619001813 ABC transporter signature motif; other site 515619001814 Walker B; other site 515619001815 D-loop; other site 515619001816 H-loop/switch region; other site 515619001817 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 515619001818 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 515619001819 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 515619001820 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 515619001821 protein binding site [polypeptide binding]; other site 515619001822 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 515619001823 Catalytic dyad [active] 515619001824 Predicted integral membrane protein [Function unknown]; Region: COG5652 515619001825 peptide chain release factor 2; Provisional; Region: PRK05589 515619001826 PCRF domain; Region: PCRF; pfam03462 515619001827 RF-1 domain; Region: RF-1; pfam00472 515619001828 Tim44-like domain; Region: Tim44; cl09208 515619001829 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 515619001830 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]; Region: COG4260 515619001831 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 515619001832 hypothetical protein; Provisional; Region: PRK04435 515619001833 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 515619001834 DNA-binding interface [nucleotide binding]; DNA binding site 515619001835 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 515619001836 homoserine dehydrogenase; Provisional; Region: PRK06349 515619001837 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 515619001838 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 515619001839 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 515619001840 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 515619001841 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 515619001842 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 515619001843 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 515619001844 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 515619001845 Rod binding protein; Region: Rod-binding; cl01626 515619001846 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 515619001847 AAA domain; Region: AAA_30; pfam13604 515619001848 Family description; Region: UvrD_C_2; pfam13538 515619001849 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 515619001850 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619001851 Coenzyme A binding pocket [chemical binding]; other site 515619001852 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12838 515619001853 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 515619001854 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 515619001855 catalytic site [active] 515619001856 subunit interface [polypeptide binding]; other site 515619001857 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 515619001858 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 515619001859 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 515619001860 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 515619001861 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 515619001862 ATP-grasp domain; Region: ATP-grasp_4; cl17255 515619001863 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 515619001864 IMP binding site; other site 515619001865 dimer interface [polypeptide binding]; other site 515619001866 interdomain contacts; other site 515619001867 partial ornithine binding site; other site 515619001868 putative acyltransferase; Provisional; Region: PRK05790 515619001869 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 515619001870 dimer interface [polypeptide binding]; other site 515619001871 active site 515619001872 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 515619001873 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 515619001874 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 515619001875 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 515619001876 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 515619001877 FAD binding site [chemical binding]; other site 515619001878 homotetramer interface [polypeptide binding]; other site 515619001879 substrate binding pocket [chemical binding]; other site 515619001880 catalytic base [active] 515619001881 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 515619001882 Ligand binding site [chemical binding]; other site 515619001883 Electron transfer flavoprotein domain; Region: ETF; pfam01012 515619001884 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 515619001885 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 515619001886 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 515619001887 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619001888 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 515619001889 non-specific DNA binding site [nucleotide binding]; other site 515619001890 salt bridge; other site 515619001891 sequence-specific DNA binding site [nucleotide binding]; other site 515619001892 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 515619001893 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 515619001894 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 515619001895 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 515619001896 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 515619001897 FeS/SAM binding site; other site 515619001898 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 515619001899 Radical SAM superfamily; Region: Radical_SAM; pfam04055 515619001900 FeS/SAM binding site; other site 515619001901 putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Region: rSAM_pep_methan; TIGR04083 515619001902 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 515619001903 FeS/SAM binding site; other site 515619001904 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 515619001905 Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is...; Region: Peptidase_C1B; cd00585 515619001906 active site 515619001907 trimer interface [polypeptide binding]; other site 515619001908 G bulge; other site 515619001909 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 515619001910 FeS/SAM binding site; other site 515619001911 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619001912 Zn2+ binding site [ion binding]; other site 515619001913 Mg2+ binding site [ion binding]; other site 515619001914 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 515619001915 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 515619001916 trimer interface [polypeptide binding]; other site 515619001917 active site 515619001918 substrate binding site [chemical binding]; other site 515619001919 CoA binding site [chemical binding]; other site 515619001920 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 515619001921 isopentenyl-diphosphate delta-isomerase, type 1; Region: IPP_isom_1; TIGR02150 515619001922 nudix motif; other site 515619001923 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619001924 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 515619001925 catalytic residues [active] 515619001926 catalytic nucleophile [active] 515619001927 Presynaptic Site I dimer interface [polypeptide binding]; other site 515619001928 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 515619001929 Synaptic Flat tetramer interface [polypeptide binding]; other site 515619001930 Synaptic Site I dimer interface [polypeptide binding]; other site 515619001931 DNA binding site [nucleotide binding] 515619001932 Recombinase; Region: Recombinase; pfam07508 515619001933 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619001934 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 515619001935 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 515619001936 DNA binding residues [nucleotide binding] 515619001937 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 515619001938 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 515619001939 putative active site [active] 515619001940 putative metal binding site [ion binding]; other site 515619001941 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 515619001942 FtsX-like permease family; Region: FtsX; pfam02687 515619001943 FtsX-like permease family; Region: FtsX; pfam02687 515619001944 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619001945 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619001946 Walker A/P-loop; other site 515619001947 ATP binding site [chemical binding]; other site 515619001948 Q-loop/lid; other site 515619001949 ABC transporter signature motif; other site 515619001950 Walker B; other site 515619001951 D-loop; other site 515619001952 H-loop/switch region; other site 515619001953 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619001954 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 515619001955 dimer interface [polypeptide binding]; other site 515619001956 phosphorylation site [posttranslational modification] 515619001957 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 515619001958 ATP binding site [chemical binding]; other site 515619001959 Mg2+ binding site [ion binding]; other site 515619001960 G-X-G motif; other site 515619001961 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619001962 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619001963 active site 515619001964 phosphorylation site [posttranslational modification] 515619001965 intermolecular recognition site; other site 515619001966 dimerization interface [polypeptide binding]; other site 515619001967 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 515619001968 DNA binding site [nucleotide binding] 515619001969 Helix-turn-helix domain; Region: HTH_17; pfam12728 515619001970 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619001971 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 515619001972 non-specific DNA binding site [nucleotide binding]; other site 515619001973 salt bridge; other site 515619001974 sequence-specific DNA binding site [nucleotide binding]; other site 515619001975 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 515619001976 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 515619001977 Protein of unknown function (DUF1559); Region: SBP_bac_10; pfam07596 515619001978 Domain of unknown function (DUF4316); Region: DUF4316; pfam14195 515619001979 Cysteine-rich VLP; Region: Cys_rich_VLP; pfam14194 515619001980 Domain of unknown function (DUF4366); Region: DUF4366; pfam14283 515619001981 Domain of unknown function (DUF4315); Region: DUF4315; pfam14193 515619001982 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619001983 NlpC/P60 family; Region: NLPC_P60; pfam00877 515619001984 AAA-like domain; Region: AAA_10; pfam12846 515619001985 Domain of unknown function DUF87; Region: DUF87; pfam01935 515619001986 SpoVG; Region: SpoVG; pfam04026 515619001987 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619001988 Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a...; Region: SR_TndX_transposase; cd03770 515619001989 putative catalytic residues [active] 515619001990 catalytic nucleophile [active] 515619001991 Recombinase; Region: Recombinase; pfam07508 515619001992 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619001993 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 515619001994 Virulence-associated protein E; Region: VirE; pfam05272 515619001995 CHC2 zinc finger; Region: zf-CHC2; cl17510 515619001996 MobA/MobL family; Region: MobA_MobL; pfam03389 515619001997 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619001998 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 515619001999 non-specific DNA binding site [nucleotide binding]; other site 515619002000 salt bridge; other site 515619002001 sequence-specific DNA binding site [nucleotide binding]; other site 515619002002 Protein of unknown function (DUF3847); Region: DUF3847; pfam12958 515619002003 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 515619002004 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619002005 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 515619002006 non-specific DNA binding site [nucleotide binding]; other site 515619002007 salt bridge; other site 515619002008 sequence-specific DNA binding site [nucleotide binding]; other site 515619002009 Transposon-encoded protein TnpV; Region: TnpV; pfam14198 515619002010 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 515619002011 salt bridge; other site 515619002012 non-specific DNA binding site [nucleotide binding]; other site 515619002013 sequence-specific DNA binding site [nucleotide binding]; other site 515619002014 Maff2 family; Region: Maff2; pfam12750 515619002015 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 515619002016 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 515619002017 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 515619002018 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 515619002019 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619002020 putative active site [active] 515619002021 putative NTP binding site [chemical binding]; other site 515619002022 putative nucleic acid binding site [nucleotide binding]; other site 515619002023 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619002024 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 515619002025 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619002026 Walker A motif; other site 515619002027 ATP binding site [chemical binding]; other site 515619002028 Protein of unknown function (DUF3801); Region: DUF3801; pfam12687 515619002029 potential frameshift: common BLAST hit: gi|126698695|ref|YP_001087592.1| putative DNA primase 515619002030 Antirestriction protein (ArdA); Region: ArdA; cl01953 515619002031 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 515619002032 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 515619002033 cofactor binding site; other site 515619002034 DNA binding site [nucleotide binding] 515619002035 substrate interaction site [chemical binding]; other site 515619002036 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 515619002037 ParB-like nuclease domain; Region: ParBc; pfam02195 515619002038 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 515619002039 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 515619002040 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 515619002041 glutaminase active site [active] 515619002042 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 515619002043 dimer interface [polypeptide binding]; other site 515619002044 active site 515619002045 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 515619002046 dimer interface [polypeptide binding]; other site 515619002047 active site 515619002048 Predicted membrane protein [Function unknown]; Region: COG4684 515619002049 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 515619002050 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 515619002051 putative active site pocket [active] 515619002052 cleavage site 515619002053 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 515619002054 Flavoprotein; Region: Flavoprotein; pfam02441 515619002055 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 515619002056 Protein of unknown function (DUF975); Region: DUF975; cl10504 515619002057 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 515619002058 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 515619002059 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 515619002060 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 515619002061 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 515619002062 RNA binding site [nucleotide binding]; other site 515619002063 Predicted membrane protein [Function unknown]; Region: COG3601 515619002064 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 515619002065 YcxB-like protein; Region: YcxB; pfam14317 515619002066 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 515619002067 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 515619002068 Glycoprotease family; Region: Peptidase_M22; pfam00814 515619002069 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 515619002070 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619002071 Coenzyme A binding pocket [chemical binding]; other site 515619002072 ribonuclease Z; Reviewed; Region: PRK00055 515619002073 UGMP family protein; Validated; Region: PRK09604 515619002074 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 515619002075 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 515619002076 substrate binding site; other site 515619002077 dimer interface; other site 515619002078 Domain of unknown function (DUF4176); Region: DUF4176; pfam13780 515619002079 LXG domain of WXG superfamily; Region: LXG; pfam04740 515619002080 Bacterial EndoU nuclease; Region: EndoU_bacteria; pfam14436 515619002081 SseB protein; Region: SseB; cl06279 515619002082 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 515619002083 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 515619002084 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 515619002085 active site 515619002086 metal binding site [ion binding]; metal-binding site 515619002087 LabA_like proteins; Region: LabA_like; cd06167 515619002088 putative metal binding site [ion binding]; other site 515619002089 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 515619002090 HsdM N-terminal domain; Region: HsdM_N; pfam12161 515619002091 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 515619002092 Methyltransferase domain; Region: Methyltransf_26; pfam13659 515619002093 NTPase; Region: NTPase_1; cl17478 515619002094 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619002095 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619002096 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619002097 Protein of unknown function (DUF3990); Region: DUF3990; pfam13151 515619002098 Domain of unknown function (DUF1768); Region: DUF1768; pfam08719 515619002099 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619002100 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619002101 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619002102 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 515619002103 Int/Topo IB signature motif; other site 515619002104 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 515619002105 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 515619002106 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 515619002107 ATP binding site [chemical binding]; other site 515619002108 putative Mg++ binding site [ion binding]; other site 515619002109 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 515619002110 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 515619002111 metal binding site [ion binding]; metal-binding site 515619002112 dimer interface [polypeptide binding]; other site 515619002113 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619002114 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619002115 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619002116 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619002117 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 515619002118 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 515619002119 Ca binding site [ion binding]; other site 515619002120 active site 515619002121 catalytic site [active] 515619002122 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 515619002123 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 515619002124 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 515619002125 Ca binding site [ion binding]; other site 515619002126 active site 515619002127 catalytic site [active] 515619002128 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 515619002129 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 515619002130 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 515619002131 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 515619002132 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 515619002133 homodimer interface [polypeptide binding]; other site 515619002134 substrate-cofactor binding pocket; other site 515619002135 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619002136 catalytic residue [active] 515619002137 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 515619002138 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 515619002139 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 515619002140 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 515619002141 CPxP motif; other site 515619002142 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 515619002143 catalytic residues [active] 515619002144 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 515619002145 thiS-thiF/thiG interaction site; other site 515619002146 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 515619002147 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 515619002148 ATP binding site [chemical binding]; other site 515619002149 substrate interface [chemical binding]; other site 515619002150 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); Region: MPN_like; cd08070 515619002151 MPN+ (JAMM) motif; other site 515619002152 Zinc-binding site [ion binding]; other site 515619002153 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 515619002154 siroheme synthase, N-terminal domain; Region: cysG_Nterm; TIGR01470 515619002155 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 515619002156 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 515619002157 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; cl17708 515619002158 domain interfaces; other site 515619002159 active site 515619002160 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 515619002161 active site 515619002162 SAM binding site [chemical binding]; other site 515619002163 homodimer interface [polypeptide binding]; other site 515619002164 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 515619002165 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 515619002166 active site 515619002167 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 515619002168 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 515619002169 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 515619002170 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 515619002171 homodimer interface [polypeptide binding]; other site 515619002172 substrate-cofactor binding pocket; other site 515619002173 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619002174 catalytic residue [active] 515619002175 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619002176 metal binding site [ion binding]; metal-binding site 515619002177 active site 515619002178 I-site; other site 515619002179 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619002180 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 515619002181 active site residue [active] 515619002182 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 515619002183 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 515619002184 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 515619002185 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cd02619 515619002186 active site 515619002187 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 515619002188 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 515619002189 active site 515619002190 metal binding site [ion binding]; metal-binding site 515619002191 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 515619002192 active site 515619002193 dimerization interface [polypeptide binding]; other site 515619002194 Predicted membrane protein [Function unknown]; Region: COG2510 515619002195 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 515619002196 Predicted membrane protein [Function unknown]; Region: COG2510 515619002197 biotin synthase; Region: bioB; TIGR00433 515619002198 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 515619002199 FeS/SAM binding site; other site 515619002200 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 515619002201 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 515619002202 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 515619002203 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619002204 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619002205 active site 515619002206 phosphorylation site [posttranslational modification] 515619002207 intermolecular recognition site; other site 515619002208 dimerization interface [polypeptide binding]; other site 515619002209 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 515619002210 DNA binding site [nucleotide binding] 515619002211 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619002212 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 515619002213 dimerization interface [polypeptide binding]; other site 515619002214 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 515619002215 dimer interface [polypeptide binding]; other site 515619002216 phosphorylation site [posttranslational modification] 515619002217 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 515619002218 ATP binding site [chemical binding]; other site 515619002219 Mg2+ binding site [ion binding]; other site 515619002220 G-X-G motif; other site 515619002221 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 515619002222 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 515619002223 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 515619002224 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 515619002225 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 515619002226 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 515619002227 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 515619002228 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 515619002229 FtsX-like permease family; Region: FtsX; pfam02687 515619002230 FtsX-like permease family; Region: FtsX; pfam02687 515619002231 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619002232 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619002233 Walker A/P-loop; other site 515619002234 ATP binding site [chemical binding]; other site 515619002235 Q-loop/lid; other site 515619002236 ABC transporter signature motif; other site 515619002237 Walker B; other site 515619002238 D-loop; other site 515619002239 H-loop/switch region; other site 515619002240 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619002241 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619002242 Walker A/P-loop; other site 515619002243 ATP binding site [chemical binding]; other site 515619002244 Q-loop/lid; other site 515619002245 ABC transporter signature motif; other site 515619002246 Walker B; other site 515619002247 D-loop; other site 515619002248 H-loop/switch region; other site 515619002249 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619002250 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619002251 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619002252 active site 515619002253 phosphorylation site [posttranslational modification] 515619002254 intermolecular recognition site; other site 515619002255 dimerization interface [polypeptide binding]; other site 515619002256 LytTr DNA-binding domain; Region: LytTR; smart00850 515619002257 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619002258 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 515619002259 non-specific DNA binding site [nucleotide binding]; other site 515619002260 salt bridge; other site 515619002261 sequence-specific DNA binding site [nucleotide binding]; other site 515619002262 cyclic lactone autoinducer peptide; Region: quorum_AgrD; TIGR04223 515619002263 Accessory gene regulator B; Region: AgrB; pfam04647 515619002264 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 515619002265 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39B; cd02418 515619002266 putative active site [active] 515619002267 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619002268 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619002269 Walker A/P-loop; other site 515619002270 ATP binding site [chemical binding]; other site 515619002271 Q-loop/lid; other site 515619002272 ABC transporter signature motif; other site 515619002273 Walker B; other site 515619002274 D-loop; other site 515619002275 H-loop/switch region; other site 515619002276 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 515619002277 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 515619002278 HlyD family secretion protein; Region: HlyD_3; pfam13437 515619002279 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619002280 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619002281 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619002282 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619002283 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 515619002284 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619002285 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619002286 active site 515619002287 phosphorylation site [posttranslational modification] 515619002288 intermolecular recognition site; other site 515619002289 dimerization interface [polypeptide binding]; other site 515619002290 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 515619002291 DNA binding site [nucleotide binding] 515619002292 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619002293 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 515619002294 dimerization interface [polypeptide binding]; other site 515619002295 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 515619002296 dimer interface [polypeptide binding]; other site 515619002297 phosphorylation site [posttranslational modification] 515619002298 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 515619002299 ATP binding site [chemical binding]; other site 515619002300 Mg2+ binding site [ion binding]; other site 515619002301 G-X-G motif; other site 515619002302 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 515619002303 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619002304 Walker A/P-loop; other site 515619002305 ATP binding site [chemical binding]; other site 515619002306 Q-loop/lid; other site 515619002307 ABC transporter signature motif; other site 515619002308 Walker B; other site 515619002309 D-loop; other site 515619002310 H-loop/switch region; other site 515619002311 S-layer domain [Cell envelope biogenesis, outer membrane]; Region: COG1361 515619002312 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 515619002313 active site 515619002314 metal binding site [ion binding]; metal-binding site 515619002315 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619002316 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619002317 active site 515619002318 phosphorylation site [posttranslational modification] 515619002319 intermolecular recognition site; other site 515619002320 dimerization interface [polypeptide binding]; other site 515619002321 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 515619002322 DNA binding site [nucleotide binding] 515619002323 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619002324 ATP-binding cassette domain of the bacitracin-resistance transporter; Region: ABC_BcrA_bacitracin_resist; cd03268 515619002325 Walker A/P-loop; other site 515619002326 ATP binding site [chemical binding]; other site 515619002327 Q-loop/lid; other site 515619002328 ABC transporter signature motif; other site 515619002329 Walker B; other site 515619002330 D-loop; other site 515619002331 H-loop/switch region; other site 515619002332 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619002333 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619002334 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 515619002335 dimer interface [polypeptide binding]; other site 515619002336 phosphorylation site [posttranslational modification] 515619002337 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 515619002338 ATP binding site [chemical binding]; other site 515619002339 Mg2+ binding site [ion binding]; other site 515619002340 G-X-G motif; other site 515619002341 Domain of unknown function, E. rectale Gene description (DUF3878); Region: DUF3878; pfam12994 515619002342 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 515619002343 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 515619002344 dimer interface [polypeptide binding]; other site 515619002345 conserved gate region; other site 515619002346 putative PBP binding loops; other site 515619002347 ABC-ATPase subunit interface; other site 515619002348 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 515619002349 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 515619002350 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 515619002351 dimer interface [polypeptide binding]; other site 515619002352 conserved gate region; other site 515619002353 putative PBP binding loops; other site 515619002354 ABC-ATPase subunit interface; other site 515619002355 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 515619002356 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 515619002357 Walker A/P-loop; other site 515619002358 ATP binding site [chemical binding]; other site 515619002359 Q-loop/lid; other site 515619002360 ABC transporter signature motif; other site 515619002361 Walker B; other site 515619002362 D-loop; other site 515619002363 H-loop/switch region; other site 515619002364 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 515619002365 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 515619002366 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 515619002367 Walker A/P-loop; other site 515619002368 ATP binding site [chemical binding]; other site 515619002369 Q-loop/lid; other site 515619002370 ABC transporter signature motif; other site 515619002371 Walker B; other site 515619002372 D-loop; other site 515619002373 H-loop/switch region; other site 515619002374 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 515619002375 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; cl01709 515619002376 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 515619002377 peptide binding site [polypeptide binding]; other site 515619002378 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 515619002379 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 515619002380 Clostridium thermocellum (Cth)TTM and similar proteins, a subgroup of the CYTH-like superfamily; Region: CYTH-like_CthTTM-like; cd07761 515619002381 putative active site [active] 515619002382 putative metal binding residues [ion binding]; other site 515619002383 signature motif; other site 515619002384 putative dimer interface [polypeptide binding]; other site 515619002385 putative phosphate binding site [ion binding]; other site 515619002386 DJ-1 family protein; Region: not_thiJ; TIGR01383 515619002387 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 515619002388 conserved cys residue [active] 515619002389 Small, acid-soluble spore proteins, alpha/beta type; Region: SASP; pfam00269 515619002390 trigger factor; Provisional; Region: tig; PRK01490 515619002391 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 515619002392 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 515619002393 Clp protease; Region: CLP_protease; pfam00574 515619002394 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 515619002395 oligomer interface [polypeptide binding]; other site 515619002396 active site residues [active] 515619002397 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 515619002398 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 515619002399 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 515619002400 Walker A motif; other site 515619002401 ATP binding site [chemical binding]; other site 515619002402 Walker B motif; other site 515619002403 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 515619002404 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 515619002405 Found in ATP-dependent protease La (LON); Region: LON; smart00464 515619002406 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 515619002407 Walker A motif; other site 515619002408 ATP binding site [chemical binding]; other site 515619002409 Walker B motif; other site 515619002410 arginine finger; other site 515619002411 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 515619002412 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 515619002413 G1 box; other site 515619002414 GTP/Mg2+ binding site [chemical binding]; other site 515619002415 Switch I region; other site 515619002416 G2 box; other site 515619002417 G3 box; other site 515619002418 Switch II region; other site 515619002419 G4 box; other site 515619002420 G5 box; other site 515619002421 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 515619002422 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 515619002423 intersubunit interface [polypeptide binding]; other site 515619002424 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 515619002425 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 515619002426 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 515619002427 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 515619002428 ABC-ATPase subunit interface; other site 515619002429 dimer interface [polypeptide binding]; other site 515619002430 putative PBP binding regions; other site 515619002431 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 515619002432 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 515619002433 dimerization interface [polypeptide binding]; other site 515619002434 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619002435 dimer interface [polypeptide binding]; other site 515619002436 putative CheW interface [polypeptide binding]; other site 515619002437 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00128 515619002438 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 515619002439 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 515619002440 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619002441 DNA-binding site [nucleotide binding]; DNA binding site 515619002442 Transcriptional regulators [Transcription]; Region: FadR; COG2186 515619002443 FCD domain; Region: FCD; pfam07729 515619002444 Bacillus/Clostridium GerA spore germination protein; Region: GerA; pfam03323 515619002445 Spore germination protein; Region: Spore_permease; cl17796 515619002446 Stage II sporulation protein R (spore_II_R); Region: Spore_II_R; pfam09551 515619002447 Domain of unknown function (DUF1934); Region: DUF1934; pfam09148 515619002448 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 515619002449 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619002450 dimerization interface [polypeptide binding]; other site 515619002451 ligand binding site [chemical binding]; other site 515619002452 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619002453 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619002454 metal binding site [ion binding]; metal-binding site 515619002455 active site 515619002456 I-site; other site 515619002457 Glycosyl hydrolase family 53; Region: Glyco_hydro_53; cl06672 515619002458 trigger factor; Region: tig; TIGR00115 515619002459 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 515619002460 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 515619002461 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 515619002462 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 515619002463 putative dimer interface [polypeptide binding]; other site 515619002464 putative anticodon binding site; other site 515619002465 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 515619002466 homodimer interface [polypeptide binding]; other site 515619002467 motif 1; other site 515619002468 motif 2; other site 515619002469 active site 515619002470 motif 3; other site 515619002471 Protein of unknown function (DUF4001); Region: DUF4001; pfam13165 515619002472 SCIFF radical SAM maturase; Region: rSAM_six_Cys; TIGR03974 515619002473 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 515619002474 FeS/SAM binding site; other site 515619002475 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 515619002476 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 515619002477 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 515619002478 Protein export membrane protein; Region: SecD_SecF; pfam02355 515619002479 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 515619002480 Alpha amylase catalytic domain found in eukaryotic and bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_euk_bac_CMD_like; cd11353 515619002481 active site 515619002482 catalytic site [active] 515619002483 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 515619002484 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 515619002485 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 515619002486 Domain of unknown function (DUF4234); Region: DUF4234; pfam14018 515619002487 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 515619002488 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 515619002489 substrate binding site [chemical binding]; other site 515619002490 oxyanion hole (OAH) forming residues; other site 515619002491 trimer interface [polypeptide binding]; other site 515619002492 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619002493 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619002494 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 515619002495 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 515619002496 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 515619002497 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 515619002498 SCP-2 sterol transfer family; Region: SCP2; pfam02036 515619002499 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 515619002500 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 515619002501 Condensation domain; Region: Condensation; pfam00668 515619002502 acyl carrier protein; Provisional; Region: acpP; PRK00982 515619002503 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 515619002504 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 515619002505 acyl-activating enzyme (AAE) consensus motif; other site 515619002506 putative AMP binding site [chemical binding]; other site 515619002507 putative active site [active] 515619002508 putative CoA binding site [chemical binding]; other site 515619002509 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 515619002510 active site 515619002511 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 515619002512 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 515619002513 active site 515619002514 NTP binding site [chemical binding]; other site 515619002515 metal binding triad [ion binding]; metal-binding site 515619002516 antibiotic binding site [chemical binding]; other site 515619002517 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 515619002518 Quinolinate synthetase A protein; Region: NadA; pfam02445 515619002519 L-aspartate oxidase; Provisional; Region: PRK06175 515619002520 FAD binding domain; Region: FAD_binding_2; pfam00890 515619002521 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 515619002522 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 515619002523 dimerization interface [polypeptide binding]; other site 515619002524 active site 515619002525 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 515619002526 HTH domain; Region: HTH_11; pfam08279 515619002527 3H domain; Region: 3H; pfam02829 515619002528 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619002529 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 515619002530 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 515619002531 Putative esterase; Region: Esterase; pfam00756 515619002532 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 515619002533 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 515619002534 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 515619002535 active site 515619002536 catalytic triad [active] 515619002537 oxyanion hole [active] 515619002538 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 515619002539 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 515619002540 inhibitor binding site; inhibition site 515619002541 active site 515619002542 Cupin domain; Region: Cupin_2; pfam07883 515619002543 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619002544 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619002545 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619002546 Probable beta-xylosidase; Provisional; Region: PLN03080 515619002547 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 515619002548 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 515619002549 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619002550 HAMP domain; Region: HAMP; pfam00672 515619002551 Histidine kinase; Region: His_kinase; pfam06580 515619002552 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 515619002553 ATP binding site [chemical binding]; other site 515619002554 Mg2+ binding site [ion binding]; other site 515619002555 G-X-G motif; other site 515619002556 Response regulator receiver domain; Region: Response_reg; pfam00072 515619002557 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619002558 active site 515619002559 phosphorylation site [posttranslational modification] 515619002560 intermolecular recognition site; other site 515619002561 dimerization interface [polypeptide binding]; other site 515619002562 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619002563 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619002564 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619002565 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619002566 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619002567 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 515619002568 dimer interface [polypeptide binding]; other site 515619002569 conserved gate region; other site 515619002570 putative PBP binding loops; other site 515619002571 ABC-ATPase subunit interface; other site 515619002572 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619002573 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 515619002574 dimer interface [polypeptide binding]; other site 515619002575 conserved gate region; other site 515619002576 ABC-ATPase subunit interface; other site 515619002577 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619002578 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619002579 dimer interface [polypeptide binding]; other site 515619002580 putative CheW interface [polypeptide binding]; other site 515619002581 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 515619002582 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 515619002583 HIGH motif; other site 515619002584 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 515619002585 active site 515619002586 KMSKS motif; other site 515619002587 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 515619002588 tRNA binding surface [nucleotide binding]; other site 515619002589 anticodon binding site; other site 515619002590 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 515619002591 homodimer interface [polypeptide binding]; other site 515619002592 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 515619002593 active site pocket [active] 515619002594 TraX protein; Region: TraX; pfam05857 515619002595 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 515619002596 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06826 515619002597 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 515619002598 active site 515619002599 PHP Thumb interface [polypeptide binding]; other site 515619002600 metal binding site [ion binding]; metal-binding site 515619002601 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 515619002602 generic binding surface II; other site 515619002603 generic binding surface I; other site 515619002604 6-phosphofructokinase; Provisional; Region: PRK03202 515619002605 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 515619002606 active site 515619002607 ADP/pyrophosphate binding site [chemical binding]; other site 515619002608 dimerization interface [polypeptide binding]; other site 515619002609 allosteric effector site; other site 515619002610 fructose-1,6-bisphosphate binding site; other site 515619002611 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 515619002612 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 515619002613 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 515619002614 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 515619002615 synthetase active site [active] 515619002616 NTP binding site [chemical binding]; other site 515619002617 metal binding site [ion binding]; metal-binding site 515619002618 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 515619002619 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619002620 ABC transporter; Region: ABC_tran_2; pfam12848 515619002621 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619002622 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 515619002623 Uncharacterized conserved protein [Function unknown]; Region: COG2966 515619002624 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 515619002625 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 515619002626 RelB antitoxin; Region: RelB; cl01171 515619002627 Stage V sporulation protein AA; Region: SporV_AA; pfam12164 515619002628 Stage V sporulation protein AB; Region: SpoVAB; pfam13782 515619002629 Domain of unknown function (DUF3837); Region: DUF3837; pfam12939 515619002630 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 515619002631 N-terminal domain of cellobiose phosphorylase (CBP) and similar proteins; Region: GH94N_CBP_like; cd11754 515619002632 catalytic domain interface [polypeptide binding]; other site 515619002633 homodimer interface [polypeptide binding]; other site 515619002634 putative active site [active] 515619002635 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619002636 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619002637 DNA binding site [nucleotide binding] 515619002638 domain linker motif; other site 515619002639 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619002640 dimerization interface [polypeptide binding]; other site 515619002641 ligand binding site [chemical binding]; other site 515619002642 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619002643 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619002644 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 515619002645 dimer interface [polypeptide binding]; other site 515619002646 conserved gate region; other site 515619002647 putative PBP binding loops; other site 515619002648 ABC-ATPase subunit interface; other site 515619002649 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619002650 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 515619002651 dimer interface [polypeptide binding]; other site 515619002652 conserved gate region; other site 515619002653 putative PBP binding loops; other site 515619002654 ABC-ATPase subunit interface; other site 515619002655 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 515619002656 EamA-like transporter family; Region: EamA; pfam00892 515619002657 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 515619002658 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 515619002659 FeS/SAM binding site; other site 515619002660 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cl04227 515619002661 carbohydrate binding site [chemical binding]; other site 515619002662 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 515619002663 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_2; cd11339 515619002664 active site 515619002665 catalytic site [active] 515619002666 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]; Region: COG2452 515619002667 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 515619002668 DNA binding residues [nucleotide binding] 515619002669 Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of...; Region: SR_IS607_transposase_like; cd03769 515619002670 catalytic residues [active] 515619002671 catalytic nucleophile [active] 515619002672 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 515619002673 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 515619002674 Probable transposase; Region: OrfB_IS605; pfam01385 515619002675 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 515619002676 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 515619002677 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619002678 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619002679 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 515619002680 dimerization interface [polypeptide binding]; other site 515619002681 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 515619002682 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 515619002683 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 515619002684 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 515619002685 GDP-binding site [chemical binding]; other site 515619002686 ACT binding site; other site 515619002687 IMP binding site; other site 515619002688 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 515619002689 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 515619002690 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619002691 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619002692 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 515619002693 dimerization interface [polypeptide binding]; other site 515619002694 L-1,2-propanediol oxidoreductase; Provisional; Region: PRK10624 515619002695 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 515619002696 dimer interface [polypeptide binding]; other site 515619002697 active site 515619002698 metal binding site [ion binding]; metal-binding site 515619002699 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 515619002700 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 515619002701 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 515619002702 YcfA-like protein; Region: YcfA; pfam07927 515619002703 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619002704 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619002705 Cupin domain; Region: Cupin_2; pfam07883 515619002706 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619002707 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 515619002708 non-specific DNA binding site [nucleotide binding]; other site 515619002709 salt bridge; other site 515619002710 sequence-specific DNA binding site [nucleotide binding]; other site 515619002711 AAA domain; Region: AAA_31; pfam13614 515619002712 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619002713 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 515619002714 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 515619002715 ATP binding site [chemical binding]; other site 515619002716 Walker A motif; other site 515619002717 hexamer interface [polypeptide binding]; other site 515619002718 Walker B motif; other site 515619002719 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 515619002720 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 515619002721 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 515619002722 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 515619002723 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 515619002724 Viral DNA-binding protein, zinc binding domain; Region: Viral_DNA_Zn_bi; pfam03728 515619002725 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 515619002726 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 515619002727 phosphopeptide binding site; other site 515619002728 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 515619002729 active site 515619002730 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 515619002731 Catalytic domain of Protein Kinases; Region: PKc; cd00180 515619002732 active site 515619002733 ATP binding site [chemical binding]; other site 515619002734 substrate binding site [chemical binding]; other site 515619002735 activation loop (A-loop); other site 515619002736 Bacterial Ig-like domain (group 3); Region: Big_3_3; pfam13750 515619002737 SpoVA protein; Region: SpoVA; pfam03862 515619002738 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 515619002739 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 515619002740 dimer interface [polypeptide binding]; other site 515619002741 active site 515619002742 glycine-pyridoxal phosphate binding site [chemical binding]; other site 515619002743 folate binding site [chemical binding]; other site 515619002744 seryl-tRNA synthetase; Provisional; Region: PRK05431 515619002745 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 515619002746 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 515619002747 motif 1; other site 515619002748 dimer interface [polypeptide binding]; other site 515619002749 active site 515619002750 motif 2; other site 515619002751 motif 3; other site 515619002752 YcfA-like protein; Region: YcfA; cl00752 515619002753 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 515619002754 HicB family; Region: HicB; pfam05534 515619002755 Uncharacterized conserved protein [Function unknown]; Region: COG1284 515619002756 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 515619002757 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 515619002758 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 515619002759 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 515619002760 dimerization interface [polypeptide binding]; other site 515619002761 putative ATP binding site [chemical binding]; other site 515619002762 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 515619002763 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 515619002764 active site 515619002765 substrate binding site [chemical binding]; other site 515619002766 cosubstrate binding site; other site 515619002767 catalytic site [active] 515619002768 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 515619002769 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 515619002770 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 515619002771 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 515619002772 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 515619002773 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cl17915 515619002774 motif II; other site 515619002775 PAS domain; Region: PAS_9; pfam13426 515619002776 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619002777 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619002778 metal binding site [ion binding]; metal-binding site 515619002779 active site 515619002780 I-site; other site 515619002781 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619002782 metal binding site [ion binding]; metal-binding site 515619002783 active site 515619002784 I-site; other site 515619002785 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619002786 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 515619002787 Y-family of DNA polymerases; Region: PolY; cl12025 515619002788 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 515619002789 active site 515619002790 Y-family of DNA polymerases; Region: PolY; cl12025 515619002791 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 515619002792 DNA binding site [nucleotide binding] 515619002793 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 515619002794 active site 515619002795 SAM binding site [chemical binding]; other site 515619002796 homodimer interface [polypeptide binding]; other site 515619002797 benzoyl-CoA reductase, bcr type, subunit B; Region: benz_CoA_red_B; TIGR02260 515619002798 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 515619002799 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 515619002800 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 515619002801 Ferredoxin [Energy production and conversion]; Region: COG1146 515619002802 4Fe-4S binding domain; Region: Fer4_6; pfam12837 515619002803 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 515619002804 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 515619002805 ligand binding site [chemical binding]; other site 515619002806 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 515619002807 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 515619002808 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 515619002809 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 515619002810 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619002811 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619002812 metal binding site [ion binding]; metal-binding site 515619002813 active site 515619002814 I-site; other site 515619002815 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 515619002816 dimerization interface [polypeptide binding]; other site 515619002817 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619002818 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619002819 dimer interface [polypeptide binding]; other site 515619002820 putative CheW interface [polypeptide binding]; other site 515619002821 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 515619002822 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 515619002823 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619002824 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619002825 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619002826 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 515619002827 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 515619002828 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 515619002829 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 515619002830 active site 515619002831 metal binding site [ion binding]; metal-binding site 515619002832 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 515619002833 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 515619002834 active site 515619002835 catalytic residues [active] 515619002836 metal binding site [ion binding]; metal-binding site 515619002837 Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly...; Region: Macro; cl00019 515619002838 Domain of unknown function (DUF4268); Region: DUF4268; pfam14088 515619002839 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 515619002840 Low molecular weight phosphatase family; Region: LMWPc; cl00105 515619002841 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 515619002842 putative deacylase active site [active] 515619002843 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 515619002844 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 515619002845 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 515619002846 motif II; other site 515619002847 Part of AAA domain; Region: AAA_19; pfam13245 515619002848 Family description; Region: UvrD_C_2; pfam13538 515619002849 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 515619002850 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 515619002851 active site 515619002852 motif I; other site 515619002853 motif II; other site 515619002854 aspartyl-tRNA synthetase; Provisional; Region: aspC; PRK05159 515619002855 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 515619002856 Dimer interface [polypeptide binding]; other site 515619002857 anticodon binding site; other site 515619002858 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 515619002859 homodimer interface [polypeptide binding]; other site 515619002860 motif 1; other site 515619002861 motif 2; other site 515619002862 active site 515619002863 motif 3; other site 515619002864 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 515619002865 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619002866 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 515619002867 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 515619002868 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 515619002869 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 515619002870 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 515619002871 GatB domain; Region: GatB_Yqey; smart00845 515619002872 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 515619002873 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 515619002874 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 515619002875 Walker A motif; other site 515619002876 ATP binding site [chemical binding]; other site 515619002877 Walker B motif; other site 515619002878 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 515619002879 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 515619002880 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 515619002881 active site 515619002882 metal binding site [ion binding]; metal-binding site 515619002883 DNA binding site [nucleotide binding] 515619002884 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619002885 AAA domain; Region: AAA_23; pfam13476 515619002886 Walker A/P-loop; other site 515619002887 ATP binding site [chemical binding]; other site 515619002888 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619002889 ABC transporter signature motif; other site 515619002890 Walker B; other site 515619002891 D-loop; other site 515619002892 Peptidase S8 family domain in CspA-like proteins; Region: Peptidases_S8_CspA-like; cd07478 515619002893 active site 515619002894 catalytic triad [active] 515619002895 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_1_2; cd06113 515619002896 dimer interface [polypeptide binding]; other site 515619002897 Citrate synthase; Region: Citrate_synt; pfam00285 515619002898 active site 515619002899 citrylCoA binding site [chemical binding]; other site 515619002900 oxalacetate/citrate binding site [chemical binding]; other site 515619002901 coenzyme A binding site [chemical binding]; other site 515619002902 catalytic triad [active] 515619002903 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 515619002904 heterotetramer interface [polypeptide binding]; other site 515619002905 active site pocket [active] 515619002906 cleavage site 515619002907 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 515619002908 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 515619002909 putative DNA binding site [nucleotide binding]; other site 515619002910 putative Zn2+ binding site [ion binding]; other site 515619002911 AsnC family; Region: AsnC_trans_reg; pfam01037 515619002912 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 515619002913 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 515619002914 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619002915 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619002916 DNA binding site [nucleotide binding] 515619002917 domain linker motif; other site 515619002918 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619002919 ligand binding site [chemical binding]; other site 515619002920 dimerization interface [polypeptide binding]; other site 515619002921 DDE domain; Region: DDE_Tnp_IS240; pfam13610 515619002922 Integrase core domain; Region: rve; pfam00665 515619002923 Integrase core domain; Region: rve_3; cl15866 515619002924 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 515619002925 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 515619002926 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 515619002927 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 515619002928 dimer interface [polypeptide binding]; other site 515619002929 conserved gate region; other site 515619002930 putative PBP binding loops; other site 515619002931 ABC-ATPase subunit interface; other site 515619002932 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619002933 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 515619002934 dimer interface [polypeptide binding]; other site 515619002935 conserved gate region; other site 515619002936 putative PBP binding loops; other site 515619002937 ABC-ATPase subunit interface; other site 515619002938 maltodextrin glucosidase; Provisional; Region: PRK10785 515619002939 N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes; Region: E_set_CDase_PDE_N; cd02857 515619002940 homodimer interface [polypeptide binding]; other site 515619002941 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 515619002942 active site 515619002943 homodimer interface [polypeptide binding]; other site 515619002944 catalytic site [active] 515619002945 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 515619002946 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 515619002947 Putative transposase; Region: Y2_Tnp; pfam04986 515619002948 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 515619002949 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 515619002950 active site 515619002951 DNA binding site [nucleotide binding] 515619002952 Int/Topo IB signature motif; other site 515619002953 Protein of unknown function (DUF1847); Region: DUF1847; pfam08901 515619002954 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 515619002955 Propionate catabolism activator; Region: PrpR_N; pfam06506 515619002956 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 515619002957 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 515619002958 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 515619002959 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 515619002960 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 515619002961 putative active site [active] 515619002962 metal binding site [ion binding]; metal-binding site 515619002963 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 515619002964 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 515619002965 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3395 515619002966 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 515619002967 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 515619002968 inhibitor site; inhibition site 515619002969 active site 515619002970 dimer interface [polypeptide binding]; other site 515619002971 catalytic residue [active] 515619002972 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 515619002973 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 515619002974 ligand binding site [chemical binding]; other site 515619002975 NAD binding site [chemical binding]; other site 515619002976 dimerization interface [polypeptide binding]; other site 515619002977 catalytic site [active] 515619002978 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 515619002979 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 515619002980 transmembrane helices; other site 515619002981 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 515619002982 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 515619002983 substrate binding site [chemical binding]; other site 515619002984 THF binding site; other site 515619002985 zinc-binding site [ion binding]; other site 515619002986 Hemerythrin; Region: Hemerythrin; cd12107 515619002987 Fe binding site [ion binding]; other site 515619002988 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 515619002989 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 515619002990 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 515619002991 catalytic residues [active] 515619002992 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 515619002993 active site residue [active] 515619002994 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 515619002995 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 515619002996 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 515619002997 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 515619002998 active site residue [active] 515619002999 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 515619003000 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 515619003001 ligand binding site [chemical binding]; other site 515619003002 flexible hinge region; other site 515619003003 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 515619003004 putative switch regulator; other site 515619003005 non-specific DNA interactions [nucleotide binding]; other site 515619003006 DNA binding site [nucleotide binding] 515619003007 sequence specific DNA binding site [nucleotide binding]; other site 515619003008 putative cAMP binding site [chemical binding]; other site 515619003009 Predicted DNA-binding proteins [General function prediction only]; Region: COG1342 515619003010 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 515619003011 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 515619003012 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 515619003013 catalytic triad [active] 515619003014 Protein of unknown function (DUF328); Region: DUF328; pfam03883 515619003015 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 515619003016 4Fe-4S binding domain; Region: Fer4; pfam00037 515619003017 4Fe-4S binding domain; Region: Fer4_6; pfam12837 515619003018 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 515619003019 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 515619003020 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619003021 Zn2+ binding site [ion binding]; other site 515619003022 Mg2+ binding site [ion binding]; other site 515619003023 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 515619003024 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619003025 Zn2+ binding site [ion binding]; other site 515619003026 Mg2+ binding site [ion binding]; other site 515619003027 Hemerythrin; Region: Hemerythrin; cd12107 515619003028 Fe binding site [ion binding]; other site 515619003029 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 515619003030 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 515619003031 Soluble P-type ATPase [General function prediction only]; Region: COG4087 515619003032 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 515619003033 active site 515619003034 NTP binding site [chemical binding]; other site 515619003035 metal binding triad [ion binding]; metal-binding site 515619003036 antibiotic binding site [chemical binding]; other site 515619003037 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 515619003038 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 515619003039 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 515619003040 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619003041 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_4; cd13144 515619003042 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619003043 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3864 515619003044 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 515619003045 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 515619003046 metal ion-dependent adhesion site (MIDAS); other site 515619003047 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 515619003048 AAA domain; Region: AAA_22; pfam13401 515619003049 Walker A motif; other site 515619003050 ATP binding site [chemical binding]; other site 515619003051 Walker B motif; other site 515619003052 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 515619003053 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 515619003054 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 515619003055 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 515619003056 classical (c) SDRs; Region: SDR_c; cd05233 515619003057 NAD(P) binding site [chemical binding]; other site 515619003058 active site 515619003059 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 515619003060 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 515619003061 FMN binding site [chemical binding]; other site 515619003062 active site 515619003063 catalytic residues [active] 515619003064 substrate binding site [chemical binding]; other site 515619003065 Thymidylate synthase; Region: Thymidylat_synt; pfam00303 515619003066 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 515619003067 dimerization interface [polypeptide binding]; other site 515619003068 active site 515619003069 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 515619003070 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 515619003071 folate binding site [chemical binding]; other site 515619003072 NADP+ binding site [chemical binding]; other site 515619003073 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 515619003074 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 515619003075 PYR/PP interface [polypeptide binding]; other site 515619003076 dimer interface [polypeptide binding]; other site 515619003077 TPP binding site [chemical binding]; other site 515619003078 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 515619003079 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 515619003080 TPP-binding site [chemical binding]; other site 515619003081 dimer interface [polypeptide binding]; other site 515619003082 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 515619003083 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 515619003084 putative valine binding site [chemical binding]; other site 515619003085 dimer interface [polypeptide binding]; other site 515619003086 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 515619003087 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 515619003088 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 515619003089 Stage II sporulation protein; Region: SpoIID; pfam08486 515619003090 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619003091 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 515619003092 catalytic residues [active] 515619003093 catalytic nucleophile [active] 515619003094 Recombinase; Region: Recombinase; pfam07508 515619003095 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619003096 Abi-like protein; Region: Abi_2; pfam07751 515619003097 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619003098 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 515619003099 non-specific DNA binding site [nucleotide binding]; other site 515619003100 salt bridge; other site 515619003101 sequence-specific DNA binding site [nucleotide binding]; other site 515619003102 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 515619003103 Catalytic site [active] 515619003104 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619003105 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 515619003106 non-specific DNA binding site [nucleotide binding]; other site 515619003107 salt bridge; other site 515619003108 sequence-specific DNA binding site [nucleotide binding]; other site 515619003109 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 515619003110 active site 515619003111 ParB-like nuclease domain; Region: ParB; smart00470 515619003112 Domain of unknown function (DUF4417); Region: DUF4417; pfam14386 515619003113 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 515619003114 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 515619003115 Terminase small subunit; Region: Terminase_2; cl01513 515619003116 Phage terminase large subunit; Region: Terminase_3; cl12054 515619003117 phage portal protein, putative, A118 family; Region: A118_put_portal; TIGR01542 515619003118 Phage minor capsid protein 2; Region: Phage_min_cap2; pfam06152 515619003119 Cysteine-rich KTR; Region: Cys_rich_KTR; pfam14205 515619003120 Phage minor structural protein GP20; Region: Phage_GP20; pfam06810 515619003121 Minor capsid protein; Region: Minor_capsid_2; pfam11114 515619003122 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 515619003123 Bacteriophage Gp15 protein; Region: Phage_Gp15; pfam06854 515619003124 Phage-related protein [Function unknown]; Region: COG5412 515619003125 Phage tail protein; Region: Sipho_tail; cl17486 515619003126 Prophage endopeptidase tail; Region: Prophage_tail; cl12123 515619003127 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 515619003128 active site 515619003129 catalytic triad [active] 515619003130 oxyanion hole [active] 515619003131 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 515619003132 active site 515619003133 catalytic triad [active] 515619003134 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 515619003135 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 515619003136 active site 515619003137 DNA binding site [nucleotide binding] 515619003138 Int/Topo IB signature motif; other site 515619003139 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 515619003140 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 515619003141 active site 515619003142 Holin family; Region: Phage_holin_4; pfam05105 515619003143 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 515619003144 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 515619003145 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 515619003146 dimerization interface 3.5A [polypeptide binding]; other site 515619003147 active site 515619003148 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 515619003149 DHH family; Region: DHH; pfam01368 515619003150 DHHA1 domain; Region: DHHA1; pfam02272 515619003151 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 515619003152 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 515619003153 active site 515619003154 Beta-galactosidase [Carbohydrate transport and metabolism]; Region: LacA; COG1874 515619003155 Beta-galactosidase; Region: Glyco_hydro_42; pfam02449 515619003156 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 515619003157 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619003158 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619003159 DNA binding site [nucleotide binding] 515619003160 domain linker motif; other site 515619003161 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619003162 ligand binding site [chemical binding]; other site 515619003163 dimerization interface [polypeptide binding]; other site 515619003164 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK14654 515619003165 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 515619003166 Mg++ binding site [ion binding]; other site 515619003167 putative catalytic motif [active] 515619003168 putative substrate binding site [chemical binding]; other site 515619003169 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA_like; cd07944 515619003170 active site 515619003171 catalytic residues [active] 515619003172 metal binding site [ion binding]; metal-binding site 515619003173 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 515619003174 non-specific DNA interactions [nucleotide binding]; other site 515619003175 DNA binding site [nucleotide binding] 515619003176 sequence specific DNA binding site [nucleotide binding]; other site 515619003177 putative cAMP binding site [chemical binding]; other site 515619003178 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 515619003179 DNA methylase; Region: N6_N4_Mtase; cl17433 515619003180 DNA methylase; Region: N6_N4_Mtase; pfam01555 515619003181 DNA methylase; Region: N6_N4_Mtase; pfam01555 515619003182 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 515619003183 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 515619003184 Divergent AAA domain; Region: AAA_4; pfam04326 515619003185 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 515619003186 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 515619003187 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619003188 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 515619003189 dimer interface [polypeptide binding]; other site 515619003190 phosphorylation site [posttranslational modification] 515619003191 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619003192 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619003193 active site 515619003194 phosphorylation site [posttranslational modification] 515619003195 intermolecular recognition site; other site 515619003196 dimerization interface [polypeptide binding]; other site 515619003197 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 515619003198 DNA binding site [nucleotide binding] 515619003199 Protein of unknown function (DUF2705); Region: DUF2705; pfam10920 515619003200 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619003201 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619003202 Walker A/P-loop; other site 515619003203 ATP binding site [chemical binding]; other site 515619003204 Q-loop/lid; other site 515619003205 ABC transporter signature motif; other site 515619003206 Walker B; other site 515619003207 D-loop; other site 515619003208 H-loop/switch region; other site 515619003209 Domain of unknown function (DUF3368); Region: DUF3368; pfam11848 515619003210 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619003211 Domain of unknown function, E. rectale Gene description (DUF3879); Region: DUF3879; pfam12995 515619003212 Protein of unknown function (DUF1761); Region: DUF1761; pfam08570 515619003213 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 515619003214 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 515619003215 active site 515619003216 active site 515619003217 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619003218 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619003219 active site 515619003220 phosphorylation site [posttranslational modification] 515619003221 intermolecular recognition site; other site 515619003222 dimerization interface [polypeptide binding]; other site 515619003223 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619003224 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 515619003225 Accessory gene regulator B; Region: AgrB; pfam04647 515619003226 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 515619003227 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 515619003228 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 515619003229 dimerization interface [polypeptide binding]; other site 515619003230 domain crossover interface; other site 515619003231 redox-dependent activation switch; other site 515619003232 NAD synthetase; Reviewed; Region: nadE; PRK02628 515619003233 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 515619003234 active site 515619003235 catalytic triad [active] 515619003236 multimer interface [polypeptide binding]; other site 515619003237 protein interface 1 [polypeptide binding]; other site 515619003238 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 515619003239 homodimer interface [polypeptide binding]; other site 515619003240 NAD binding pocket [chemical binding]; other site 515619003241 ATP binding pocket [chemical binding]; other site 515619003242 Mg binding site [ion binding]; other site 515619003243 active-site loop [active] 515619003244 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 515619003245 putative active site [active] 515619003246 asparagine synthetase AsnA; Provisional; Region: PRK05425 515619003247 motif 1; other site 515619003248 dimer interface [polypeptide binding]; other site 515619003249 active site 515619003250 motif 2; other site 515619003251 motif 3; other site 515619003252 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 515619003253 active site residue [active] 515619003254 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 515619003255 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 515619003256 Ligand Binding Site [chemical binding]; other site 515619003257 Protein of unknown function (DUF2974); Region: DUF2974; pfam11187 515619003258 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 515619003259 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 515619003260 putative ATP binding site [chemical binding]; other site 515619003261 putative substrate interface [chemical binding]; other site 515619003262 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 515619003263 Walker A motif; other site 515619003264 ATP binding site [chemical binding]; other site 515619003265 Walker B motif; other site 515619003266 arginine finger; other site 515619003267 aminotransferase AlaT; Validated; Region: PRK09265 515619003268 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 515619003269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619003270 homodimer interface [polypeptide binding]; other site 515619003271 catalytic residue [active] 515619003272 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619003273 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619003274 Walker A/P-loop; other site 515619003275 ATP binding site [chemical binding]; other site 515619003276 Q-loop/lid; other site 515619003277 ABC transporter signature motif; other site 515619003278 Walker B; other site 515619003279 D-loop; other site 515619003280 H-loop/switch region; other site 515619003281 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 515619003282 FtsX-like permease family; Region: FtsX; pfam02687 515619003283 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 515619003284 FtsX-like permease family; Region: FtsX; pfam02687 515619003285 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619003286 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619003287 active site 515619003288 phosphorylation site [posttranslational modification] 515619003289 intermolecular recognition site; other site 515619003290 dimerization interface [polypeptide binding]; other site 515619003291 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 515619003292 DNA binding site [nucleotide binding] 515619003293 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619003294 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 515619003295 dimer interface [polypeptide binding]; other site 515619003296 phosphorylation site [posttranslational modification] 515619003297 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 515619003298 ATP binding site [chemical binding]; other site 515619003299 Mg2+ binding site [ion binding]; other site 515619003300 G-X-G motif; other site 515619003301 FeoA domain; Region: FeoA; pfam04023 515619003302 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 515619003303 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 515619003304 G1 box; other site 515619003305 GTP/Mg2+ binding site [chemical binding]; other site 515619003306 Switch I region; other site 515619003307 G2 box; other site 515619003308 G3 box; other site 515619003309 Switch II region; other site 515619003310 G4 box; other site 515619003311 G5 box; other site 515619003312 Nucleoside recognition; Region: Gate; pfam07670 515619003313 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 515619003314 Nucleoside recognition; Region: Gate; pfam07670 515619003315 Aldose 1-epimerase, similar to Lactococcus lactis lacX; Region: Aldose_epim_lacX; cd09024 515619003316 active site 515619003317 catalytic residues [active] 515619003318 Protein of unknown function (DUF1700); Region: DUF1700; pfam08006 515619003319 Predicted transcriptional regulators [Transcription]; Region: COG1695 515619003320 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 515619003321 DNA helicase II; Region: uvrD; TIGR01075 515619003322 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 515619003323 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 515619003324 active site 515619003325 motif I; other site 515619003326 motif II; other site 515619003327 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 515619003328 motif II; other site 515619003329 Uncharacterized protein family (UPF0175); Region: UPF0175; pfam03683 515619003330 Cupin domain; Region: Cupin_2; cl17218 515619003331 Apovitellenin I (Apo-VLDL-II); Region: Apo-VLDL-II; pfam05418 515619003332 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619003333 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619003334 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619003335 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619003336 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619003337 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 515619003338 dimer interface [polypeptide binding]; other site 515619003339 conserved gate region; other site 515619003340 putative PBP binding loops; other site 515619003341 ABC-ATPase subunit interface; other site 515619003342 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619003343 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 515619003344 dimer interface [polypeptide binding]; other site 515619003345 conserved gate region; other site 515619003346 putative PBP binding loops; other site 515619003347 ABC-ATPase subunit interface; other site 515619003348 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 515619003349 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 515619003350 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 515619003351 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 515619003352 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 515619003353 Glycosyl hydrolase family 53; Region: Glyco_hydro_53; cl06672 515619003354 galactokinase; Provisional; Region: PRK05322 515619003355 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 515619003356 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 515619003357 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 515619003358 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK05270 515619003359 Galactose-1-phosphate uridyl transferase, N-terminal domain; Region: GalP_UDP_transf; pfam01087 515619003360 Galactose-1-phosphate uridyl transferase, C-terminal domain; Region: GalP_UDP_tr_C; pfam02744 515619003361 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619003362 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619003363 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 515619003364 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 515619003365 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619003366 homodimer interface [polypeptide binding]; other site 515619003367 catalytic residue [active] 515619003368 Putative small multi-drug export protein; Region: Sm_multidrug_ex; pfam06695 515619003369 CAAX protease self-immunity; Region: Abi; pfam02517 515619003370 Trp repressor protein; Region: Trp_repressor; cl17266 515619003371 Domain of unknown function (DUF1836); Region: DUF1836; pfam08876 515619003372 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 515619003373 Part of AAA domain; Region: AAA_19; pfam13245 515619003374 Family description; Region: UvrD_C_2; pfam13538 515619003375 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 515619003376 TRAM domain; Region: TRAM; cl01282 515619003377 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 515619003378 S-adenosylmethionine binding site [chemical binding]; other site 515619003379 NACHT domain; Region: NACHT; pfam05729 515619003380 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 515619003381 HsdM N-terminal domain; Region: HsdM_N; pfam12161 515619003382 Methyltransferase domain; Region: Methyltransf_26; pfam13659 515619003383 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 515619003384 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619003385 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619003386 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619003387 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619003388 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619003389 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 515619003390 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 515619003391 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 515619003392 ATP binding site [chemical binding]; other site 515619003393 putative Mg++ binding site [ion binding]; other site 515619003394 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea; Region: GIY-YIG_unchar_2; cd10447 515619003395 GIY-YIG motif/motif A; other site 515619003396 putative active site [active] 515619003397 putative metal binding site [ion binding]; other site 515619003398 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 515619003399 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 515619003400 FtsX-like permease family; Region: FtsX; pfam02687 515619003401 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 515619003402 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 515619003403 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 515619003404 nucleotide binding site [chemical binding]; other site 515619003405 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 515619003406 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH7; cd08261 515619003407 putative NAD(P) binding site [chemical binding]; other site 515619003408 catalytic Zn binding site [ion binding]; other site 515619003409 structural Zn binding site [ion binding]; other site 515619003410 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 515619003411 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 515619003412 active site 515619003413 metal binding site [ion binding]; metal-binding site 515619003414 MFS/sugar transport protein; Region: MFS_2; pfam13347 515619003415 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 515619003416 putative substrate translocation pore; other site 515619003417 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 515619003418 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 515619003419 putative substrate binding site [chemical binding]; other site 515619003420 putative ATP binding site [chemical binding]; other site 515619003421 Uncharacterized conserved protein [Function unknown]; Region: COG1284 515619003422 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 515619003423 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 515619003424 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 515619003425 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 515619003426 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 515619003427 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 515619003428 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 515619003429 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 515619003430 active site 515619003431 motif I; other site 515619003432 motif II; other site 515619003433 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 515619003434 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 515619003435 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 515619003436 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 515619003437 Na2 binding site [ion binding]; other site 515619003438 putative substrate binding site 1 [chemical binding]; other site 515619003439 Na binding site 1 [ion binding]; other site 515619003440 putative substrate binding site 2 [chemical binding]; other site 515619003441 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 515619003442 MoxR-like ATPases [General function prediction only]; Region: COG0714 515619003443 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 515619003444 Walker A motif; other site 515619003445 ATP binding site [chemical binding]; other site 515619003446 Walker B motif; other site 515619003447 arginine finger; other site 515619003448 Protein of unknown function DUF58; Region: DUF58; pfam01882 515619003449 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 515619003450 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 515619003451 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 515619003452 PTS system, glucose-specific IIBC component; Region: PTS-II-BC-glcB; TIGR02002 515619003453 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 515619003454 active site turn [active] 515619003455 phosphorylation site [posttranslational modification] 515619003456 Phosphotransferase system IIA components [Carbohydrate transport and metabolism]; Region: NagE; COG2190 515619003457 HPr interaction site; other site 515619003458 glycerol kinase (GK) interaction site [polypeptide binding]; other site 515619003459 active site 515619003460 phosphorylation site [posttranslational modification] 515619003461 PRD domain; Region: PRD; pfam00874 515619003462 GTP-binding protein YchF; Reviewed; Region: PRK09601 515619003463 YchF GTPase; Region: YchF; cd01900 515619003464 G1 box; other site 515619003465 GTP/Mg2+ binding site [chemical binding]; other site 515619003466 Switch I region; other site 515619003467 G2 box; other site 515619003468 Switch II region; other site 515619003469 G3 box; other site 515619003470 G4 box; other site 515619003471 G5 box; other site 515619003472 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 515619003473 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]; Region: COG1873; cl17889 515619003474 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 515619003475 ATP cone domain; Region: ATP-cone; pfam03477 515619003476 Predicted hydrolase of the HAD superfamily [General function prediction only]; Region: COG2179 515619003477 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 515619003478 active site 515619003479 motif I; other site 515619003480 motif II; other site 515619003481 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 515619003482 elongation factor P; Validated; Region: PRK00529 515619003483 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 515619003484 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 515619003485 RNA binding site [nucleotide binding]; other site 515619003486 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 515619003487 RNA binding site [nucleotide binding]; other site 515619003488 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619003489 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 515619003490 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 515619003491 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 515619003492 active site 515619003493 motif I; other site 515619003494 motif II; other site 515619003495 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 515619003496 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 515619003497 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 515619003498 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 515619003499 substrate binding pocket [chemical binding]; other site 515619003500 dimer interface [polypeptide binding]; other site 515619003501 inhibitor binding site; inhibition site 515619003502 B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or...; Region: corrinoid_protein_B12-BD; cd02070 515619003503 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 515619003504 B12 binding site [chemical binding]; other site 515619003505 cobalt ligand [ion binding]; other site 515619003506 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); Region: NT5C; cl17836 515619003507 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 515619003508 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 515619003509 active site 515619003510 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 515619003511 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 515619003512 homodimer interface [polypeptide binding]; other site 515619003513 substrate-cofactor binding pocket; other site 515619003514 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619003515 catalytic residue [active] 515619003516 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 515619003517 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 515619003518 homotrimer interaction site [polypeptide binding]; other site 515619003519 zinc binding site [ion binding]; other site 515619003520 CDP-binding sites; other site 515619003521 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 515619003522 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619003523 active site 515619003524 HIGH motif; other site 515619003525 nucleotide binding site [chemical binding]; other site 515619003526 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 515619003527 KMSKS motif; other site 515619003528 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 515619003529 tRNA binding surface [nucleotide binding]; other site 515619003530 anticodon binding site; other site 515619003531 Ribonuclease III family protein [Replication, recombination, and repair]; Region: COG1939 515619003532 active site 515619003533 metal binding site [ion binding]; metal-binding site 515619003534 dimerization interface [polypeptide binding]; other site 515619003535 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 515619003536 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 515619003537 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 515619003538 RNA polymerase factor sigma-70; Validated; Region: PRK08295 515619003539 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619003540 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; cl17315 515619003541 DNA binding residues [nucleotide binding] 515619003542 Negative regulator of genetic competence (MecA); Region: MecA; cl02022 515619003543 Response regulator receiver domain; Region: Response_reg; pfam00072 515619003544 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619003545 active site 515619003546 phosphorylation site [posttranslational modification] 515619003547 intermolecular recognition site; other site 515619003548 dimerization interface [polypeptide binding]; other site 515619003549 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 515619003550 CheC-like family; Region: CheC; pfam04509 515619003551 Chemotaxis phosphatase CheX; Region: CheX; cl15816 515619003552 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 515619003553 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 515619003554 Predicted phosphoesterases, related to the Icc protein [General function prediction only]; Region: COG2129 515619003555 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 515619003556 active site 515619003557 metal binding site [ion binding]; metal-binding site 515619003558 Thermus thermophilus TTHA0053 and related proteins, metallophosphatase domain; Region: MPP_TTHA0053; cd07403 515619003559 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 515619003560 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 515619003561 N-acetyl-D-glucosamine binding site [chemical binding]; other site 515619003562 catalytic residue [active] 515619003563 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 515619003564 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 515619003565 active site 515619003566 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 515619003567 substrate binding site [chemical binding]; other site 515619003568 catalytic residues [active] 515619003569 dimer interface [polypeptide binding]; other site 515619003570 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619003571 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 515619003572 non-specific DNA binding site [nucleotide binding]; other site 515619003573 salt bridge; other site 515619003574 sequence-specific DNA binding site [nucleotide binding]; other site 515619003575 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 515619003576 Catalytic site [active] 515619003577 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 515619003578 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 515619003579 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619003580 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619003581 active site 515619003582 phosphorylation site [posttranslational modification] 515619003583 intermolecular recognition site; other site 515619003584 dimerization interface [polypeptide binding]; other site 515619003585 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 515619003586 DNA binding site [nucleotide binding] 515619003587 HAMP domain; Region: HAMP; pfam00672 515619003588 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 515619003589 dimer interface [polypeptide binding]; other site 515619003590 phosphorylation site [posttranslational modification] 515619003591 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 515619003592 ATP binding site [chemical binding]; other site 515619003593 Mg2+ binding site [ion binding]; other site 515619003594 G-X-G motif; other site 515619003595 Domain of unknown function (DUF4352); Region: DUF4352; pfam11611 515619003596 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 515619003597 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 515619003598 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619003599 active site 515619003600 phosphorylation site [posttranslational modification] 515619003601 intermolecular recognition site; other site 515619003602 dimerization interface [polypeptide binding]; other site 515619003603 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 515619003604 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 515619003605 putative active site [active] 515619003606 oxyanion strand; other site 515619003607 catalytic triad [active] 515619003608 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 515619003609 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 515619003610 substrate binding site [chemical binding]; other site 515619003611 glutamase interaction surface [polypeptide binding]; other site 515619003612 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 515619003613 ligand binding site [chemical binding]; other site 515619003614 active site 515619003615 UGI interface [polypeptide binding]; other site 515619003616 catalytic site [active] 515619003617 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 515619003618 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 515619003619 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619003620 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619003621 ABC transporter; Region: ABC_tran_2; pfam12848 515619003622 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619003623 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 515619003624 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 515619003625 dimer interface [polypeptide binding]; other site 515619003626 PYR/PP interface [polypeptide binding]; other site 515619003627 TPP binding site [chemical binding]; other site 515619003628 substrate binding site [chemical binding]; other site 515619003629 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 515619003630 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 515619003631 Domain of unknown function; Region: EKR; pfam10371 515619003632 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 515619003633 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 515619003634 TPP-binding site [chemical binding]; other site 515619003635 dimer interface [polypeptide binding]; other site 515619003636 phosphodiesterase; Provisional; Region: PRK12704 515619003637 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK14869 515619003638 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 515619003639 DRTGG domain; Region: DRTGG; pfam07085 515619003640 DHHA2 domain; Region: DHHA2; pfam02833 515619003641 Cupin domain; Region: Cupin_2; cl17218 515619003642 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 515619003643 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619003644 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619003645 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 515619003646 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 515619003647 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 515619003648 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 515619003649 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 515619003650 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 515619003651 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 515619003652 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 515619003653 dihydrodipicolinate synthase; Region: dapA; TIGR00674 515619003654 dimer interface [polypeptide binding]; other site 515619003655 active site 515619003656 catalytic residue [active] 515619003657 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 515619003658 Domain of unknown function (DUF4364); Region: DUF4364; pfam14277 515619003659 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 515619003660 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 515619003661 FeS/SAM binding site; other site 515619003662 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 515619003663 Malic enzyme, N-terminal domain; Region: malic; pfam00390 515619003664 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 515619003665 putative NAD(P) binding site [chemical binding]; other site 515619003666 transcription termination factor Rho; Provisional; Region: rho; PRK09376 515619003667 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 515619003668 RNA binding site [nucleotide binding]; other site 515619003669 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619003670 Walker A motif; other site 515619003671 ATP binding site [chemical binding]; other site 515619003672 Walker B motif; other site 515619003673 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 515619003674 Protein of unknown function (DUF1385); Region: DUF1385; pfam07136 515619003675 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 515619003676 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 515619003677 S-adenosylmethionine binding site [chemical binding]; other site 515619003678 peptide chain release factor 1; Validated; Region: prfA; PRK00591 515619003679 This domain is found in peptide chain release factors; Region: PCRF; smart00937 515619003680 RF-1 domain; Region: RF-1; pfam00472 515619003681 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 515619003682 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 515619003683 membrane-bound complex binding site; other site 515619003684 hinge residues; other site 515619003685 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 515619003686 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 515619003687 substrate binding pocket [chemical binding]; other site 515619003688 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 515619003689 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 515619003690 dimer interface [polypeptide binding]; other site 515619003691 conserved gate region; other site 515619003692 putative PBP binding loops; other site 515619003693 ABC-ATPase subunit interface; other site 515619003694 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 515619003695 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 515619003696 Walker A/P-loop; other site 515619003697 ATP binding site [chemical binding]; other site 515619003698 Q-loop/lid; other site 515619003699 ABC transporter signature motif; other site 515619003700 Walker B; other site 515619003701 D-loop; other site 515619003702 H-loop/switch region; other site 515619003703 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]; Region: COG3341 515619003704 Caulimovirus viroplasmin; Region: Cauli_VI; pfam01693 515619003705 Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Region: RNase_HI_bacteria_HBD; cd09277 515619003706 RNA/DNA hybrid binding site [nucleotide binding]; other site 515619003707 active site 515619003708 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 515619003709 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 515619003710 active site 515619003711 dimer interface [polypeptide binding]; other site 515619003712 metal binding site [ion binding]; metal-binding site 515619003713 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 515619003714 hypothetical protein; Provisional; Region: PRK13670 515619003715 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 515619003716 propionate/acetate kinase; Provisional; Region: PRK12379 515619003717 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 515619003718 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 515619003719 Restriction alleviation protein Lar; Region: Lar_restr_allev; pfam14354 515619003720 putative phosphate acyltransferase; Provisional; Region: PRK05331 515619003721 acyl carrier protein; Provisional; Region: acpP; PRK00982 515619003722 ribonuclease III; Reviewed; Region: rnc; PRK00102 515619003723 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 515619003724 dimerization interface [polypeptide binding]; other site 515619003725 active site 515619003726 metal binding site [ion binding]; metal-binding site 515619003727 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 515619003728 dsRNA binding site [nucleotide binding]; other site 515619003729 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 515619003730 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 515619003731 Walker A/P-loop; other site 515619003732 ATP binding site [chemical binding]; other site 515619003733 Q-loop/lid; other site 515619003734 Ubiquitin elongating factor core; Region: Ufd2P_core; pfam10408 515619003735 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 515619003736 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 515619003737 ABC transporter signature motif; other site 515619003738 Walker B; other site 515619003739 D-loop; other site 515619003740 H-loop/switch region; other site 515619003741 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 515619003742 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 515619003743 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619003744 threonine dehydratase; Provisional; Region: PRK08198 515619003745 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 515619003746 tetramer interface [polypeptide binding]; other site 515619003747 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619003748 catalytic residue [active] 515619003749 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 515619003750 putative DNA-binding protein; Validated; Region: PRK00118 515619003751 signal recognition particle protein; Provisional; Region: PRK10867 515619003752 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 515619003753 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 515619003754 P loop; other site 515619003755 GTP binding site [chemical binding]; other site 515619003756 Signal peptide binding domain; Region: SRP_SPB; pfam02978 515619003757 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 515619003758 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 515619003759 hypothetical protein; Provisional; Region: PRK00468 515619003760 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 515619003761 RimM N-terminal domain; Region: RimM; pfam01782 515619003762 PRC-barrel domain; Region: PRC; pfam05239 515619003763 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 515619003764 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 515619003765 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 515619003766 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 515619003767 Catalytic site [active] 515619003768 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 515619003769 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 515619003770 GTP/Mg2+ binding site [chemical binding]; other site 515619003771 G4 box; other site 515619003772 G5 box; other site 515619003773 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 515619003774 G1 box; other site 515619003775 G1 box; other site 515619003776 GTP/Mg2+ binding site [chemical binding]; other site 515619003777 Switch I region; other site 515619003778 G2 box; other site 515619003779 G2 box; other site 515619003780 G3 box; other site 515619003781 G3 box; other site 515619003782 Switch II region; other site 515619003783 Switch II region; other site 515619003784 G4 box; other site 515619003785 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 515619003786 RNA/DNA hybrid binding site [nucleotide binding]; other site 515619003787 active site 515619003788 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619003789 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619003790 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 515619003791 dimerization interface [polypeptide binding]; other site 515619003792 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; cl00206 515619003793 regulatory protein interface [polypeptide binding]; other site 515619003794 regulatory phosphorylation site [posttranslational modification]; other site 515619003795 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 515619003796 DEAD_2; Region: DEAD_2; pfam06733 515619003797 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 515619003798 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619003799 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619003800 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 515619003801 dimerization interface [polypeptide binding]; other site 515619003802 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 515619003803 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 515619003804 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 515619003805 dimerization interface [polypeptide binding]; other site 515619003806 ATP binding site [chemical binding]; other site 515619003807 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 515619003808 dimerization interface [polypeptide binding]; other site 515619003809 ATP binding site [chemical binding]; other site 515619003810 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 515619003811 putative active site [active] 515619003812 catalytic triad [active] 515619003813 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 515619003814 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 515619003815 active site 515619003816 histidinol-phosphatase; Provisional; Region: PRK05588 515619003817 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 515619003818 active site 515619003819 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 515619003820 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 515619003821 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 515619003822 Phosphoglycerate kinase; Region: PGK; pfam00162 515619003823 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 515619003824 substrate binding site [chemical binding]; other site 515619003825 hinge regions; other site 515619003826 ADP binding site [chemical binding]; other site 515619003827 catalytic site [active] 515619003828 triosephosphate isomerase; Provisional; Region: PRK14567 515619003829 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 515619003830 substrate binding site [chemical binding]; other site 515619003831 dimer interface [polypeptide binding]; other site 515619003832 catalytic triad [active] 515619003833 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 515619003834 phosphoglyceromutase; Provisional; Region: PRK05434 515619003835 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 515619003836 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 515619003837 ATP binding site [chemical binding]; other site 515619003838 active site 515619003839 substrate binding site [chemical binding]; other site 515619003840 amidophosphoribosyltransferase; Provisional; Region: PRK05793 515619003841 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 515619003842 active site 515619003843 tetramer interface [polypeptide binding]; other site 515619003844 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619003845 active site 515619003846 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 515619003847 Adenylsuccinate lyase (ASL)_subgroup 2; Region: Adenylsuccinate_lyase_2; cd03302 515619003848 tetramer interface [polypeptide binding]; other site 515619003849 active site 515619003850 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 515619003851 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619003852 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619003853 Walker A motif; other site 515619003854 Walker A/P-loop; other site 515619003855 ATP binding site [chemical binding]; other site 515619003856 ATP binding site [chemical binding]; other site 515619003857 Walker B motif; other site 515619003858 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional; Region: PRK10110 515619003859 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 515619003860 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 515619003861 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 515619003862 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 515619003863 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 515619003864 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 515619003865 Preprotein translocase SecG subunit; Region: SecG; pfam03840 515619003866 ribonuclease R; Region: RNase_R; TIGR02063 515619003867 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 515619003868 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 515619003869 RNB domain; Region: RNB; pfam00773 515619003870 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 515619003871 RNA binding site [nucleotide binding]; other site 515619003872 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 515619003873 SmpB-tmRNA interface; other site 515619003874 uracil-xanthine permease; Region: ncs2; TIGR00801 515619003875 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 515619003876 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619003877 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619003878 metal binding site [ion binding]; metal-binding site 515619003879 active site 515619003880 I-site; other site 515619003881 Sulfatase; Region: Sulfatase; pfam00884 515619003882 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 515619003883 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 515619003884 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 515619003885 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 515619003886 ATP binding site [chemical binding]; other site 515619003887 putative Mg++ binding site [ion binding]; other site 515619003888 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 515619003889 nucleotide binding region [chemical binding]; other site 515619003890 ATP-binding site [chemical binding]; other site 515619003891 Mitochondrial degradasome RNA helicase subunit C terminal; Region: SUV3_C; pfam12513 515619003892 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 515619003893 active site 515619003894 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 515619003895 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 515619003896 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 515619003897 active site 515619003898 DNA polymerase I; Provisional; Region: PRK05755 515619003899 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 515619003900 active site 515619003901 metal binding site 1 [ion binding]; metal-binding site 515619003902 putative 5' ssDNA interaction site; other site 515619003903 metal binding site 3; metal-binding site 515619003904 metal binding site 2 [ion binding]; metal-binding site 515619003905 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 515619003906 putative DNA binding site [nucleotide binding]; other site 515619003907 putative metal binding site [ion binding]; other site 515619003908 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 515619003909 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 515619003910 active site 515619003911 DNA binding site [nucleotide binding] 515619003912 catalytic site [active] 515619003913 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 515619003914 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 515619003915 CoA-binding site [chemical binding]; other site 515619003916 ATP-binding [chemical binding]; other site 515619003917 cell division protein FtsA; Region: ftsA; TIGR01174 515619003918 Cell division protein FtsA; Region: FtsA; smart00842 515619003919 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 515619003920 nucleotide binding site [chemical binding]; other site 515619003921 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 515619003922 ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; Region: ACT_1ZPV; cd04872 515619003923 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 515619003924 IMP cyclohydrolase-like protein; Region: IMP_cyclohyd; cl01330 515619003925 5-aminoimidazole-4-carboxamide ribonucleotide transformylase; Provisional; Region: PRK07106 515619003926 AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) [Nucleotide transport and metabolism]; Region: PurH; COG0138 515619003927 helicase-exonuclease AddAB, AddB subunit; Region: addB_Gpos; TIGR02773 515619003928 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 515619003929 helicase-exonuclease AddAB, AddA subunit, Firmicutes type; Region: addA_Gpos; TIGR02785 515619003930 Part of AAA domain; Region: AAA_19; pfam13245 515619003931 Family description; Region: UvrD_C_2; pfam13538 515619003932 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 515619003933 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 515619003934 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 515619003935 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 515619003936 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 515619003937 active site 515619003938 heat shock protein 90; Provisional; Region: PRK05218 515619003939 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 515619003940 ATP binding site [chemical binding]; other site 515619003941 Mg2+ binding site [ion binding]; other site 515619003942 G-X-G motif; other site 515619003943 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; cd03440 515619003944 active site 1 [active] 515619003945 active site 2 [active] 515619003946 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 515619003947 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 515619003948 serine O-acetyltransferase; Region: cysE; TIGR01172 515619003949 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 515619003950 trimer interface [polypeptide binding]; other site 515619003951 active site 515619003952 substrate binding site [chemical binding]; other site 515619003953 CoA binding site [chemical binding]; other site 515619003954 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619003955 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619003956 putative active site [active] 515619003957 putative NTP binding site [chemical binding]; other site 515619003958 putative nucleic acid binding site [nucleotide binding]; other site 515619003959 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619003960 FeoA domain; Region: FeoA; pfam04023 515619003961 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 515619003962 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 515619003963 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 515619003964 G1 box; other site 515619003965 GTP/Mg2+ binding site [chemical binding]; other site 515619003966 Switch I region; other site 515619003967 G2 box; other site 515619003968 G3 box; other site 515619003969 Switch II region; other site 515619003970 G4 box; other site 515619003971 G5 box; other site 515619003972 Nucleoside recognition; Region: Gate; pfam07670 515619003973 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 515619003974 Nucleoside recognition; Region: Gate; pfam07670 515619003975 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 515619003976 putative DNA binding helix; other site 515619003977 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 515619003978 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 515619003979 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 515619003980 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 515619003981 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 515619003982 MFS/sugar transport protein; Region: MFS_2; pfam13347 515619003983 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 515619003984 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619003985 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619003986 Domain of unknown function (DUF4190); Region: DUF4190; pfam13828 515619003987 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 515619003988 nucleotide binding site [chemical binding]; other site 515619003989 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 515619003990 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 515619003991 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3580 515619003992 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 515619003993 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 515619003994 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 515619003995 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 515619003996 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619003997 active site 515619003998 HIGH motif; other site 515619003999 nucleotide binding site [chemical binding]; other site 515619004000 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619004001 active site 515619004002 KMSKS motif; other site 515619004003 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 515619004004 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1655 515619004005 Uncharacterized protein conserved in bacteria (DUF2225); Region: DUF2225; pfam09986 515619004006 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619004007 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619004008 putative active site [active] 515619004009 putative NTP binding site [chemical binding]; other site 515619004010 putative nucleic acid binding site [nucleotide binding]; other site 515619004011 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619004012 argininosuccinate synthase; Provisional; Region: PRK13820 515619004013 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 515619004014 ANP binding site [chemical binding]; other site 515619004015 Substrate Binding Site II [chemical binding]; other site 515619004016 Substrate Binding Site I [chemical binding]; other site 515619004017 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 515619004018 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 515619004019 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 515619004020 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619004021 Coenzyme A binding pocket [chemical binding]; other site 515619004022 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 515619004023 feedback inhibition sensing region; other site 515619004024 homohexameric interface [polypeptide binding]; other site 515619004025 nucleotide binding site [chemical binding]; other site 515619004026 N-acetyl-L-glutamate binding site [chemical binding]; other site 515619004027 acetylornithine aminotransferase; Provisional; Region: PRK02627 515619004028 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 515619004029 inhibitor-cofactor binding pocket; inhibition site 515619004030 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619004031 catalytic residue [active] 515619004032 SLBB domain; Region: SLBB; pfam10531 515619004033 comEA protein; Region: comE; TIGR01259 515619004034 Helix-hairpin-helix motif; Region: HHH; pfam00633 515619004035 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619004036 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619004037 active site 515619004038 phosphorylation site [posttranslational modification] 515619004039 intermolecular recognition site; other site 515619004040 dimerization interface [polypeptide binding]; other site 515619004041 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 515619004042 DNA binding site [nucleotide binding] 515619004043 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619004044 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 515619004045 dimer interface [polypeptide binding]; other site 515619004046 phosphorylation site [posttranslational modification] 515619004047 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 515619004048 ATP binding site [chemical binding]; other site 515619004049 Mg2+ binding site [ion binding]; other site 515619004050 G-X-G motif; other site 515619004051 Sporulation and spore germination; Region: Germane; pfam10646 515619004052 Sporulation and spore germination; Region: Germane; pfam10646 515619004053 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 515619004054 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 515619004055 Competence protein; Region: Competence; pfam03772 515619004056 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 515619004057 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 515619004058 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 515619004059 germination protease; Provisional; Region: PRK12362 515619004060 Stage II sporulation protein P (SpoIIP); Region: SpoIIP; pfam07454 515619004061 stage II sporulation protein P; Region: spore_II_P; TIGR02867 515619004062 GTP-binding protein LepA; Provisional; Region: PRK05433 515619004063 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 515619004064 G1 box; other site 515619004065 putative GEF interaction site [polypeptide binding]; other site 515619004066 GTP/Mg2+ binding site [chemical binding]; other site 515619004067 Switch I region; other site 515619004068 G2 box; other site 515619004069 G3 box; other site 515619004070 Switch II region; other site 515619004071 G4 box; other site 515619004072 G5 box; other site 515619004073 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 515619004074 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 515619004075 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 515619004076 coproporphyrinogen III oxidase; Provisional; Region: PRK05799 515619004077 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 515619004078 FeS/SAM binding site; other site 515619004079 HemN C-terminal domain; Region: HemN_C; pfam06969 515619004080 segregation and condensation protein A; Reviewed; Region: scpA; PRK00104 515619004081 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 515619004082 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 515619004083 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 515619004084 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 515619004085 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 515619004086 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 515619004087 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 515619004088 carboxyltransferase (CT) interaction site; other site 515619004089 biotinylation site [posttranslational modification]; other site 515619004090 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 515619004091 oxaloacetate decarboxylase; Provisional; Region: PRK12331 515619004092 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 515619004093 active site 515619004094 catalytic residues [active] 515619004095 metal binding site [ion binding]; metal-binding site 515619004096 homodimer binding site [polypeptide binding]; other site 515619004097 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 515619004098 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 515619004099 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 515619004100 putative active site [active] 515619004101 flavoprotein, HI0933 family; Region: TIGR00275 515619004102 cytidylate kinase; Provisional; Region: cmk; PRK00023 515619004103 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 515619004104 CMP-binding site; other site 515619004105 The sites determining sugar specificity; other site 515619004106 LytB protein; Region: LYTB; cl00507 515619004107 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 515619004108 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06676 515619004109 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 515619004110 RNA binding site [nucleotide binding]; other site 515619004111 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 515619004112 RNA binding site [nucleotide binding]; other site 515619004113 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 515619004114 RNA binding site [nucleotide binding]; other site 515619004115 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 515619004116 RNA binding site [nucleotide binding]; other site 515619004117 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 515619004118 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 515619004119 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 515619004120 RNase_H superfamily; Region: RNase_H_2; pfam13482 515619004121 active site 515619004122 catalytic site [active] 515619004123 substrate binding site [chemical binding]; other site 515619004124 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 515619004125 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 515619004126 SLBB domain; Region: SLBB; pfam10531 515619004127 4Fe-4S binding domain; Region: Fer4_6; pfam12837 515619004128 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 515619004129 FMN-binding domain; Region: FMN_bind; cl01081 515619004130 electron transport complex RsxE subunit; Provisional; Region: PRK12405 515619004131 electron transport complex, RnfABCDGE type, A subunit; Region: rnfA; TIGR01943 515619004132 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]; Region: COG2878 515619004133 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 515619004134 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 515619004135 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 515619004136 ApbE family; Region: ApbE; pfam02424 515619004137 Glutamate 5-kinase [Amino acid transport and metabolism]; Region: ProB; COG0263 515619004138 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 515619004139 nucleotide binding site [chemical binding]; other site 515619004140 homotetrameric interface [polypeptide binding]; other site 515619004141 putative phosphate binding site [ion binding]; other site 515619004142 putative allosteric binding site; other site 515619004143 Bacterial protein of unknown function (DUF896); Region: DUF896; pfam05979 515619004144 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 515619004145 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 515619004146 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 515619004147 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 515619004148 putative catalytic cysteine [active] 515619004149 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14328 515619004150 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 515619004151 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 515619004152 FeS/SAM binding site; other site 515619004153 TRAM domain; Region: TRAM; cl01282 515619004154 Listerrria innocua Lin0431 is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (DII); Region: Lin0431_like; cd09911 515619004155 trimer interface [polypeptide binding]; other site 515619004156 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 515619004157 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 515619004158 RuvA N terminal domain; Region: RuvA_N; pfam01330 515619004159 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 515619004160 Holliday junction DNA helicase ruvB N-terminus; Region: RuvB_N; pfam05496 515619004161 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 515619004162 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 515619004163 Walker B motif; other site 515619004164 arginine finger; other site 515619004165 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 515619004166 Cell division protein ZapA; Region: ZapA; pfam05164 515619004167 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 515619004168 Peptidase family U32; Region: Peptidase_U32; pfam01136 515619004169 Collagenase; Region: DUF3656; pfam12392 515619004170 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 515619004171 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 515619004172 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 515619004173 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 515619004174 active site 515619004175 Ap6A binding site [chemical binding]; other site 515619004176 nudix motif; other site 515619004177 metal binding site [ion binding]; metal-binding site 515619004178 Sporulation protein YtfJ (Spore_YtfJ); Region: Spore_YtfJ; pfam09579 515619004179 Asp23 family; Region: Asp23; pfam03780 515619004180 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 515619004181 DAK2 domain; Region: Dak2; pfam02734 515619004182 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 515619004183 Y-family of DNA polymerases; Region: PolY; cl12025 515619004184 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 515619004185 ssDNA binding site; other site 515619004186 generic binding surface II; other site 515619004187 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 515619004188 ATP binding site [chemical binding]; other site 515619004189 putative Mg++ binding site [ion binding]; other site 515619004190 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 515619004191 nucleotide binding region [chemical binding]; other site 515619004192 ATP-binding site [chemical binding]; other site 515619004193 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 515619004194 Domain of unknown function (DUF814); Region: DUF814; pfam05670 515619004195 hypothetical protein; Provisional; Region: PRK11820 515619004196 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 515619004197 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 515619004198 Guanylate kinase; Region: Guanylate_kin; pfam00625 515619004199 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 515619004200 catalytic site [active] 515619004201 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 515619004202 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 515619004203 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 515619004204 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 515619004205 FeS/SAM binding site; other site 515619004206 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 515619004207 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 515619004208 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 515619004209 S-adenosylmethionine binding site [chemical binding]; other site 515619004210 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 515619004211 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 515619004212 active site 515619004213 (T/H)XGH motif; other site 515619004214 sporulation integral membrane protein YlbJ; Region: spore_ylbJ; TIGR02871 515619004215 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 515619004216 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 515619004217 RNA binding surface [nucleotide binding]; other site 515619004218 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 515619004219 active site 515619004220 uracil binding [chemical binding]; other site 515619004221 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 515619004222 hypothetical protein; Provisional; Region: PRK00955 515619004223 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 515619004224 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 515619004225 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 515619004226 RNA binding surface [nucleotide binding]; other site 515619004227 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 515619004228 active site 515619004229 Recombination protein U; Region: RecU; cl01314 515619004230 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 515619004231 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 515619004232 dimer interface [polypeptide binding]; other site 515619004233 motif 1; other site 515619004234 active site 515619004235 motif 2; other site 515619004236 motif 3; other site 515619004237 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 515619004238 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 515619004239 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 515619004240 histidinol dehydrogenase; Region: hisD; TIGR00069 515619004241 NAD binding site [chemical binding]; other site 515619004242 dimerization interface [polypeptide binding]; other site 515619004243 product binding site; other site 515619004244 substrate binding site [chemical binding]; other site 515619004245 zinc binding site [ion binding]; other site 515619004246 catalytic residues [active] 515619004247 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 515619004248 putative active site pocket [active] 515619004249 4-fold oligomerization interface [polypeptide binding]; other site 515619004250 metal binding residues [ion binding]; metal-binding site 515619004251 3-fold/trimer interface [polypeptide binding]; other site 515619004252 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 515619004253 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 515619004254 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 515619004255 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 515619004256 metal binding site [ion binding]; metal-binding site 515619004257 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 515619004258 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 515619004259 FeS/SAM binding site; other site 515619004260 radical SAM-linked protein; Region: sam_1_link_chp; TIGR03936 515619004261 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; pfam10105 515619004262 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 515619004263 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 515619004264 homodimer interface [polypeptide binding]; other site 515619004265 oligonucleotide binding site [chemical binding]; other site 515619004266 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 515619004267 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 515619004268 Protein of unknown function (DUF464); Region: DUF464; pfam04327 515619004269 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 515619004270 GTPase CgtA; Reviewed; Region: obgE; PRK12297 515619004271 GTP1/OBG; Region: GTP1_OBG; pfam01018 515619004272 Obg GTPase; Region: Obg; cd01898 515619004273 G1 box; other site 515619004274 GTP/Mg2+ binding site [chemical binding]; other site 515619004275 Switch I region; other site 515619004276 G2 box; other site 515619004277 G3 box; other site 515619004278 Switch II region; other site 515619004279 G4 box; other site 515619004280 G5 box; other site 515619004281 Domain of unknown function (DUF1967); Region: DUF1967; pfam09269 515619004282 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 515619004283 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 515619004284 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 515619004285 active site 515619004286 (T/H)XGH motif; other site 515619004287 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619004288 Zn2+ binding site [ion binding]; other site 515619004289 Mg2+ binding site [ion binding]; other site 515619004290 Oligomerisation domain; Region: Oligomerisation; pfam02410 515619004291 LexA repressor; Validated; Region: PRK00215 515619004292 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 515619004293 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 515619004294 Catalytic site [active] 515619004295 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 515619004296 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 515619004297 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 515619004298 putative acyl-acceptor binding pocket; other site 515619004299 site-specific tyrosine recombinase XerS; Reviewed; Region: xerS; PRK05084 515619004300 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 515619004301 active site 515619004302 Int/Topo IB signature motif; other site 515619004303 DNA binding site [nucleotide binding] 515619004304 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 515619004305 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 515619004306 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 515619004307 dinuclear metal binding motif [ion binding]; other site 515619004308 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 515619004309 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 515619004310 putative active site [active] 515619004311 dimerization interface [polypeptide binding]; other site 515619004312 putative tRNAtyr binding site [nucleotide binding]; other site 515619004313 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 515619004314 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 515619004315 Ligand Binding Site [chemical binding]; other site 515619004316 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619004317 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619004318 dimer interface [polypeptide binding]; other site 515619004319 putative CheW interface [polypeptide binding]; other site 515619004320 CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI; Region: cas_Csn1; TIGR01865 515619004321 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 515619004322 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 515619004323 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09638 515619004324 Stu0660-like CRISPR/Cas system-associated protein Csn2; Region: Stu0660_Csn2; cd12217 515619004325 tetramer interface [polypeptide binding]; other site 515619004326 putative DNA binding site [nucleotide binding]; other site 515619004327 Uncharacterized protein conserved in bacteria (DUF2128); Region: DUF2128; pfam09901 515619004328 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cd02062 515619004329 FMN binding site [chemical binding]; other site 515619004330 dimer interface [polypeptide binding]; other site 515619004331 WYL domain; Region: WYL; pfam13280 515619004332 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 515619004333 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619004334 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619004335 ABC transporter; Region: ABC_tran_2; pfam12848 515619004336 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619004337 potential frameshift: common BLAST hit: gi|226949384|ref|YP_002804475.1| transporter, AEC family 515619004338 Membrane transport protein; Region: Mem_trans; cl09117 515619004339 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 515619004340 active site 515619004341 substrate binding site [chemical binding]; other site 515619004342 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 515619004343 FMN binding site [chemical binding]; other site 515619004344 putative catalytic residues [active] 515619004345 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 515619004346 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK12315 515619004347 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 515619004348 TPP-binding site; other site 515619004349 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 515619004350 PYR/PP interface [polypeptide binding]; other site 515619004351 dimer interface [polypeptide binding]; other site 515619004352 TPP binding site [chemical binding]; other site 515619004353 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 515619004354 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619004355 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 515619004356 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 515619004357 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 515619004358 RNA binding surface [nucleotide binding]; other site 515619004359 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 515619004360 active site 515619004361 lipoprotein signal peptidase; Provisional; Region: PRK14767 515619004362 lipoprotein signal peptidase; Provisional; Region: PRK14787 515619004363 Protein of unknown function (DUF552); Region: DUF552; pfam04472 515619004364 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 515619004365 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 515619004366 catalytic residue [active] 515619004367 HlyD family secretion protein; Region: HlyD_2; pfam12700 515619004368 putative membrane fusion protein; Region: TIGR02828 515619004369 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 515619004370 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 515619004371 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 515619004372 active site 515619004373 dimer interfaces [polypeptide binding]; other site 515619004374 catalytic residues [active] 515619004375 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 515619004376 Septum formation topological specificity factor MinE; Region: MinE; cl00538 515619004377 septum site-determining protein MinD; Region: minD_bact; TIGR01968 515619004378 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 515619004379 P-loop; other site 515619004380 ADP binding residues [chemical binding]; other site 515619004381 Switch I; other site 515619004382 Switch II; other site 515619004383 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 515619004384 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 515619004385 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 515619004386 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 515619004387 rod shape-determining protein MreC; Provisional; Region: PRK13922 515619004388 rod shape-determining protein MreC; Region: MreC; pfam04085 515619004389 rod shape-determining protein MreB; Provisional; Region: PRK13927 515619004390 MreB and similar proteins; Region: MreB_like; cd10225 515619004391 nucleotide binding site [chemical binding]; other site 515619004392 Mg binding site [ion binding]; other site 515619004393 putative protofilament interaction site [polypeptide binding]; other site 515619004394 RodZ interaction site [polypeptide binding]; other site 515619004395 hypothetical protein; Reviewed; Region: PRK00024 515619004396 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 515619004397 MPN+ (JAMM) motif; other site 515619004398 Zinc-binding site [ion binding]; other site 515619004399 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 515619004400 Aluminium resistance protein; Region: Alum_res; pfam06838 515619004401 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 515619004402 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 515619004403 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 515619004404 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 515619004405 ATP binding site [chemical binding]; other site 515619004406 Mg2+ binding site [ion binding]; other site 515619004407 G-X-G motif; other site 515619004408 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 515619004409 ATP binding site [chemical binding]; other site 515619004410 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 515619004411 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 515619004412 MutS domain I; Region: MutS_I; pfam01624 515619004413 MutS domain II; Region: MutS_II; pfam05188 515619004414 MutS domain III; Region: MutS_III; pfam05192 515619004415 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 515619004416 Walker A/P-loop; other site 515619004417 ATP binding site [chemical binding]; other site 515619004418 Q-loop/lid; other site 515619004419 ABC transporter signature motif; other site 515619004420 Walker B; other site 515619004421 D-loop; other site 515619004422 H-loop/switch region; other site 515619004423 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 515619004424 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 515619004425 flavoprotein, HI0933 family; Region: TIGR00275 515619004426 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 515619004427 stage V sporulation protein B; Region: spore_V_B; TIGR02900 515619004428 metal-binding heat shock protein; Provisional; Region: PRK00016 515619004429 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 515619004430 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 515619004431 PhoH-like protein; Region: PhoH; pfam02562 515619004432 sporulation protein YqfD; Region: spore_yqfD; TIGR02876 515619004433 YabP family; Region: YabP; cl06766 515619004434 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 515619004435 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619004436 active site 515619004437 DNA polymerase III PolC; Validated; Region: polC; PRK00448 515619004438 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 515619004439 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 515619004440 generic binding surface II; other site 515619004441 generic binding surface I; other site 515619004442 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 515619004443 active site 515619004444 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 515619004445 active site 515619004446 catalytic site [active] 515619004447 substrate binding site [chemical binding]; other site 515619004448 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; Region: PHP_PolIIIA_POLC; cd07435 515619004449 GcpE protein; Region: GcpE; pfam04551 515619004450 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 515619004451 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 515619004452 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 515619004453 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 515619004454 active site 515619004455 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 515619004456 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 515619004457 putative substrate binding region [chemical binding]; other site 515619004458 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 515619004459 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 515619004460 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 515619004461 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 515619004462 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 515619004463 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 515619004464 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 515619004465 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 515619004466 catalytic residue [active] 515619004467 putative FPP diphosphate binding site; other site 515619004468 putative FPP binding hydrophobic cleft; other site 515619004469 dimer interface [polypeptide binding]; other site 515619004470 putative IPP diphosphate binding site; other site 515619004471 ribosome recycling factor; Reviewed; Region: frr; PRK00083 515619004472 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 515619004473 hinge region; other site 515619004474 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 515619004475 putative nucleotide binding site [chemical binding]; other site 515619004476 uridine monophosphate binding site [chemical binding]; other site 515619004477 homohexameric interface [polypeptide binding]; other site 515619004478 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 515619004479 delta-lactam-biosynthetic de-N-acetylase; Region: spore_pdaA; TIGR02884 515619004480 Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; Region: CE4_SmPgdA_like; cd10944 515619004481 NodB motif; other site 515619004482 active site 515619004483 catalytic site [active] 515619004484 Zn binding site [ion binding]; other site 515619004485 translation elongation factor Ts; Region: tsf; TIGR00116 515619004486 UBA/TS-N domain; Region: UBA; pfam00627 515619004487 Elongation factor TS; Region: EF_TS; pfam00889 515619004488 Elongation factor TS; Region: EF_TS; pfam00889 515619004489 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 515619004490 rRNA interaction site [nucleotide binding]; other site 515619004491 S8 interaction site; other site 515619004492 putative laminin-1 binding site; other site 515619004493 YceG-like family; Region: YceG; pfam02618 515619004494 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 515619004495 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619004496 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 515619004497 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 515619004498 DNA binding residues [nucleotide binding] 515619004499 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13488 515619004500 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 515619004501 CheC-like family; Region: CheC; pfam04509 515619004502 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 515619004503 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 515619004504 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 515619004505 putative binding surface; other site 515619004506 active site 515619004507 P2 response regulator binding domain; Region: P2; pfam07194 515619004508 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 515619004509 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 515619004510 ATP binding site [chemical binding]; other site 515619004511 Mg2+ binding site [ion binding]; other site 515619004512 G-X-G motif; other site 515619004513 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 515619004514 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 515619004515 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619004516 active site 515619004517 phosphorylation site [posttranslational modification] 515619004518 intermolecular recognition site; other site 515619004519 dimerization interface [polypeptide binding]; other site 515619004520 CheB methylesterase; Region: CheB_methylest; pfam01339 515619004521 Flagellar protein YcgR; Region: YcgR_2; pfam12945 515619004522 PilZ domain; Region: PilZ; pfam07238 515619004523 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 515619004524 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 515619004525 P-loop; other site 515619004526 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 515619004527 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619004528 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 515619004529 FHIPEP family; Region: FHIPEP; pfam00771 515619004530 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 515619004531 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 515619004532 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 515619004533 Bacterial export proteins, family 3; Region: Bac_export_3; pfam01313 515619004534 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 515619004535 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 515619004536 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 515619004537 CheC-like family; Region: CheC; pfam04509 515619004538 CheC-like family; Region: CheC; pfam04509 515619004539 flagellar motor switch protein FliN; Region: fliN; TIGR02480 515619004540 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 515619004541 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 515619004542 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 515619004543 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 515619004544 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 515619004545 ligand binding site [chemical binding]; other site 515619004546 flagellar motor protein MotA; Validated; Region: PRK08124 515619004547 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 515619004548 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 515619004549 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 515619004550 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 515619004551 Protein of unknown function (DUF3766); Region: DUF3766; cl11797 515619004552 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 515619004553 flagellar basal body rod modification protein; Provisional; Region: flgD; PRK09618 515619004554 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 515619004555 Uncharacterized conserved protein [Function unknown]; Region: COG3334 515619004556 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK07720 515619004557 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 515619004558 flagellar protein export ATPase FliI; Region: FliI_clade2; TIGR03497 515619004559 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619004560 Walker A motif; other site 515619004561 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619004562 Walker B motif; other site 515619004563 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 515619004564 Flagellar assembly protein FliH; Region: FliH; pfam02108 515619004565 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 515619004566 MgtE intracellular N domain; Region: MgtE_N; cl15244 515619004567 FliG C-terminal domain; Region: FliG_C; pfam01706 515619004568 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 515619004569 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 515619004570 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 515619004571 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 515619004572 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 515619004573 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 515619004574 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 515619004575 flagellar basal-body rod protein FlgB; Region: FlgB; TIGR01396 515619004576 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 515619004577 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 515619004578 transcriptional repressor CodY; Validated; Region: PRK04158 515619004579 CodY GAF-like domain; Region: CodY; pfam06018 515619004580 CodY helix-turn-helix domain; Region: HTH_CodY; pfam08222 515619004581 DNA topoisomerase I; Validated; Region: PRK05582 515619004582 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 515619004583 active site 515619004584 interdomain interaction site; other site 515619004585 putative metal-binding site [ion binding]; other site 515619004586 nucleotide binding site [chemical binding]; other site 515619004587 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 515619004588 domain I; other site 515619004589 DNA binding groove [nucleotide binding] 515619004590 phosphate binding site [ion binding]; other site 515619004591 domain II; other site 515619004592 domain III; other site 515619004593 nucleotide binding site [chemical binding]; other site 515619004594 catalytic site [active] 515619004595 domain IV; other site 515619004596 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 515619004597 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 515619004598 DNA protecting protein DprA; Region: dprA; TIGR00732 515619004599 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 515619004600 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 515619004601 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 515619004602 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 515619004603 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 515619004604 sporulation sigma factor SigG; Reviewed; Region: PRK08215 515619004605 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619004606 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 515619004607 DNA binding residues [nucleotide binding] 515619004608 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 515619004609 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 515619004610 active site 515619004611 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 515619004612 Type II secretory pathway, pullulanase PulA and related glycosidases [Carbohydrate transport and metabolism]; Region: PulA; COG1523 515619004613 Alpha amylase catalytic domain family; Region: AmyAc_family; cd00551 515619004614 active site 515619004615 catalytic site [active] 515619004616 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 515619004617 Protein of unknown function (DUF1292); Region: DUF1292; pfam06949 515619004618 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 515619004619 Part of AAA domain; Region: AAA_19; pfam13245 515619004620 Family description; Region: UvrD_C_2; pfam13538 515619004621 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 515619004622 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619004623 active site 515619004624 HIGH motif; other site 515619004625 nucleotide binding site [chemical binding]; other site 515619004626 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 515619004627 active site 515619004628 KMSKS motif; other site 515619004629 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 515619004630 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 515619004631 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619004632 homodimer interface [polypeptide binding]; other site 515619004633 catalytic residue [active] 515619004634 putative oxidoreductase; Provisional; Region: PRK12831 515619004635 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 515619004636 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 515619004637 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 515619004638 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 515619004639 FAD binding pocket [chemical binding]; other site 515619004640 FAD binding motif [chemical binding]; other site 515619004641 phosphate binding motif [ion binding]; other site 515619004642 beta-alpha-beta structure motif; other site 515619004643 NAD binding pocket [chemical binding]; other site 515619004644 Iron coordination center [ion binding]; other site 515619004645 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619004646 Domain of unknown function (DUF1980); Region: DUF1980; cl01492 515619004647 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 515619004648 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 515619004649 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 515619004650 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 515619004651 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 515619004652 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 515619004653 HAMP domain; Region: HAMP; pfam00672 515619004654 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619004655 dimer interface [polypeptide binding]; other site 515619004656 putative CheW interface [polypeptide binding]; other site 515619004657 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 515619004658 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 515619004659 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 515619004660 motif 1; other site 515619004661 active site 515619004662 motif 2; other site 515619004663 motif 3; other site 515619004664 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 515619004665 DHHA1 domain; Region: DHHA1; pfam02272 515619004666 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 515619004667 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 515619004668 Stage IV sporulation protein A (spore_IV_A); Region: Spore_IV_A; pfam09547 515619004669 stage IV sporulation protein A; Region: spore_IV_A; TIGR02836 515619004670 4-alpha-glucanotransferase; Provisional; Region: PRK14508 515619004671 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 515619004672 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cl02915 515619004673 Cl- selectivity filter; other site 515619004674 Cl- binding residues [ion binding]; other site 515619004675 pore gating glutamate residue; other site 515619004676 dimer interface [polypeptide binding]; other site 515619004677 pullulanase, type I; Region: pulA_typeI; TIGR02104 515619004678 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 515619004679 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 515619004680 Ca binding site [ion binding]; other site 515619004681 active site 515619004682 catalytic site [active] 515619004683 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 515619004684 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 515619004685 classical (c) SDRs; Region: SDR_c; cd05233 515619004686 NAD(P) binding site [chemical binding]; other site 515619004687 active site 515619004688 Sortase B (SrtB) or subfamily-2 sortases are membrane cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the...; Region: Sortase_B_2; cd05826 515619004689 active site 515619004690 catalytic site [active] 515619004691 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 515619004692 Catalytic site [active] 515619004693 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 515619004694 DNA binding site [nucleotide binding] 515619004695 Bacterial transcriptional activator domain; Region: BTAD; smart01043 515619004696 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 515619004697 binding surface 515619004698 TPR motif; other site 515619004699 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 515619004700 metal binding site [ion binding]; metal-binding site 515619004701 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 515619004702 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 515619004703 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 515619004704 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 515619004705 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 515619004706 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 515619004707 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 515619004708 ribonuclease R; Region: RNase_R; TIGR02063 515619004709 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 515619004710 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 515619004711 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 515619004712 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619004713 dimer interface [polypeptide binding]; other site 515619004714 putative CheW interface [polypeptide binding]; other site 515619004715 PilZ domain; Region: PilZ; pfam07238 515619004716 pyruvate phosphate dikinase; Provisional; Region: PRK09279 515619004717 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 515619004718 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 515619004719 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 515619004720 Cell-wall surface anchor repeat; Region: C-term_anchor; pfam13461 515619004721 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the...; Region: Sortase_C_3; cd05827 515619004722 active site 515619004723 catalytic site [active] 515619004724 fimbrial isopeptide formation D2 domain; Region: RrgB_K2N_iso_D2; TIGR04226 515619004725 Cna protein B-type domain; Region: Cna_B; pfam05738 515619004726 Collagen binding domain; Region: Collagen_bind; pfam05737 515619004727 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 515619004728 domain interaction interfaces [polypeptide binding]; other site 515619004729 LPXTG-motif cell wall anchor domain; Region: LPXTG_anchor; TIGR01167 515619004730 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 515619004731 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 515619004732 Catalytic site [active] 515619004733 glycyl-tRNA synthetase; Provisional; Region: PRK04173 515619004734 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 515619004735 motif 1; other site 515619004736 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 515619004737 active site 515619004738 motif 2; other site 515619004739 motif 3; other site 515619004740 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 515619004741 anticodon binding site; other site 515619004742 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 515619004743 Recombination protein O N terminal; Region: RecO_N; pfam11967 515619004744 Recombination protein O C terminal; Region: RecO_C; pfam02565 515619004745 GTPase Era; Reviewed; Region: era; PRK00089 515619004746 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 515619004747 G1 box; other site 515619004748 GTP/Mg2+ binding site [chemical binding]; other site 515619004749 Switch I region; other site 515619004750 G2 box; other site 515619004751 Switch II region; other site 515619004752 G3 box; other site 515619004753 G4 box; other site 515619004754 G5 box; other site 515619004755 KH domain; Region: KH_2; pfam07650 515619004756 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]; Region: COG1026 515619004757 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 515619004758 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 515619004759 Peptidase M16C associated; Region: M16C_assoc; pfam08367 515619004760 Mechanosensitive ion channel; Region: MS_channel; pfam00924 515619004761 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 515619004762 putative ligand binding site [chemical binding]; other site 515619004763 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 515619004764 putative NAD binding site [chemical binding]; other site 515619004765 putative catalytic site [active] 515619004766 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 515619004767 L-serine binding site [chemical binding]; other site 515619004768 ACT domain interface; other site 515619004769 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 515619004770 homodimer interface [polypeptide binding]; other site 515619004771 substrate-cofactor binding pocket; other site 515619004772 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619004773 catalytic residue [active] 515619004774 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 515619004775 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 515619004776 PYR/PP interface [polypeptide binding]; other site 515619004777 dimer interface [polypeptide binding]; other site 515619004778 TPP binding site [chemical binding]; other site 515619004779 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 515619004780 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 515619004781 TPP-binding site [chemical binding]; other site 515619004782 dimer interface [polypeptide binding]; other site 515619004783 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 515619004784 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 515619004785 tartrate dehydrogenase; Region: TTC; TIGR02089 515619004786 Preprotein translocase subunit; Region: YajC; pfam02699 515619004787 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 515619004788 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 515619004789 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 515619004790 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 515619004791 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 515619004792 Tetramer interface [polypeptide binding]; other site 515619004793 active site 515619004794 FMN-binding site [chemical binding]; other site 515619004795 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619004796 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 515619004797 Walker A/P-loop; other site 515619004798 ATP binding site [chemical binding]; other site 515619004799 Q-loop/lid; other site 515619004800 ABC transporter signature motif; other site 515619004801 Walker B; other site 515619004802 D-loop; other site 515619004803 H-loop/switch region; other site 515619004804 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 515619004805 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 515619004806 Domain of unknown function (DUF3502); Region: DUF3502; pfam12010 515619004807 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619004808 ATP binding site [chemical binding]; other site 515619004809 Mg2+ binding site [ion binding]; other site 515619004810 G-X-G motif; other site 515619004811 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619004812 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619004813 active site 515619004814 phosphorylation site [posttranslational modification] 515619004815 intermolecular recognition site; other site 515619004816 dimerization interface [polypeptide binding]; other site 515619004817 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619004818 Accessory gene regulator B; Region: AgrB; pfam04647 515619004819 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 515619004820 Peptidase family U32; Region: Peptidase_U32; pfam01136 515619004821 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 515619004822 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 515619004823 S-adenosylmethionine binding site [chemical binding]; other site 515619004824 YceG-like family; Region: YceG; pfam02618 515619004825 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 515619004826 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 515619004827 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 515619004828 Protein of unknown function (DUF1292); Region: DUF1292; pfam06949 515619004829 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 515619004830 hypothetical protein; Provisional; Region: PRK05473 515619004831 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 515619004832 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 515619004833 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 515619004834 FeS/SAM binding site; other site 515619004835 PTS HPr component phosphorylation site; Region: PTS-HPr; pfam00381 515619004836 regulatory protein interface [polypeptide binding]; other site 515619004837 regulatory phosphorylation site [posttranslational modification]; other site 515619004838 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 515619004839 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 515619004840 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 515619004841 Ligand Binding Site [chemical binding]; other site 515619004842 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 515619004843 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 515619004844 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619004845 catalytic residue [active] 515619004846 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 515619004847 RNA methyltransferase, RsmE family; Region: TIGR00046 515619004848 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 515619004849 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 515619004850 S-adenosylmethionine binding site [chemical binding]; other site 515619004851 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 515619004852 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 515619004853 dimer interface [polypeptide binding]; other site 515619004854 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 515619004855 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 515619004856 HSP70 interaction site [polypeptide binding]; other site 515619004857 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 515619004858 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 515619004859 nucleotide binding site [chemical binding]; other site 515619004860 NEF interaction site [polypeptide binding]; other site 515619004861 SBD interface [polypeptide binding]; other site 515619004862 hypothetical protein; Provisional; Region: PRK10318 515619004863 GrpE; Region: GrpE; pfam01025 515619004864 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 515619004865 dimer interface [polypeptide binding]; other site 515619004866 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 515619004867 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 515619004868 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 515619004869 RelB antitoxin; Region: RelB; cl01171 515619004870 Cysteine-rich small domain; Region: zf-like; cl00946 515619004871 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 515619004872 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619004873 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 515619004874 catalytic triad [active] 515619004875 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; pfam02571 515619004876 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 515619004877 active site 515619004878 putative homodimer interface [polypeptide binding]; other site 515619004879 SAM binding site [chemical binding]; other site 515619004880 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 515619004881 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 515619004882 S-adenosylmethionine binding site [chemical binding]; other site 515619004883 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 515619004884 active site 515619004885 SAM binding site [chemical binding]; other site 515619004886 homodimer interface [polypeptide binding]; other site 515619004887 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 515619004888 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 515619004889 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 515619004890 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 515619004891 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 515619004892 active site 515619004893 SAM binding site [chemical binding]; other site 515619004894 homodimer interface [polypeptide binding]; other site 515619004895 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 515619004896 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 515619004897 Precorrin-8X methylmutase; Region: CbiC; pfam02570 515619004898 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 515619004899 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 515619004900 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619004901 homodimer interface [polypeptide binding]; other site 515619004902 catalytic residue [active] 515619004903 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 515619004904 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 515619004905 catalytic core [active] 515619004906 Cobinamide kinase / cobinamide phosphate guanyltransferase; Region: CobU; cl17363 515619004907 cobalamin synthase; Reviewed; Region: cobS; PRK00235 515619004908 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619004909 Walker A motif; other site 515619004910 ATP binding site [chemical binding]; other site 515619004911 Walker B motif; other site 515619004912 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 515619004913 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 515619004914 putative dimer interface [polypeptide binding]; other site 515619004915 active site pocket [active] 515619004916 putative cataytic base [active] 515619004917 cobyric acid synthase; Provisional; Region: PRK00784 515619004918 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 515619004919 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 515619004920 catalytic triad [active] 515619004921 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 515619004922 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 515619004923 Walker A/P-loop; other site 515619004924 ATP binding site [chemical binding]; other site 515619004925 Q-loop/lid; other site 515619004926 ABC transporter signature motif; other site 515619004927 Walker B; other site 515619004928 D-loop; other site 515619004929 H-loop/switch region; other site 515619004930 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 515619004931 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 515619004932 ABC-ATPase subunit interface; other site 515619004933 dimer interface [polypeptide binding]; other site 515619004934 putative PBP binding regions; other site 515619004935 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 515619004936 intersubunit interface [polypeptide binding]; other site 515619004937 NEAr Transport domain, a component of cell surface proteins; Region: NEAT; cl02760 515619004938 heme-binding site [chemical binding]; other site 515619004939 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 515619004940 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 515619004941 active site 515619004942 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_C; cd03413 515619004943 active site 515619004944 N-terminal domain interface [polypeptide binding]; other site 515619004945 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 515619004946 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 515619004947 Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_1; cd09154 515619004948 putative active site [active] 515619004949 catalytic site [active] 515619004950 Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_2; cd09160 515619004951 putative active site [active] 515619004952 catalytic site [active] 515619004953 Peptidase S8 family domain, uncharacterized subfamily 1; Region: Peptidases_S8_1; cd07487 515619004954 active site 515619004955 catalytic triad [active] 515619004956 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 515619004957 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 515619004958 RNase E interface [polypeptide binding]; other site 515619004959 trimer interface [polypeptide binding]; other site 515619004960 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 515619004961 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 515619004962 RNase E interface [polypeptide binding]; other site 515619004963 trimer interface [polypeptide binding]; other site 515619004964 active site 515619004965 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 515619004966 putative nucleic acid binding region [nucleotide binding]; other site 515619004967 G-X-X-G motif; other site 515619004968 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 515619004969 RNA binding site [nucleotide binding]; other site 515619004970 domain interface; other site 515619004971 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 515619004972 16S/18S rRNA binding site [nucleotide binding]; other site 515619004973 S13e-L30e interaction site [polypeptide binding]; other site 515619004974 25S rRNA binding site [nucleotide binding]; other site 515619004975 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619004976 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619004977 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619004978 NlpC/P60 family; Region: NLPC_P60; pfam00877 515619004979 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 515619004980 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 515619004981 active site 515619004982 Riboflavin kinase; Region: Flavokinase; pfam01687 515619004983 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 515619004984 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 515619004985 RNA binding site [nucleotide binding]; other site 515619004986 active site 515619004987 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 515619004988 DHH family; Region: DHH; pfam01368 515619004989 DHHA1 domain; Region: DHHA1; pfam02272 515619004990 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 515619004991 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 515619004992 translation initiation factor IF-2; Region: IF-2; TIGR00487 515619004993 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 515619004994 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 515619004995 G1 box; other site 515619004996 putative GEF interaction site [polypeptide binding]; other site 515619004997 GTP/Mg2+ binding site [chemical binding]; other site 515619004998 Switch I region; other site 515619004999 G2 box; other site 515619005000 G3 box; other site 515619005001 Switch II region; other site 515619005002 G4 box; other site 515619005003 G5 box; other site 515619005004 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 515619005005 Translation-initiation factor 2; Region: IF-2; pfam11987 515619005006 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 515619005007 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 515619005008 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 515619005009 putative RNA binding cleft [nucleotide binding]; other site 515619005010 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 515619005011 NusA N-terminal domain; Region: NusA_N; pfam08529 515619005012 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 515619005013 RNA binding site [nucleotide binding]; other site 515619005014 homodimer interface [polypeptide binding]; other site 515619005015 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 515619005016 G-X-X-G motif; other site 515619005017 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 515619005018 G-X-X-G motif; other site 515619005019 ribosome maturation protein RimP; Reviewed; Region: PRK00092 515619005020 Sm and related proteins; Region: Sm_like; cl00259 515619005021 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 515619005022 putative oligomer interface [polypeptide binding]; other site 515619005023 putative RNA binding site [nucleotide binding]; other site 515619005024 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 515619005025 UDP-glucose 4-epimerase; Region: PLN02240 515619005026 NAD binding site [chemical binding]; other site 515619005027 homodimer interface [polypeptide binding]; other site 515619005028 active site 515619005029 substrate binding site [chemical binding]; other site 515619005030 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619005031 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619005032 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005033 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005034 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 515619005035 23S rRNA binding site [nucleotide binding]; other site 515619005036 L21 binding site [polypeptide binding]; other site 515619005037 L13 binding site [polypeptide binding]; other site 515619005038 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 515619005039 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 515619005040 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 515619005041 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 515619005042 Chorismate mutase type II; Region: CM_2; pfam01817 515619005043 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 515619005044 Prephenate dehydratase; Region: PDT; pfam00800 515619005045 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 515619005046 putative L-Phe binding site [chemical binding]; other site 515619005047 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 515619005048 TPR repeat; Region: TPR_11; pfam13414 515619005049 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 515619005050 binding surface 515619005051 TPR motif; other site 515619005052 Tetratricopeptide repeat; Region: TPR_16; pfam13432 515619005053 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 515619005054 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 515619005055 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 515619005056 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 515619005057 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 515619005058 homodimer interface [polypeptide binding]; other site 515619005059 NADP binding site [chemical binding]; other site 515619005060 substrate binding site [chemical binding]; other site 515619005061 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 515619005062 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 515619005063 Potassium binding sites [ion binding]; other site 515619005064 Cesium cation binding sites [ion binding]; other site 515619005065 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619005066 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 515619005067 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 515619005068 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 515619005069 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 515619005070 glycogen synthase; Provisional; Region: glgA; PRK00654 515619005071 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 515619005072 ADP-binding pocket [chemical binding]; other site 515619005073 homodimer interface [polypeptide binding]; other site 515619005074 hypothetical protein; Validated; Region: PRK00110 515619005075 FOG: CBS domain [General function prediction only]; Region: COG0517 515619005076 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 515619005077 Transporter associated domain; Region: CorC_HlyC; pfam03471 515619005078 PemK-like protein; Region: PemK; pfam02452 515619005079 alanine racemase; Reviewed; Region: alr; PRK00053 515619005080 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 515619005081 active site 515619005082 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 515619005083 dimer interface [polypeptide binding]; other site 515619005084 substrate binding site [chemical binding]; other site 515619005085 catalytic residues [active] 515619005086 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 515619005087 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 515619005088 putative substrate binding site [chemical binding]; other site 515619005089 putative ATP binding site [chemical binding]; other site 515619005090 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 515619005091 CoA binding domain; Region: CoA_binding; pfam02629 515619005092 isocitrate dehydrogenase; Validated; Region: PRK08299 515619005093 Transcriptional regulators [Transcription]; Region: FadR; COG2186 515619005094 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619005095 DNA-binding site [nucleotide binding]; DNA binding site 515619005096 FCD domain; Region: FCD; pfam07729 515619005097 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 515619005098 Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_Re_CS; cd07947 515619005099 active site 515619005100 catalytic residues [active] 515619005101 metal binding site [ion binding]; metal-binding site 515619005102 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 515619005103 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 515619005104 elongation factor G; Reviewed; Region: PRK12740 515619005105 G1 box; other site 515619005106 putative GEF interaction site [polypeptide binding]; other site 515619005107 GTP/Mg2+ binding site [chemical binding]; other site 515619005108 Switch I region; other site 515619005109 G2 box; other site 515619005110 G3 box; other site 515619005111 Switch II region; other site 515619005112 G4 box; other site 515619005113 G5 box; other site 515619005114 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 515619005115 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 515619005116 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 515619005117 prephenate dehydrogenase; Validated; Region: PRK06545 515619005118 prephenate dehydrogenase; Validated; Region: PRK08507 515619005119 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 515619005120 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 515619005121 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 515619005122 hinge; other site 515619005123 active site 515619005124 PilZ domain; Region: PilZ; pfam07238 515619005125 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 515619005126 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 515619005127 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 515619005128 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 515619005129 putative tRNA-binding site [nucleotide binding]; other site 515619005130 B3/4 domain; Region: B3_4; pfam03483 515619005131 tRNA synthetase B5 domain; Region: B5; smart00874 515619005132 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 515619005133 dimer interface [polypeptide binding]; other site 515619005134 motif 1; other site 515619005135 motif 3; other site 515619005136 motif 2; other site 515619005137 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 515619005138 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 515619005139 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 515619005140 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 515619005141 dimer interface [polypeptide binding]; other site 515619005142 motif 1; other site 515619005143 active site 515619005144 motif 2; other site 515619005145 motif 3; other site 515619005146 EUBREC_1985; RF00230 T-box leader; T-box leader 515619005147 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 515619005148 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 515619005149 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 515619005150 Stage II sporulation protein; Region: SpoIID; pfam08486 515619005151 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 515619005152 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 515619005153 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619005154 active site 515619005155 phosphorylation site [posttranslational modification] 515619005156 intermolecular recognition site; other site 515619005157 dimerization interface [polypeptide binding]; other site 515619005158 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 515619005159 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 515619005160 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK15489 515619005161 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 515619005162 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 515619005163 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619005164 catalytic residue [active] 515619005165 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 515619005166 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 515619005167 substrate binding site [chemical binding]; other site 515619005168 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 515619005169 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 515619005170 substrate binding site [chemical binding]; other site 515619005171 ligand binding site [chemical binding]; other site 515619005172 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619005173 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619005174 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 515619005175 dimerization interface [polypeptide binding]; other site 515619005176 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 515619005177 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 515619005178 HIGH motif; other site 515619005179 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 515619005180 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619005181 KMSKS motif; other site 515619005182 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 515619005183 tRNA binding surface [nucleotide binding]; other site 515619005184 ketol-acid reductoisomerase; Provisional; Region: PRK05479 515619005185 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 515619005186 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 515619005187 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 515619005188 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 515619005189 putative valine binding site [chemical binding]; other site 515619005190 dimer interface [polypeptide binding]; other site 515619005191 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 515619005192 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 515619005193 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 515619005194 active site 515619005195 substrate-binding site [chemical binding]; other site 515619005196 metal-binding site [ion binding] 515619005197 ATP binding site [chemical binding]; other site 515619005198 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 515619005199 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 515619005200 Walker A/P-loop; other site 515619005201 ATP binding site [chemical binding]; other site 515619005202 Q-loop/lid; other site 515619005203 ABC transporter signature motif; other site 515619005204 Walker B; other site 515619005205 D-loop; other site 515619005206 H-loop/switch region; other site 515619005207 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 515619005208 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 515619005209 dimer interface [polypeptide binding]; other site 515619005210 conserved gate region; other site 515619005211 putative PBP binding loops; other site 515619005212 ABC-ATPase subunit interface; other site 515619005213 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 515619005214 membrane-bound complex binding site; other site 515619005215 hinge residues; other site 515619005216 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 515619005217 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 515619005218 substrate binding pocket [chemical binding]; other site 515619005219 Predicted permeases [General function prediction only]; Region: COG0679 515619005220 diacylglycerol glucosyltransferase; Provisional; Region: PRK13609 515619005221 Monogalactosyldiacylglycerol (MGDG) synthase; Region: MGDG_synth; pfam06925 515619005222 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 515619005223 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; pfam02660 515619005224 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 515619005225 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619005226 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619005227 metal binding site [ion binding]; metal-binding site 515619005228 active site 515619005229 I-site; other site 515619005230 Domain of unknown function (DUF4300); Region: DUF4300; pfam14133 515619005231 DDE domain; Region: DDE_Tnp_IS240; pfam13610 515619005232 Integrase core domain; Region: rve; pfam00665 515619005233 Integrase core domain; Region: rve_3; cl15866 515619005234 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619005235 LytTr DNA-binding domain; Region: LytTR; smart00850 515619005236 Protein of unknown function (DUF3021); Region: DUF3021; pfam11457 515619005237 Abi-like protein; Region: Abi_2; pfam07751 515619005238 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 515619005239 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 515619005240 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 515619005241 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 515619005242 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 515619005243 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 515619005244 MFS/sugar transport protein; Region: MFS_2; pfam13347 515619005245 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 515619005246 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619005247 Helix-turn-helix domain; Region: HTH_18; pfam12833 515619005248 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005249 Helix-turn-helix domain; Region: HTH_17; pfam12728 515619005250 Fic family protein [Function unknown]; Region: COG3177 515619005251 Fic/DOC family; Region: Fic; pfam02661 515619005252 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619005253 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 515619005254 dimerization interface [polypeptide binding]; other site 515619005255 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 515619005256 dimer interface [polypeptide binding]; other site 515619005257 phosphorylation site [posttranslational modification] 515619005258 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 515619005259 ATP binding site [chemical binding]; other site 515619005260 Mg2+ binding site [ion binding]; other site 515619005261 G-X-G motif; other site 515619005262 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619005263 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619005264 active site 515619005265 phosphorylation site [posttranslational modification] 515619005266 intermolecular recognition site; other site 515619005267 dimerization interface [polypeptide binding]; other site 515619005268 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 515619005269 DNA binding site [nucleotide binding] 515619005270 4Fe-4S binding domain; Region: Fer4_5; pfam12801 515619005271 4Fe-4S binding domain; Region: Fer4_5; pfam12801 515619005272 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 515619005273 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 515619005274 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 515619005275 catalytic residues [active] 515619005276 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619005277 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619005278 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005279 MFS/sugar transport protein; Region: MFS_2; pfam13347 515619005280 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 515619005281 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619005282 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619005283 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005284 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005285 Beta galactosidase small chain; Region: Bgal_small_N; pfam02929 515619005286 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 515619005287 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 515619005288 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 515619005289 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619005290 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 515619005291 dimerization interface [polypeptide binding]; other site 515619005292 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 515619005293 dimer interface [polypeptide binding]; other site 515619005294 phosphorylation site [posttranslational modification] 515619005295 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 515619005296 ATP binding site [chemical binding]; other site 515619005297 Mg2+ binding site [ion binding]; other site 515619005298 G-X-G motif; other site 515619005299 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619005300 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619005301 active site 515619005302 phosphorylation site [posttranslational modification] 515619005303 intermolecular recognition site; other site 515619005304 dimerization interface [polypeptide binding]; other site 515619005305 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 515619005306 DNA binding site [nucleotide binding] 515619005307 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 515619005308 putative active site [active] 515619005309 SdpI/YhfL protein family; Region: SdpI; pfam13630 515619005310 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 515619005311 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 515619005312 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 515619005313 dimer interface [polypeptide binding]; other site 515619005314 ssDNA binding site [nucleotide binding]; other site 515619005315 tetramer (dimer of dimers) interface [polypeptide binding]; other site 515619005316 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 515619005317 Active Sites [active] 515619005318 PemK-like protein; Region: PemK; pfam02452 515619005319 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 515619005320 ParB-like nuclease domain; Region: ParB; smart00470 515619005321 Domain of unknown function (DUF4313); Region: DUF4313; pfam14190 515619005322 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 515619005323 non-specific DNA binding site [nucleotide binding]; other site 515619005324 salt bridge; other site 515619005325 sequence-specific DNA binding site [nucleotide binding]; other site 515619005326 HNH endonuclease; Region: HNH_3; pfam13392 515619005327 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 515619005328 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 515619005329 active site 515619005330 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 515619005331 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 515619005332 Uncharacterized protein family UPF0027; Region: UPF0027; cl17455 515619005333 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons; Region: RT_like; cl02808 515619005334 NTP binding site [chemical binding]; other site 515619005335 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 515619005336 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 515619005337 Uncharacterized homolog of phage Mu protein gp47 [Function unknown]; Region: XkdT; COG3299 515619005338 Protein of unknown function (DUF2634); Region: DUF2634; pfam10934 515619005339 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 515619005340 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 515619005341 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 515619005342 Learning-associated protein; Region: Laps; pfam10169 515619005343 Phage XkdN-like protein; Region: XkdN; pfam08890 515619005344 Phage tail sheath protein; Region: Phage_sheath_1; pfam04984 515619005345 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 515619005346 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 515619005347 Protein of unknown function (DUF935); Region: DUF935; pfam06074 515619005348 Terminase-like family; Region: Terminase_6; pfam03237 515619005349 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 515619005350 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 515619005351 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 515619005352 ParB-like nuclease domain; Region: ParB; smart00470 515619005353 transcription termination factor Rho; Provisional; Region: PRK12608 515619005354 Protein of unknown function (DUF1351); Region: DUF1351; pfam07083 515619005355 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 515619005356 hypothetical protein; Validated; Region: PRK08116 515619005357 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 515619005358 Walker A motif; other site 515619005359 ATP binding site [chemical binding]; other site 515619005360 Walker B motif; other site 515619005361 N-terminal phage replisome organiser (Phage_rep_org_N); Region: Phage_rep_org_N; pfam09681 515619005362 PDDEXK-like domain of unknown function (DUF3799); Region: DUF3799; pfam12684 515619005363 RecT family; Region: RecT; cl04285 515619005364 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 515619005365 non-specific DNA binding site [nucleotide binding]; other site 515619005366 Helix-turn-helix domain; Region: HTH_31; pfam13560 515619005367 sequence-specific DNA binding site [nucleotide binding]; other site 515619005368 salt bridge; other site 515619005369 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619005370 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 515619005371 non-specific DNA binding site [nucleotide binding]; other site 515619005372 salt bridge; other site 515619005373 sequence-specific DNA binding site [nucleotide binding]; other site 515619005374 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 515619005375 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 515619005376 non-specific DNA binding site [nucleotide binding]; other site 515619005377 salt bridge; other site 515619005378 sequence-specific DNA binding site [nucleotide binding]; other site 515619005379 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619005380 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 515619005381 non-specific DNA binding site [nucleotide binding]; other site 515619005382 salt bridge; other site 515619005383 sequence-specific DNA binding site [nucleotide binding]; other site 515619005384 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 515619005385 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 515619005386 active site 515619005387 DNA binding site [nucleotide binding] 515619005388 Int/Topo IB signature motif; other site 515619005389 GGGtGRT protein; Region: GGGtGRT; pfam14057 515619005390 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 515619005391 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 515619005392 Putative glucose-1-phosphate thymidylyltransferase, C-terminal Left-handed parallel beta-Helix (LbH) domain: Proteins in this family show simlarity to glucose-1-phosphate adenylyltransferases in that they contain N-terminal catalytic domains that...; Region: LbH_G1P_TT_C_like; cd05636 515619005393 DNA topoisomerase III; Provisional; Region: PRK07726 515619005394 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 515619005395 active site 515619005396 putative interdomain interaction site [polypeptide binding]; other site 515619005397 putative metal-binding site [ion binding]; other site 515619005398 putative nucleotide binding site [chemical binding]; other site 515619005399 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 515619005400 domain I; other site 515619005401 DNA binding groove [nucleotide binding] 515619005402 phosphate binding site [ion binding]; other site 515619005403 domain II; other site 515619005404 domain III; other site 515619005405 nucleotide binding site [chemical binding]; other site 515619005406 catalytic site [active] 515619005407 domain IV; other site 515619005408 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 515619005409 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 515619005410 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 515619005411 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 515619005412 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 515619005413 Archaeal ATPase; Region: Arch_ATPase; pfam01637 515619005414 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 515619005415 Walker A motif; other site 515619005416 ATP binding site [chemical binding]; other site 515619005417 Walker B motif; other site 515619005418 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 515619005419 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619005420 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619005421 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK08664 515619005422 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 515619005423 argininosuccinate lyase; Provisional; Region: PRK00855 515619005424 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 515619005425 active sites [active] 515619005426 tetramer interface [polypeptide binding]; other site 515619005427 Uncharacterized BCR, COG1636; Region: DUF208; pfam02677 515619005428 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619005429 Zn2+ binding site [ion binding]; other site 515619005430 Mg2+ binding site [ion binding]; other site 515619005431 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 515619005432 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 515619005433 Walker A/P-loop; other site 515619005434 ATP binding site [chemical binding]; other site 515619005435 Q-loop/lid; other site 515619005436 ABC transporter signature motif; other site 515619005437 Walker B; other site 515619005438 D-loop; other site 515619005439 H-loop/switch region; other site 515619005440 Predicted transcriptional regulators [Transcription]; Region: COG1725 515619005441 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619005442 DNA-binding site [nucleotide binding]; DNA binding site 515619005443 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 515619005444 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 515619005445 non-specific DNA binding site [nucleotide binding]; other site 515619005446 salt bridge; other site 515619005447 sequence-specific DNA binding site [nucleotide binding]; other site 515619005448 Cupin domain; Region: Cupin_2; pfam07883 515619005449 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 515619005450 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619005451 Walker A/P-loop; other site 515619005452 ATP binding site [chemical binding]; other site 515619005453 Q-loop/lid; other site 515619005454 ABC transporter signature motif; other site 515619005455 Walker B; other site 515619005456 D-loop; other site 515619005457 H-loop/switch region; other site 515619005458 TOBE domain; Region: TOBE_2; pfam08402 515619005459 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 515619005460 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 515619005461 dimer interface [polypeptide binding]; other site 515619005462 conserved gate region; other site 515619005463 putative PBP binding loops; other site 515619005464 ABC-ATPase subunit interface; other site 515619005465 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 515619005466 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 515619005467 dimer interface [polypeptide binding]; other site 515619005468 conserved gate region; other site 515619005469 putative PBP binding loops; other site 515619005470 ABC-ATPase subunit interface; other site 515619005471 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 515619005472 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 515619005473 glycogen synthase; Provisional; Region: glgA; PRK00654 515619005474 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 515619005475 ADP-binding pocket [chemical binding]; other site 515619005476 homodimer interface [polypeptide binding]; other site 515619005477 Sporulation initiation factor Spo0A C terminal; Region: Spo0A_C; pfam08769 515619005478 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619005479 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619005480 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 515619005481 Walker A/P-loop; other site 515619005482 ATP binding site [chemical binding]; other site 515619005483 Q-loop/lid; other site 515619005484 ABC transporter signature motif; other site 515619005485 Walker B; other site 515619005486 D-loop; other site 515619005487 H-loop/switch region; other site 515619005488 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619005489 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 515619005490 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619005491 Walker A/P-loop; other site 515619005492 ATP binding site [chemical binding]; other site 515619005493 Q-loop/lid; other site 515619005494 ABC transporter signature motif; other site 515619005495 Walker B; other site 515619005496 D-loop; other site 515619005497 H-loop/switch region; other site 515619005498 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 515619005499 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 515619005500 type IV pilus assembly protein PilM; Region: pilM; TIGR01175 515619005501 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 515619005502 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 515619005503 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 515619005504 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 515619005505 putative transposase OrfB; Reviewed; Region: PHA02517 515619005506 HTH-like domain; Region: HTH_21; pfam13276 515619005507 Integrase core domain; Region: rve; pfam00665 515619005508 Integrase core domain; Region: rve_2; pfam13333 515619005509 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 515619005510 Helix-turn-helix domain; Region: HTH_28; pfam13518 515619005511 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 515619005512 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 515619005513 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 515619005514 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 515619005515 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 515619005516 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619005517 Walker A motif; other site 515619005518 ATP binding site [chemical binding]; other site 515619005519 Walker B motif; other site 515619005520 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 515619005521 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 515619005522 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 515619005523 Walker A motif; other site 515619005524 ATP binding site [chemical binding]; other site 515619005525 Walker B motif; other site 515619005526 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 515619005527 Na2 binding site [ion binding]; other site 515619005528 putative substrate binding site 1 [chemical binding]; other site 515619005529 Na binding site 1 [ion binding]; other site 515619005530 putative substrate binding site 2 [chemical binding]; other site 515619005531 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619005532 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619005533 putative active site [active] 515619005534 putative NTP binding site [chemical binding]; other site 515619005535 putative nucleic acid binding site [nucleotide binding]; other site 515619005536 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619005537 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 515619005538 FAD binding site [chemical binding]; other site 515619005539 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619005540 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 515619005541 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 515619005542 protein binding site [polypeptide binding]; other site 515619005543 SpoIVB peptidase S55; Region: Peptidase_S55; pfam05580 515619005544 potassium/proton antiporter; Reviewed; Region: PRK05326 515619005545 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 515619005546 TrkA-C domain; Region: TrkA_C; pfam02080 515619005547 TrkA-C domain; Region: TrkA_C; pfam02080 515619005548 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 515619005549 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 515619005550 Walker A/P-loop; other site 515619005551 ATP binding site [chemical binding]; other site 515619005552 Q-loop/lid; other site 515619005553 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 515619005554 ABC transporter signature motif; other site 515619005555 Walker B; other site 515619005556 D-loop; other site 515619005557 H-loop/switch region; other site 515619005558 arginine repressor; Provisional; Region: argR; PRK00441 515619005559 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 515619005560 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 515619005561 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 515619005562 ATP-NAD kinase; Region: NAD_kinase; pfam01513 515619005563 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 515619005564 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 515619005565 RNA binding surface [nucleotide binding]; other site 515619005566 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 515619005567 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 515619005568 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 515619005569 TPP-binding site; other site 515619005570 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 515619005571 PYR/PP interface [polypeptide binding]; other site 515619005572 dimer interface [polypeptide binding]; other site 515619005573 TPP binding site [chemical binding]; other site 515619005574 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 515619005575 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 515619005576 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 515619005577 substrate binding pocket [chemical binding]; other site 515619005578 chain length determination region; other site 515619005579 substrate-Mg2+ binding site; other site 515619005580 catalytic residues [active] 515619005581 aspartate-rich region 1; other site 515619005582 active site lid residues [active] 515619005583 aspartate-rich region 2; other site 515619005584 Exonuclease VII small subunit; Region: Exonuc_VII_S; pfam02609 515619005585 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 515619005586 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 515619005587 generic binding surface II; other site 515619005588 generic binding surface I; other site 515619005589 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 515619005590 putative RNA binding site [nucleotide binding]; other site 515619005591 Asp23 family; Region: Asp23; pfam03780 515619005592 glucose-1-phosphate adenylyltransferase, GlgD subunit; Region: glgD; TIGR02092 515619005593 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 515619005594 ligand binding site; other site 515619005595 oligomer interface; other site 515619005596 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 515619005597 dimer interface [polypeptide binding]; other site 515619005598 N-terminal domain interface [polypeptide binding]; other site 515619005599 sulfate 1 binding site; other site 515619005600 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 515619005601 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 515619005602 ligand binding site; other site 515619005603 oligomer interface; other site 515619005604 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 515619005605 dimer interface [polypeptide binding]; other site 515619005606 N-terminal domain interface [polypeptide binding]; other site 515619005607 sulfate 1 binding site; other site 515619005608 Homoserine O-succinyltransferase; Region: HTS; pfam04204 515619005609 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 515619005610 proposed active site lysine [active] 515619005611 conserved cys residue [active] 515619005612 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 515619005613 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; cl03295 515619005614 nucleotide binding pocket [chemical binding]; other site 515619005615 K-X-D-G motif; other site 515619005616 catalytic site [active] 515619005617 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 515619005618 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 515619005619 Dimer interface [polypeptide binding]; other site 515619005620 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 515619005621 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 515619005622 RNA binding surface [nucleotide binding]; other site 515619005623 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 515619005624 probable active site [active] 515619005625 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 515619005626 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 515619005627 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 515619005628 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 515619005629 dimer interface [polypeptide binding]; other site 515619005630 ADP-ribose binding site [chemical binding]; other site 515619005631 active site 515619005632 nudix motif; other site 515619005633 metal binding site [ion binding]; metal-binding site 515619005634 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 515619005635 NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria; Region: NADPH_BDH; cd08179 515619005636 putative active site [active] 515619005637 metal binding site [ion binding]; metal-binding site 515619005638 phosphodiesterase; Provisional; Region: PRK12704 515619005639 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619005640 Zn2+ binding site [ion binding]; other site 515619005641 Mg2+ binding site [ion binding]; other site 515619005642 recombination regulator RecX; Reviewed; Region: recX; PRK00117 515619005643 recombinase A; Provisional; Region: recA; PRK09354 515619005644 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 515619005645 hexamer interface [polypeptide binding]; other site 515619005646 Walker A motif; other site 515619005647 ATP binding site [chemical binding]; other site 515619005648 Walker B motif; other site 515619005649 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 515619005650 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 515619005651 G1 box; other site 515619005652 putative GEF interaction site [polypeptide binding]; other site 515619005653 GTP/Mg2+ binding site [chemical binding]; other site 515619005654 Switch I region; other site 515619005655 G2 box; other site 515619005656 G3 box; other site 515619005657 Switch II region; other site 515619005658 G4 box; other site 515619005659 G5 box; other site 515619005660 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 515619005661 SpoIIIAH-like protein; Region: SpoIIIAH; pfam12685 515619005662 stage III sporulation protein AG; Region: spore_III_AG; TIGR02830 515619005663 Stage III sporulation protein AF (Spore_III_AF); Region: Spore_III_AF; cl17562 515619005664 Stage III sporulation protein AE (spore_III_AE); Region: Spore_III_AE; cl09771 515619005665 Stage III sporulation protein AC/AD protein family; Region: SpoIIIAC; cl05961 515619005666 stage III sporulation protein AC; Region: spore_III_AC; TIGR02848 515619005667 stage III sporulation protein AA; Region: spore_III_AA; TIGR02858 515619005668 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 515619005669 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 515619005670 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619005671 active site 515619005672 HIGH motif; other site 515619005673 nucleotide binding site [chemical binding]; other site 515619005674 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 515619005675 KMSK motif region; other site 515619005676 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 515619005677 tRNA binding surface [nucleotide binding]; other site 515619005678 anticodon binding site; other site 515619005679 sporulation sigma factor SigG; Reviewed; Region: PRK08215 515619005680 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619005681 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 515619005682 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 515619005683 DNA binding residues [nucleotide binding] 515619005684 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 515619005685 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619005686 Zn2+ binding site [ion binding]; other site 515619005687 Mg2+ binding site [ion binding]; other site 515619005688 QueT transporter; Region: QueT; pfam06177 515619005689 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 515619005690 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 515619005691 Beta-Casp domain; Region: Beta-Casp; smart01027 515619005692 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 515619005693 sporulation sigma factor SigE; Reviewed; Region: PRK08301 515619005694 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619005695 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 515619005696 DNA binding residues [nucleotide binding] 515619005697 sigma-E processing peptidase SpoIIGA; Region: spore_II_GA; TIGR02854 515619005698 cell division protein FtsZ; Validated; Region: PRK09330 515619005699 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 515619005700 nucleotide binding site [chemical binding]; other site 515619005701 SulA interaction site; other site 515619005702 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 515619005703 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 515619005704 cell division protein FtsW; Region: ftsW; TIGR02614 515619005705 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK14106 515619005706 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 515619005707 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 515619005708 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 515619005709 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 515619005710 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 515619005711 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 515619005712 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 515619005713 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 515619005714 MraW methylase family; Region: Methyltransf_5; pfam01795 515619005715 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 515619005716 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 515619005717 MraZ protein; Region: MraZ; pfam02381 515619005718 MraZ protein; Region: MraZ; pfam02381 515619005719 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 515619005720 Domain of Unknown Function (DUF1540); Region: DUF1540; pfam07561 515619005721 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 515619005722 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 515619005723 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 515619005724 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 515619005725 active site 515619005726 dimer interface [polypeptide binding]; other site 515619005727 motif 1; other site 515619005728 motif 2; other site 515619005729 motif 3; other site 515619005730 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 515619005731 anticodon binding site; other site 515619005732 hypothetical protein; Provisional; Region: PRK05590 515619005733 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 515619005734 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 515619005735 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 515619005736 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 515619005737 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619005738 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 515619005739 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 515619005740 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 515619005741 Walker A/P-loop; other site 515619005742 ATP binding site [chemical binding]; other site 515619005743 Q-loop/lid; other site 515619005744 ABC transporter signature motif; other site 515619005745 Walker B; other site 515619005746 D-loop; other site 515619005747 H-loop/switch region; other site 515619005748 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 515619005749 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619005750 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 515619005751 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619005752 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 515619005753 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 515619005754 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 515619005755 ring oligomerisation interface [polypeptide binding]; other site 515619005756 ATP/Mg binding site [chemical binding]; other site 515619005757 stacking interactions; other site 515619005758 hinge regions; other site 515619005759 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 515619005760 oligomerisation interface [polypeptide binding]; other site 515619005761 mobile loop; other site 515619005762 roof hairpin; other site 515619005763 Predicted hydrolases of the HAD superfamily [General function prediction only]; Region: Cof; COG0561 515619005764 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 515619005765 active site 515619005766 motif I; other site 515619005767 motif II; other site 515619005768 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 515619005769 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 515619005770 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 515619005771 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 515619005772 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 515619005773 active site 515619005774 dimer interface [polypeptide binding]; other site 515619005775 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 515619005776 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 515619005777 active site 515619005778 FMN binding site [chemical binding]; other site 515619005779 substrate binding site [chemical binding]; other site 515619005780 3Fe-4S cluster binding site [ion binding]; other site 515619005781 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 515619005782 domain interface; other site 515619005783 CAAX protease self-immunity; Region: Abi; pfam02517 515619005784 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 515619005785 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 515619005786 motif II; other site 515619005787 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 515619005788 metal ion-dependent adhesion site (MIDAS); other site 515619005789 MoxR-like ATPases [General function prediction only]; Region: COG0714 515619005790 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 515619005791 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 515619005792 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 515619005793 CAP-like domain; other site 515619005794 active site 515619005795 primary dimer interface [polypeptide binding]; other site 515619005796 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 515619005797 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 515619005798 Mg2+ binding site [ion binding]; other site 515619005799 G-X-G motif; other site 515619005800 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 515619005801 anchoring element; other site 515619005802 dimer interface [polypeptide binding]; other site 515619005803 ATP binding site [chemical binding]; other site 515619005804 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 515619005805 active site 515619005806 putative metal-binding site [ion binding]; other site 515619005807 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 515619005808 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 515619005809 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 515619005810 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 515619005811 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 515619005812 Walker A/P-loop; other site 515619005813 ATP binding site [chemical binding]; other site 515619005814 Q-loop/lid; other site 515619005815 ABC transporter signature motif; other site 515619005816 Walker B; other site 515619005817 D-loop; other site 515619005818 H-loop/switch region; other site 515619005819 TOBE domain; Region: TOBE_2; pfam08402 515619005820 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 515619005821 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 515619005822 trimer interface [polypeptide binding]; other site 515619005823 active site 515619005824 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 515619005825 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 515619005826 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 515619005827 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; pfam02660 515619005828 GTP-binding protein Der; Reviewed; Region: PRK00093 515619005829 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 515619005830 G1 box; other site 515619005831 GTP/Mg2+ binding site [chemical binding]; other site 515619005832 Switch I region; other site 515619005833 G2 box; other site 515619005834 Switch II region; other site 515619005835 G3 box; other site 515619005836 G4 box; other site 515619005837 G5 box; other site 515619005838 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 515619005839 G1 box; other site 515619005840 GTP/Mg2+ binding site [chemical binding]; other site 515619005841 Switch I region; other site 515619005842 G2 box; other site 515619005843 G3 box; other site 515619005844 Switch II region; other site 515619005845 G4 box; other site 515619005846 G5 box; other site 515619005847 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619005848 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 515619005849 Walker A/P-loop; other site 515619005850 ATP binding site [chemical binding]; other site 515619005851 Q-loop/lid; other site 515619005852 ABC transporter signature motif; other site 515619005853 Walker B; other site 515619005854 D-loop; other site 515619005855 H-loop/switch region; other site 515619005856 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619005857 DNA-binding site [nucleotide binding]; DNA binding site 515619005858 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 515619005859 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 515619005860 hypothetical protein; Reviewed; Region: PRK12497 515619005861 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 515619005862 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 515619005863 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 515619005864 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 515619005865 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 515619005866 FeS/SAM binding site; other site 515619005867 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 515619005868 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 515619005869 DNA repair protein RadA; Provisional; Region: PRK11823 515619005870 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 515619005871 Walker A motif/ATP binding site; other site 515619005872 ATP binding site [chemical binding]; other site 515619005873 Walker B motif; other site 515619005874 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 515619005875 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 515619005876 Clp amino terminal domain; Region: Clp_N; pfam02861 515619005877 Clp amino terminal domain; Region: Clp_N; pfam02861 515619005878 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 515619005879 Walker A motif; other site 515619005880 ATP binding site [chemical binding]; other site 515619005881 Walker B motif; other site 515619005882 arginine finger; other site 515619005883 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 515619005884 Walker A motif; other site 515619005885 ATP binding site [chemical binding]; other site 515619005886 Walker B motif; other site 515619005887 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 515619005888 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 515619005889 Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]; Region: LytD; COG4193 515619005890 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 515619005891 Predicted secreted protein [Function unknown]; Region: COG4086 515619005892 Protein of unknown function (DUF1002); Region: DUF1002; pfam06207 515619005893 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 515619005894 putative dimer interface [polypeptide binding]; other site 515619005895 catalytic triad [active] 515619005896 Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]; Region: PflX; COG1313 515619005897 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 515619005898 FeS/SAM binding site; other site 515619005899 6-phosphofructokinase; Provisional; Region: PRK14072 515619005900 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 515619005901 active site 515619005902 ADP/pyrophosphate binding site [chemical binding]; other site 515619005903 dimerization interface [polypeptide binding]; other site 515619005904 allosteric effector site; other site 515619005905 fructose-1,6-bisphosphate binding site; other site 515619005906 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 515619005907 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 515619005908 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 515619005909 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 515619005910 Vacuolar ATP synthase subunit S1 (ATP6S1); Region: ATP-synt_S1; pfam05827 515619005911 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619005912 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619005913 active site 515619005914 phosphorylation site [posttranslational modification] 515619005915 intermolecular recognition site; other site 515619005916 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619005917 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619005918 putative active site [active] 515619005919 putative NTP binding site [chemical binding]; other site 515619005920 putative nucleic acid binding site [nucleotide binding]; other site 515619005921 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619005922 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619005923 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619005924 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 515619005925 Walker A/P-loop; other site 515619005926 ATP binding site [chemical binding]; other site 515619005927 Q-loop/lid; other site 515619005928 ABC transporter signature motif; other site 515619005929 Walker B; other site 515619005930 D-loop; other site 515619005931 H-loop/switch region; other site 515619005932 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619005933 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619005934 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619005935 Walker A/P-loop; other site 515619005936 ATP binding site [chemical binding]; other site 515619005937 Q-loop/lid; other site 515619005938 ABC transporter signature motif; other site 515619005939 Walker B; other site 515619005940 D-loop; other site 515619005941 H-loop/switch region; other site 515619005942 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 515619005943 Helix-turn-helix diphteria tox regulatory element; Region: HTH_DTXR; smart00529 515619005944 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 515619005945 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 515619005946 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 515619005947 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619005948 homodimer interface [polypeptide binding]; other site 515619005949 catalytic residue [active] 515619005950 Protein of unknown function (DUF3737); Region: DUF3737; pfam12541 515619005951 L-lactate dehydrogenase; Reviewed; Region: ldh; PRK00066 515619005952 A subgroup of L-lactate dehydrogenases; Region: LDH_2; cd05292 515619005953 NAD binding site [chemical binding]; other site 515619005954 dimer interface [polypeptide binding]; other site 515619005955 substrate binding site [chemical binding]; other site 515619005956 tetramer (dimer of dimers) interface [polypeptide binding]; other site 515619005957 2-isopropylmalate synthase; Validated; Region: PRK03739 515619005958 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 515619005959 active site 515619005960 catalytic residues [active] 515619005961 metal binding site [ion binding]; metal-binding site 515619005962 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 515619005963 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619005964 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619005965 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619005966 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 515619005967 Acetyltransferase (GNAT) domain; Region: Acetyltransf_9; pfam13527 515619005968 Sterol carrier protein domain; Region: SCP2_2; pfam13530 515619005969 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619005970 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619005971 metal binding site [ion binding]; metal-binding site 515619005972 active site 515619005973 I-site; other site 515619005974 Thiamine pyrophosphokinase; Region: TPK; cd07995 515619005975 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 515619005976 active site 515619005977 dimerization interface [polypeptide binding]; other site 515619005978 thiamine binding site [chemical binding]; other site 515619005979 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 515619005980 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 515619005981 substrate binding site [chemical binding]; other site 515619005982 hexamer interface [polypeptide binding]; other site 515619005983 metal binding site [ion binding]; metal-binding site 515619005984 GTPase RsgA; Reviewed; Region: PRK00098 515619005985 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 515619005986 RNA binding site [nucleotide binding]; other site 515619005987 homodimer interface [polypeptide binding]; other site 515619005988 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 515619005989 GTPase/Zn-binding domain interface [polypeptide binding]; other site 515619005990 GTP/Mg2+ binding site [chemical binding]; other site 515619005991 G4 box; other site 515619005992 G5 box; other site 515619005993 G1 box; other site 515619005994 Switch I region; other site 515619005995 G2 box; other site 515619005996 G3 box; other site 515619005997 Switch II region; other site 515619005998 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 515619005999 Catalytic domain of Protein Kinases; Region: PKc; cd00180 515619006000 active site 515619006001 ATP binding site [chemical binding]; other site 515619006002 substrate binding site [chemical binding]; other site 515619006003 activation loop (A-loop); other site 515619006004 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 515619006005 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 515619006006 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 515619006007 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 515619006008 Protein phosphatase 2C; Region: PP2C; pfam00481 515619006009 active site 515619006010 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 515619006011 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 515619006012 FeS/SAM binding site; other site 515619006013 16S rRNA methyltransferase B; Provisional; Region: PRK14902 515619006014 NusB family; Region: NusB; pfam01029 515619006015 putative RNA binding site [nucleotide binding]; other site 515619006016 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 515619006017 S-adenosylmethionine binding site [chemical binding]; other site 515619006018 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 515619006019 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 515619006020 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 515619006021 putative active site [active] 515619006022 substrate binding site [chemical binding]; other site 515619006023 putative cosubstrate binding site; other site 515619006024 catalytic site [active] 515619006025 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 515619006026 substrate binding site [chemical binding]; other site 515619006027 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 515619006028 active site 515619006029 catalytic residues [active] 515619006030 metal binding site [ion binding]; metal-binding site 515619006031 primosome assembly protein PriA; Validated; Region: PRK05580 515619006032 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 515619006033 ATP binding site [chemical binding]; other site 515619006034 putative Mg++ binding site [ion binding]; other site 515619006035 helicase superfamily c-terminal domain; Region: HELICc; smart00490 515619006036 ATP-binding site [chemical binding]; other site 515619006037 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 515619006038 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 515619006039 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 515619006040 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 515619006041 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 515619006042 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 515619006043 Bacterial PH domain; Region: DUF304; pfam03703 515619006044 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 515619006045 HSP70 interaction site [polypeptide binding]; other site 515619006046 Mitochondria Fission Protein Fis1, cytosolic domain; Region: Fis1; cd12212 515619006047 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 515619006048 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 515619006049 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 515619006050 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 515619006051 active site 515619006052 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 515619006053 Family of unknown function (DUF633); Region: DUF633; pfam04816 515619006054 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 515619006055 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 515619006056 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619006057 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 515619006058 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 515619006059 DNA binding residues [nucleotide binding] 515619006060 DNA primase; Validated; Region: dnaG; PRK05667 515619006061 CHC2 zinc finger; Region: zf-CHC2; pfam01807 515619006062 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 515619006063 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 515619006064 active site 515619006065 metal binding site [ion binding]; metal-binding site 515619006066 interdomain interaction site; other site 515619006067 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 515619006068 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 515619006069 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619006070 Zn2+ binding site [ion binding]; other site 515619006071 Mg2+ binding site [ion binding]; other site 515619006072 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 515619006073 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 515619006074 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 515619006075 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619006076 catalytic residue [active] 515619006077 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 515619006078 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619006079 Coenzyme A binding pocket [chemical binding]; other site 515619006080 Abi-like protein; Region: Abi_2; pfam07751 515619006081 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 515619006082 non-specific DNA binding site [nucleotide binding]; other site 515619006083 salt bridge; other site 515619006084 sequence-specific DNA binding site [nucleotide binding]; other site 515619006085 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 515619006086 putative metal binding site [ion binding]; other site 515619006087 Predicted transcriptional regulators [Transcription]; Region: COG1695 515619006088 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 515619006089 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619006090 Walker A/P-loop; other site 515619006091 ATP binding site [chemical binding]; other site 515619006092 Q-loop/lid; other site 515619006093 ABC transporter signature motif; other site 515619006094 Walker B; other site 515619006095 D-loop; other site 515619006096 H-loop/switch region; other site 515619006097 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 515619006098 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619006099 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619006100 metal binding site [ion binding]; metal-binding site 515619006101 active site 515619006102 I-site; other site 515619006103 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619006104 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 515619006105 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 515619006106 amidase catalytic site [active] 515619006107 Zn binding residues [ion binding]; other site 515619006108 substrate binding site [chemical binding]; other site 515619006109 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 515619006110 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 515619006111 homodimer interface [polypeptide binding]; other site 515619006112 substrate-cofactor binding pocket; other site 515619006113 catalytic residue [active] 515619006114 Predicted membrane protein [Function unknown]; Region: COG1511 515619006115 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 515619006116 FlxA-like protein; Region: FlxA; pfam14282 515619006117 YhgE/Pip C-terminal domain; Region: pip_yhgE_Cterm; TIGR03062 515619006118 Predicted membrane protein [Function unknown]; Region: COG1511 515619006119 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 515619006120 Plant nuclear matrix protein 1 (NMP1); Region: Plant_NMP1; pfam06694 515619006121 YhgE/Pip C-terminal domain; Region: pip_yhgE_Cterm; TIGR03062 515619006122 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 515619006123 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 515619006124 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 515619006125 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619006126 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 515619006127 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 515619006128 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 515619006129 active site 515619006130 metal binding site [ion binding]; metal-binding site 515619006131 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 515619006132 DNA-binding site [nucleotide binding]; DNA binding site 515619006133 RNA-binding motif; other site 515619006134 Bacterial Ig-like domain (group 3); Region: Big_3; pfam07523 515619006135 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 515619006136 Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; Region: CE4_SmPgdA_like; cd10944 515619006137 NodB motif; other site 515619006138 active site 515619006139 catalytic site [active] 515619006140 Zn binding site [ion binding]; other site 515619006141 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 515619006142 4Fe-4S binding domain; Region: Fer4; pfam00037 515619006143 4Fe-4S binding domain; Region: Fer4; pfam00037 515619006144 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 515619006145 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 515619006146 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 515619006147 FtsX-like permease family; Region: FtsX; pfam02687 515619006148 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 515619006149 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 515619006150 HlyD family secretion protein; Region: HlyD_3; pfam13437 515619006151 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619006152 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619006153 Walker A/P-loop; other site 515619006154 ATP binding site [chemical binding]; other site 515619006155 Q-loop/lid; other site 515619006156 ABC transporter signature motif; other site 515619006157 Walker B; other site 515619006158 D-loop; other site 515619006159 H-loop/switch region; other site 515619006160 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 515619006161 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 515619006162 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 515619006163 Peptidase S8 family domain in CspA-like proteins; Region: Peptidases_S8_CspA-like; cd07478 515619006164 active site 515619006165 catalytic triad [active] 515619006166 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 515619006167 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 515619006168 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 515619006169 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 515619006170 Na binding site [ion binding]; other site 515619006171 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 515619006172 ATP cone domain; Region: ATP-cone; pfam03477 515619006173 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 515619006174 MarR family; Region: MarR_2; pfam12802 515619006175 MarR family; Region: MarR_2; cl17246 515619006176 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619006177 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619006178 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619006179 Walker A/P-loop; other site 515619006180 ATP binding site [chemical binding]; other site 515619006181 Q-loop/lid; other site 515619006182 ABC transporter signature motif; other site 515619006183 Walker B; other site 515619006184 D-loop; other site 515619006185 H-loop/switch region; other site 515619006186 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619006187 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619006188 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 515619006189 Walker A/P-loop; other site 515619006190 ATP binding site [chemical binding]; other site 515619006191 Q-loop/lid; other site 515619006192 ABC transporter signature motif; other site 515619006193 Walker B; other site 515619006194 D-loop; other site 515619006195 H-loop/switch region; other site 515619006196 NAD synthetase; Reviewed; Region: nadE; PRK02628 515619006197 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 515619006198 multimer interface [polypeptide binding]; other site 515619006199 active site 515619006200 catalytic triad [active] 515619006201 protein interface 1 [polypeptide binding]; other site 515619006202 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 515619006203 homodimer interface [polypeptide binding]; other site 515619006204 NAD binding pocket [chemical binding]; other site 515619006205 ATP binding pocket [chemical binding]; other site 515619006206 Mg binding site [ion binding]; other site 515619006207 active-site loop [active] 515619006208 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 515619006209 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 515619006210 active site 515619006211 Isochorismatase family; Region: Isochorismatase; pfam00857 515619006212 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 515619006213 catalytic triad [active] 515619006214 conserved cis-peptide bond; other site 515619006215 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 515619006216 nudix motif; other site 515619006217 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619006218 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 515619006219 active site 515619006220 HIGH motif; other site 515619006221 nucleotide binding site [chemical binding]; other site 515619006222 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 515619006223 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 515619006224 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 515619006225 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 515619006226 ATP binding site [chemical binding]; other site 515619006227 putative Mg++ binding site [ion binding]; other site 515619006228 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 515619006229 nucleotide binding region [chemical binding]; other site 515619006230 ATP-binding site [chemical binding]; other site 515619006231 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619006232 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619006233 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619006234 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619006235 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619006236 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 515619006237 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 515619006238 active site 515619006239 DNA binding site [nucleotide binding] 515619006240 Int/Topo IB signature motif; other site 515619006241 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 515619006242 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 515619006243 active site 515619006244 NTP binding site [chemical binding]; other site 515619006245 metal binding triad [ion binding]; metal-binding site 515619006246 antibiotic binding site [chemical binding]; other site 515619006247 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 515619006248 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619006249 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 515619006250 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 515619006251 HsdM N-terminal domain; Region: HsdM_N; pfam12161 515619006252 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 515619006253 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 515619006254 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 515619006255 Nucleolar RNA-binding protein, Nop10p family; Region: Nop10p; cl00977 515619006256 acyltransferase, WS/DGAT/MGAT; Region: acyl_WS_DGAT; TIGR02946 515619006257 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 515619006258 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 515619006259 HflX GTPase family; Region: HflX; cd01878 515619006260 G1 box; other site 515619006261 GTP/Mg2+ binding site [chemical binding]; other site 515619006262 Switch I region; other site 515619006263 G2 box; other site 515619006264 G3 box; other site 515619006265 Switch II region; other site 515619006266 G4 box; other site 515619006267 G5 box; other site 515619006268 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 515619006269 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 515619006270 binding surface 515619006271 TPR motif; other site 515619006272 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 515619006273 binding surface 515619006274 TPR motif; other site 515619006275 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 515619006276 binding surface 515619006277 TPR motif; other site 515619006278 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 515619006279 binding surface 515619006280 TPR motif; other site 515619006281 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 515619006282 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 515619006283 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 515619006284 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619006285 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619006286 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619006287 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 515619006288 active site 515619006289 SpoVA protein; Region: SpoVA; pfam03862 515619006290 stage V sporulation protein AD; Validated; Region: PRK08304 515619006291 stage V sporulation protein AD; Provisional; Region: PRK12404 515619006292 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619006293 active site 515619006294 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 515619006295 homodimer interaction site [polypeptide binding]; other site 515619006296 cofactor binding site; other site 515619006297 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 515619006298 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 515619006299 active site 515619006300 NAD binding site [chemical binding]; other site 515619006301 metal binding site [ion binding]; metal-binding site 515619006302 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619006303 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619006304 metal binding site [ion binding]; metal-binding site 515619006305 active site 515619006306 I-site; other site 515619006307 Uncharacterized protein family (UPF0160); Region: UPF0160; cl01749 515619006308 Predicted transcriptional regulators [Transcription]; Region: COG1725 515619006309 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619006310 DNA-binding site [nucleotide binding]; DNA binding site 515619006311 Predicted membrane protein [General function prediction only]; Region: COG4194 515619006312 Protein of unknown function (DUF419); Region: DUF419; pfam04237 515619006313 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 515619006314 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 515619006315 active site 515619006316 DNA binding site [nucleotide binding] 515619006317 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619006318 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619006319 Walker A/P-loop; other site 515619006320 ATP binding site [chemical binding]; other site 515619006321 Q-loop/lid; other site 515619006322 ABC transporter signature motif; other site 515619006323 Walker B; other site 515619006324 D-loop; other site 515619006325 H-loop/switch region; other site 515619006326 Accessory gene regulator B; Region: AgrB; pfam04647 515619006327 cyclic lactone autoinducer peptide; Region: quorum_AgrD; TIGR04223 515619006328 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619006329 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 515619006330 sequence-specific DNA binding site [nucleotide binding]; other site 515619006331 salt bridge; other site 515619006332 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619006333 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619006334 active site 515619006335 phosphorylation site [posttranslational modification] 515619006336 intermolecular recognition site; other site 515619006337 dimerization interface [polypeptide binding]; other site 515619006338 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619006339 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 515619006340 ATP binding site [chemical binding]; other site 515619006341 Mg2+ binding site [ion binding]; other site 515619006342 G-X-G motif; other site 515619006343 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 515619006344 active site 515619006345 NTP binding site [chemical binding]; other site 515619006346 metal binding triad [ion binding]; metal-binding site 515619006347 antibiotic binding site [chemical binding]; other site 515619006348 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619006349 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619006350 Beta-galactosidase [Carbohydrate transport and metabolism]; Region: LacA; COG1874 515619006351 Beta-galactosidase; Region: Glyco_hydro_42; pfam02449 515619006352 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 515619006353 Beta-galactosidase C-terminal domain; Region: Glyco_hydro_42C; pfam08533 515619006354 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 515619006355 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; pfam06964 515619006356 Predicted transcriptional regulator [Transcription]; Region: COG4189 515619006357 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 515619006358 dimerization interface [polypeptide binding]; other site 515619006359 putative DNA binding site [nucleotide binding]; other site 515619006360 putative Zn2+ binding site [ion binding]; other site 515619006361 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619006362 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619006363 putative active site [active] 515619006364 putative NTP binding site [chemical binding]; other site 515619006365 putative nucleic acid binding site [nucleotide binding]; other site 515619006366 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619006367 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 515619006368 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 515619006369 PYR/PP interface [polypeptide binding]; other site 515619006370 dimer interface [polypeptide binding]; other site 515619006371 TPP binding site [chemical binding]; other site 515619006372 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 515619006373 transketolase; Reviewed; Region: PRK05899 515619006374 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 515619006375 TPP-binding site [chemical binding]; other site 515619006376 dimer interface [polypeptide binding]; other site 515619006377 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 515619006378 active site 515619006379 intersubunit interactions; other site 515619006380 catalytic residue [active] 515619006381 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 515619006382 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 515619006383 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 515619006384 Tetratricopeptide repeat; Region: TPR_12; pfam13424 515619006385 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 515619006386 TPR motif; other site 515619006387 binding surface 515619006388 Tetratricopeptide repeat; Region: TPR_12; pfam13424 515619006389 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619006390 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619006391 metal binding site [ion binding]; metal-binding site 515619006392 active site 515619006393 I-site; other site 515619006394 AIR carboxylase; Region: AIRC; cl00310 515619006395 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 515619006396 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619006397 active site 515619006398 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 515619006399 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 515619006400 CysD dimerization site [polypeptide binding]; other site 515619006401 G1 box; other site 515619006402 putative GEF interaction site [polypeptide binding]; other site 515619006403 GTP/Mg2+ binding site [chemical binding]; other site 515619006404 Switch I region; other site 515619006405 G2 box; other site 515619006406 G3 box; other site 515619006407 Switch II region; other site 515619006408 G4 box; other site 515619006409 G5 box; other site 515619006410 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 515619006411 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 515619006412 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 515619006413 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 515619006414 Active Sites [active] 515619006415 Ferredoxin [Energy production and conversion]; Region: COG1146 515619006416 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 515619006417 adenylylsulfate reductase subunit alpha; Validated; Region: PRK06854 515619006418 L-aspartate oxidase; Provisional; Region: PRK06175 515619006419 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 515619006420 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 515619006421 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 515619006422 Walker A/P-loop; other site 515619006423 ATP binding site [chemical binding]; other site 515619006424 Q-loop/lid; other site 515619006425 ABC transporter signature motif; other site 515619006426 Walker B; other site 515619006427 D-loop; other site 515619006428 H-loop/switch region; other site 515619006429 TOBE domain; Region: TOBE_2; pfam08402 515619006430 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 515619006431 dimer interface [polypeptide binding]; other site 515619006432 conserved gate region; other site 515619006433 ABC-ATPase subunit interface; other site 515619006434 sulfate transport protein; Provisional; Region: cysT; CHL00187 515619006435 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 515619006436 dimer interface [polypeptide binding]; other site 515619006437 conserved gate region; other site 515619006438 putative PBP binding loops; other site 515619006439 ABC-ATPase subunit interface; other site 515619006440 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 515619006441 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 515619006442 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 515619006443 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 515619006444 dimer interface [polypeptide binding]; other site 515619006445 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619006446 catalytic residue [active] 515619006447 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 515619006448 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 515619006449 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 515619006450 heterodimer interface [polypeptide binding]; other site 515619006451 active site 515619006452 FMN binding site [chemical binding]; other site 515619006453 homodimer interface [polypeptide binding]; other site 515619006454 substrate binding site [chemical binding]; other site 515619006455 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 515619006456 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 515619006457 FAD binding pocket [chemical binding]; other site 515619006458 FAD binding motif [chemical binding]; other site 515619006459 phosphate binding motif [ion binding]; other site 515619006460 beta-alpha-beta structure motif; other site 515619006461 NAD binding pocket [chemical binding]; other site 515619006462 Iron coordination center [ion binding]; other site 515619006463 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 515619006464 active site 515619006465 dimer interface [polypeptide binding]; other site 515619006466 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619006467 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619006468 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 515619006469 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-C; cd09721 515619006470 Domain of unknown function DUF83; Region: Cas_Cas4; pfam01930 515619006471 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 515619006472 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cd09757 515619006473 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 515619006474 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-C; cd09752 515619006475 Protein of unknown function (DUF3990); Region: DUF3990; pfam13151 515619006476 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 515619006477 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 515619006478 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 515619006479 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 515619006480 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 515619006481 active site 515619006482 catalytic tetrad [active] 515619006483 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 515619006484 tetramerization interface [polypeptide binding]; other site 515619006485 active site 515619006486 pantoate--beta-alanine ligase; Region: panC; TIGR00018 515619006487 Pantoate-beta-alanine ligase; Region: PanC; cd00560 515619006488 active site 515619006489 ATP-binding site [chemical binding]; other site 515619006490 pantoate-binding site; other site 515619006491 HXXH motif; other site 515619006492 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 515619006493 oligomerization interface [polypeptide binding]; other site 515619006494 active site 515619006495 metal binding site [ion binding]; metal-binding site 515619006496 Uncharacterized conserved protein [Function unknown]; Region: COG5495 515619006497 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 515619006498 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 515619006499 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 515619006500 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619006501 Zn2+ binding site [ion binding]; other site 515619006502 Mg2+ binding site [ion binding]; other site 515619006503 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619006504 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619006505 metal binding site [ion binding]; metal-binding site 515619006506 active site 515619006507 I-site; other site 515619006508 accessory Sec system glycosyltransferase GtfB; Region: TIGR02919 515619006509 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 515619006510 accessory Sec system glycosylation protein GtfA; Region: TIGR02918 515619006511 This family is most closely related to the GT1 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding. In...; Region: GT1_gtfA_like; cd04949 515619006512 preprotein translocase subunit SecA; Reviewed; Region: PRK09200 515619006513 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 515619006514 ATP binding site [chemical binding]; other site 515619006515 putative Mg++ binding site [ion binding]; other site 515619006516 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 515619006517 accessory Sec system protein Asp3; Region: acc_sec_asp3; TIGR03711 515619006518 accessory Sec system protein Asp2; Region: acc_sec_asp2; TIGR03712 515619006519 accessory Sec system protein Asp1; Region: acc_sec_asp1; TIGR03713 515619006520 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 515619006521 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK12417 515619006522 SecY translocase; Region: SecY; pfam00344 515619006523 beta-1,6-galactofuranosyltransferase; Provisional; Region: PRK09814 515619006524 beta-1,6-galactofuranosyltransferase; Provisional; Region: PRK09814 515619006525 accessory Sec system glycosylation protein GtfA; Region: TIGR02918 515619006526 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 515619006527 accessory Sec system glycosyltransferase GtfB; Region: TIGR02919 515619006528 putative glycosyl transferase; Provisional; Region: PRK10073 515619006529 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 515619006530 active site 515619006531 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 515619006532 Ligand binding site; other site 515619006533 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 515619006534 metal-binding site 515619006535 Bacterial transcriptional activator domain; Region: BTAD; smart01043 515619006536 Response regulator receiver domain; Region: Response_reg; pfam00072 515619006537 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619006538 active site 515619006539 phosphorylation site [posttranslational modification] 515619006540 intermolecular recognition site; other site 515619006541 dimerization interface [polypeptide binding]; other site 515619006542 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619006543 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 515619006544 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619006545 Mg2+ binding site [ion binding]; other site 515619006546 G-X-G motif; other site 515619006547 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619006548 Thiamine-precursor transporter protein (ThiW); Region: ThiW; pfam09512 515619006549 thiamine biosynthesis protein ThiC; Provisional; Region: PRK13352 515619006550 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 515619006551 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 515619006552 dimer interface [polypeptide binding]; other site 515619006553 substrate binding site [chemical binding]; other site 515619006554 ATP binding site [chemical binding]; other site 515619006555 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 515619006556 thiamine phosphate binding site [chemical binding]; other site 515619006557 active site 515619006558 pyrophosphate binding site [ion binding]; other site 515619006559 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 515619006560 substrate binding site [chemical binding]; other site 515619006561 multimerization interface [polypeptide binding]; other site 515619006562 ATP binding site [chemical binding]; other site 515619006563 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619006564 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619006565 putative active site [active] 515619006566 putative NTP binding site [chemical binding]; other site 515619006567 putative nucleic acid binding site [nucleotide binding]; other site 515619006568 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619006569 dihydrodipicolinate reductase; Provisional; Region: PRK00048 515619006570 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 515619006571 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 515619006572 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 515619006573 dihydrodipicolinate synthase; Region: dapA; TIGR00674 515619006574 dimer interface [polypeptide binding]; other site 515619006575 active site 515619006576 catalytic residue [active] 515619006577 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619006578 Walker A motif; other site 515619006579 ATP binding site [chemical binding]; other site 515619006580 Walker B motif; other site 515619006581 single-stranded DNA-binding protein; Provisional; Region: PRK05813 515619006582 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 515619006583 dimer interface [polypeptide binding]; other site 515619006584 ssDNA binding site [nucleotide binding]; other site 515619006585 tetramer (dimer of dimers) interface [polypeptide binding]; other site 515619006586 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 515619006587 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 515619006588 G1 box; other site 515619006589 putative GEF interaction site [polypeptide binding]; other site 515619006590 GTP/Mg2+ binding site [chemical binding]; other site 515619006591 Switch I region; other site 515619006592 G2 box; other site 515619006593 G3 box; other site 515619006594 Switch II region; other site 515619006595 G4 box; other site 515619006596 G5 box; other site 515619006597 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 515619006598 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 515619006599 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619006600 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619006601 putative active site [active] 515619006602 putative NTP binding site [chemical binding]; other site 515619006603 putative nucleic acid binding site [nucleotide binding]; other site 515619006604 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619006605 L,L-diaminopimelate aminotransferase; Validated; Region: PRK07590 515619006606 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 515619006607 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619006608 homodimer interface [polypeptide binding]; other site 515619006609 catalytic residue [active] 515619006610 ANTAR domain; Region: ANTAR; pfam03861 515619006611 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 515619006612 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 515619006613 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 515619006614 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an...; Region: HisA_HisF; cd04723 515619006615 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 515619006616 active site 515619006617 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 515619006618 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 515619006619 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 515619006620 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 515619006621 active site 515619006622 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 515619006623 Domain of unknown function DUF21; Region: DUF21; pfam01595 515619006624 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 515619006625 Transporter associated domain; Region: CorC_HlyC; pfam03471 515619006626 Type II/IV secretion system protein; Region: T2SE; pfam00437 515619006627 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619006628 Walker A motif; other site 515619006629 ATP binding site [chemical binding]; other site 515619006630 Walker B motif; other site 515619006631 Alanine-glyoxylate amino-transferase; Region: Aminotran_MocR; pfam12897 515619006632 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 515619006633 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619006634 catalytic residue [active] 515619006635 recombination factor protein RarA; Reviewed; Region: PRK13342 515619006636 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 515619006637 Walker A motif; other site 515619006638 ATP binding site [chemical binding]; other site 515619006639 Walker B motif; other site 515619006640 arginine finger; other site 515619006641 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 515619006642 Escherichia coli xylulokinase-like D-xylulose kinases; a subgroup of the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 515619006643 N- and C-terminal domain interface [polypeptide binding]; other site 515619006644 D-xylulose kinase; Region: XylB; TIGR01312 515619006645 active site 515619006646 MgATP binding site [chemical binding]; other site 515619006647 catalytic site [active] 515619006648 metal binding site [ion binding]; metal-binding site 515619006649 xylulose binding site [chemical binding]; other site 515619006650 homodimer interface [polypeptide binding]; other site 515619006651 L-fucose isomerase and related proteins [Carbohydrate transport and metabolism]; Region: FucI; COG2407 515619006652 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 515619006653 hexamer (dimer of trimers) interface [polypeptide binding]; other site 515619006654 substrate binding site [chemical binding]; other site 515619006655 trimer interface [polypeptide binding]; other site 515619006656 Mn binding site [ion binding]; other site 515619006657 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619006658 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619006659 DNA binding site [nucleotide binding] 515619006660 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 515619006661 ligand binding site [chemical binding]; other site 515619006662 dimerization interface [polypeptide binding]; other site 515619006663 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 515619006664 Clp amino terminal domain; Region: Clp_N; pfam02861 515619006665 Clp amino terminal domain; Region: Clp_N; pfam02861 515619006666 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 515619006667 Walker A motif; other site 515619006668 ATP binding site [chemical binding]; other site 515619006669 Walker B motif; other site 515619006670 arginine finger; other site 515619006671 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 515619006672 Walker A motif; other site 515619006673 ATP binding site [chemical binding]; other site 515619006674 Walker B motif; other site 515619006675 arginine finger; other site 515619006676 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 515619006677 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 515619006678 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 515619006679 synthetase active site [active] 515619006680 NTP binding site [chemical binding]; other site 515619006681 metal binding site [ion binding]; metal-binding site 515619006682 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 515619006683 active site 515619006684 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 515619006685 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 515619006686 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 515619006687 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 515619006688 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619006689 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 515619006690 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 515619006691 transmembrane helices; other site 515619006692 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 515619006693 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 515619006694 motif II; other site 515619006695 RNA polymerase sigma-F factor; Region: spore_sigF; TIGR02885 515619006696 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619006697 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 515619006698 DNA binding residues [nucleotide binding] 515619006699 Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]; Region: RsbW; COG2172 515619006700 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 515619006701 ATP binding site [chemical binding]; other site 515619006702 Mg2+ binding site [ion binding]; other site 515619006703 G-X-G motif; other site 515619006704 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 515619006705 anti sigma factor interaction site; other site 515619006706 regulatory phosphorylation site [posttranslational modification]; other site 515619006707 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 515619006708 binding surface 515619006709 TPR motif; other site 515619006710 Protein of unknown function (DUF342); Region: DUF342; pfam03961 515619006711 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 515619006712 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_2; cd09001 515619006713 active site 515619006714 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 515619006715 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619006716 active site 515619006717 HIGH motif; other site 515619006718 nucleotide binding site [chemical binding]; other site 515619006719 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 515619006720 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 515619006721 active site 515619006722 KMSKS motif; other site 515619006723 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 515619006724 tRNA binding surface [nucleotide binding]; other site 515619006725 anticodon binding site; other site 515619006726 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 515619006727 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 515619006728 RelB antitoxin; Region: RelB; cl01171 515619006729 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 515619006730 putative DNA binding site [nucleotide binding]; other site 515619006731 putative Zn2+ binding site [ion binding]; other site 515619006732 ROK family protein (putative glucokinase); Region: ROK_glcA_fam; TIGR00744 515619006733 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 515619006734 Uncharacterized protein with conserved CXXC pairs [Function unknown]; Region: COG3862 515619006735 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 515619006736 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 515619006737 Predicted dehydrogenase [General function prediction only]; Region: COG0579 515619006738 hydroxyglutarate oxidase; Provisional; Region: PRK11728 515619006739 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 515619006740 glycerol kinase; Provisional; Region: glpK; PRK00047 515619006741 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 515619006742 N- and C-terminal domain interface [polypeptide binding]; other site 515619006743 active site 515619006744 MgATP binding site [chemical binding]; other site 515619006745 catalytic site [active] 515619006746 metal binding site [ion binding]; metal-binding site 515619006747 glycerol binding site [chemical binding]; other site 515619006748 homotetramer interface [polypeptide binding]; other site 515619006749 homodimer interface [polypeptide binding]; other site 515619006750 FBP binding site [chemical binding]; other site 515619006751 protein IIAGlc interface [polypeptide binding]; other site 515619006752 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 515619006753 hexamer (dimer of trimers) interface [polypeptide binding]; other site 515619006754 trimer interface [polypeptide binding]; other site 515619006755 substrate binding site [chemical binding]; other site 515619006756 Mn binding site [ion binding]; other site 515619006757 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 515619006758 alpha-glucosidase; Provisional; Region: PRK10426 515619006759 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 515619006760 YihQ is a bacterial alpha-glucosidase with a conserved glycosyl hydrolase family 31 (GH31) domain that catalyzes the release of an alpha-glucosyl residue from the non-reducing end of alpha-glucoside substrates such as alpha-glucosyl fluoride. Orthologs...; Region: GH31_glucosidase_YihQ; cd06594 515619006761 putative active site [active] 515619006762 putative catalytic site [active] 515619006763 putative transporter; Provisional; Region: PRK10484 515619006764 uncharacterized SLC5 subfamily, Escherichia coli YidK-like; solute binding domain; Region: SLC5sbd_YidK; cd10328 515619006765 Na binding site [ion binding]; other site 515619006766 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 515619006767 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 515619006768 Class I aldolases; Region: Aldolase_Class_I; cl17187 515619006769 catalytic residue [active] 515619006770 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 515619006771 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 515619006772 Protein export membrane protein; Region: SecD_SecF; cl14618 515619006773 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 515619006774 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 515619006775 NodB motif; other site 515619006776 active site 515619006777 catalytic site [active] 515619006778 metal binding site [ion binding]; metal-binding site 515619006779 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 515619006780 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 515619006781 S-ribosylhomocysteinase; Provisional; Region: PRK02260 515619006782 oligoendopeptidase F; Region: pepF; TIGR00181 515619006783 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 515619006784 active site 515619006785 Zn binding site [ion binding]; other site 515619006786 carbamate kinase; Reviewed; Region: PRK12686 515619006787 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 515619006788 putative substrate binding site [chemical binding]; other site 515619006789 nucleotide binding site [chemical binding]; other site 515619006790 nucleotide binding site [chemical binding]; other site 515619006791 homodimer interface [polypeptide binding]; other site 515619006792 BCCT family transporter; Region: BCCT; pfam02028 515619006793 Transposase; Region: DEDD_Tnp_IS110; pfam01548 515619006794 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 515619006795 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 515619006796 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 515619006797 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 515619006798 active site 515619006799 metal-binding site 515619006800 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 515619006801 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 515619006802 CTP:phosphocholine cytidylyltransferase involved in choline phosphorylation for cell surface LPS epitopes [Cell envelope biogenesis, outer membrane]; Region: LicC; COG4750 515619006803 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 515619006804 Phosphotransferase enzyme family; Region: APH; pfam01636 515619006805 active site 515619006806 ATP binding site [chemical binding]; other site 515619006807 substrate binding site [chemical binding]; other site 515619006808 dimer interface [polypeptide binding]; other site 515619006809 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 515619006810 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 515619006811 protein binding site [polypeptide binding]; other site 515619006812 UDPGlcNAc pyrophosphorylase catalayzes the synthesis of UDPGlcNAc; Region: UDPGlcNAc_PPase; cd04193 515619006813 substrate binding site; other site 515619006814 dimerization interface; other site 515619006815 Transcriptional regulator [Transcription]; Region: LytR; COG1316 515619006816 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 515619006817 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 515619006818 active site 515619006819 substrate binding site [chemical binding]; other site 515619006820 metal binding site [ion binding]; metal-binding site 515619006821 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 515619006822 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 515619006823 active site 515619006824 Bacterial sugar transferase; Region: Bac_transf; pfam02397 515619006825 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 515619006826 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 515619006827 inhibitor-cofactor binding pocket; inhibition site 515619006828 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619006829 catalytic residue [active] 515619006830 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 515619006831 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 515619006832 CoA binding domain; Region: CoA_binding; cl17356 515619006833 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 515619006834 NAD(P) binding site [chemical binding]; other site 515619006835 homodimer interface [polypeptide binding]; other site 515619006836 substrate binding site [chemical binding]; other site 515619006837 active site 515619006838 Predicted membrane protein [Function unknown]; Region: COG2246 515619006839 GtrA-like protein; Region: GtrA; pfam04138 515619006840 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 515619006841 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 515619006842 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 515619006843 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 515619006844 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 515619006845 This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1); Region: GT1_CapH_like; cd03812 515619006846 putative ADP-binding pocket [chemical binding]; other site 515619006847 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 515619006848 active site 515619006849 Domain of unknown function (DUF4422); Region: DUF4422; pfam14393 515619006850 Domain of unknown function (DUF4422); Region: DUF4422; pfam14393 515619006851 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 515619006852 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 515619006853 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 515619006854 Acyltransferase family; Region: Acyl_transf_3; pfam01757 515619006855 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619006856 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619006857 putative active site [active] 515619006858 putative NTP binding site [chemical binding]; other site 515619006859 putative nucleic acid binding site [nucleotide binding]; other site 515619006860 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619006861 glucan-binding repeat; Region: glucan_65_rpt; TIGR04035 515619006862 FOG: Glucan-binding domain (YG repeat) [General function prediction only]; Region: COG5263 515619006863 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 515619006864 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 515619006865 The LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains. LytC is composed of a...; Region: GH25_LytC-like; cd06414 515619006866 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 515619006867 active site 515619006868 FOG: Glucan-binding domain (YG repeat) [General function prediction only]; Region: COG5263 515619006869 Acyltransferase family; Region: Acyl_transf_3; pfam01757 515619006870 potential frameshift: common BLAST hit: gi|220930335|ref|YP_002507244.1| transposase IS66 515619006871 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 515619006872 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 515619006873 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 515619006874 hypothetical protein; Provisional; Region: PRK07208 515619006875 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 515619006876 Acyltransferase family; Region: Acyl_transf_3; pfam01757 515619006877 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 515619006878 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 515619006879 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619006880 Coenzyme A binding pocket [chemical binding]; other site 515619006881 LicD family; Region: LicD; pfam04991 515619006882 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 515619006883 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 515619006884 active site 515619006885 nucleotide binding site [chemical binding]; other site 515619006886 HIGH motif; other site 515619006887 KMSKS motif; other site 515619006888 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 515619006889 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 515619006890 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 515619006891 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619006892 catalytic residue [active] 515619006893 CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase; Region: Glyphos_transf; pfam04464 515619006894 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 515619006895 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 515619006896 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 515619006897 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 515619006898 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 515619006899 trimer interface [polypeptide binding]; other site 515619006900 active site 515619006901 substrate binding site [chemical binding]; other site 515619006902 CoA binding site [chemical binding]; other site 515619006903 LicD family; Region: LicD; pfam04991 515619006904 O-Antigen ligase; Region: Wzy_C; cl04850 515619006905 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 515619006906 trimer interface [polypeptide binding]; other site 515619006907 active site 515619006908 substrate binding site [chemical binding]; other site 515619006909 CoA binding site [chemical binding]; other site 515619006910 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 515619006911 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 515619006912 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 515619006913 This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1); Region: GT1_CapH_like; cd03812 515619006914 putative ADP-binding pocket [chemical binding]; other site 515619006915 Glycosyltransferase family 28 C-terminal domain; Region: Glyco_tran_28_C; pfam04101 515619006916 Oligosaccharide biosynthesis protein Alg14 like; Region: Alg14; pfam08660 515619006917 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 515619006918 Bacterial sugar transferase; Region: Bac_transf; pfam02397 515619006919 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 515619006920 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 515619006921 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 515619006922 catalytic residue [active] 515619006923 Phosphopantetheine attachment site; Region: PP-binding; cl09936 515619006924 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 515619006925 AMP-binding enzyme; Region: AMP-binding; pfam00501 515619006926 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 515619006927 acyl-activating enzyme (AAE) consensus motif; other site 515619006928 AMP binding site [chemical binding]; other site 515619006929 active site 515619006930 CoA binding site [chemical binding]; other site 515619006931 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 515619006932 Ligand binding site; other site 515619006933 Putative Catalytic site; other site 515619006934 DXD motif; other site 515619006935 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 515619006936 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 515619006937 dimer interface [polypeptide binding]; other site 515619006938 active site 515619006939 ADP-ribose binding site [chemical binding]; other site 515619006940 nudix motif; other site 515619006941 metal binding site [ion binding]; metal-binding site 515619006942 TIR domain; Region: TIR_2; cl17458 515619006943 sporulation transcription factor Spo0A; Region: spore_0_A; TIGR02875 515619006944 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619006945 active site 515619006946 phosphorylation site [posttranslational modification] 515619006947 intermolecular recognition site; other site 515619006948 dimerization interface [polypeptide binding]; other site 515619006949 Sporulation initiation factor Spo0A C terminal; Region: Spo0A_C; pfam08769 515619006950 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619006951 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 515619006952 ATP binding site [chemical binding]; other site 515619006953 Mg2+ binding site [ion binding]; other site 515619006954 G-X-G motif; other site 515619006955 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619006956 RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_I; cd01646 515619006957 putative active site [active] 515619006958 putative NTP binding site [chemical binding]; other site 515619006959 putative nucleic acid binding site [nucleotide binding]; other site 515619006960 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 515619006961 active site 515619006962 catalytic triad [active] 515619006963 dimer interface [polypeptide binding]; other site 515619006964 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 515619006965 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 515619006966 active site 515619006967 DNA binding site [nucleotide binding] 515619006968 Int/Topo IB signature motif; other site 515619006969 D-alanine--D-alanine ligase; Region: D_ala_D_alaTIGR; TIGR01205 515619006970 ATP-grasp domain; Region: ATP-grasp_4; cl17255 515619006971 Tetratricopeptide repeat; Region: TPR_12; pfam13424 515619006972 ParB-like nuclease domain; Region: ParBc; pfam02195 515619006973 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 515619006974 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 515619006975 cofactor binding site; other site 515619006976 DNA binding site [nucleotide binding] 515619006977 substrate interaction site [chemical binding]; other site 515619006978 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 515619006979 potential frameshift: common BLAST hit: gi|126698695|ref|YP_001087592.1| putative DNA primase 515619006980 Antirestriction protein (ArdA); Region: ArdA; cl01953 515619006981 Protein of unknown function (DUF3801); Region: DUF3801; pfam12687 515619006982 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 515619006983 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619006984 Walker A motif; other site 515619006985 ATP binding site [chemical binding]; other site 515619006986 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 515619006987 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 515619006988 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619006989 putative active site [active] 515619006990 putative NTP binding site [chemical binding]; other site 515619006991 putative nucleic acid binding site [nucleotide binding]; other site 515619006992 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619006993 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 515619006994 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 515619006995 Maff2 family; Region: Maff2; pfam12750 515619006996 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 515619006997 salt bridge; other site 515619006998 non-specific DNA binding site [nucleotide binding]; other site 515619006999 sequence-specific DNA binding site [nucleotide binding]; other site 515619007000 Transposon-encoded protein TnpV; Region: TnpV; pfam14198 515619007001 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619007002 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 515619007003 non-specific DNA binding site [nucleotide binding]; other site 515619007004 salt bridge; other site 515619007005 sequence-specific DNA binding site [nucleotide binding]; other site 515619007006 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 515619007007 Protein of unknown function (DUF3847); Region: DUF3847; pfam12958 515619007008 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619007009 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 515619007010 non-specific DNA binding site [nucleotide binding]; other site 515619007011 salt bridge; other site 515619007012 sequence-specific DNA binding site [nucleotide binding]; other site 515619007013 MobA/MobL family; Region: MobA_MobL; pfam03389 515619007014 CHC2 zinc finger; Region: zf-CHC2; cl17510 515619007015 Virulence-associated protein E; Region: VirE; pfam05272 515619007016 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619007017 Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a...; Region: SR_TndX_transposase; cd03770 515619007018 putative catalytic residues [active] 515619007019 catalytic nucleophile [active] 515619007020 Recombinase; Region: Recombinase; pfam07508 515619007021 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619007022 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 515619007023 SpoVG; Region: SpoVG; pfam04026 515619007024 AAA-like domain; Region: AAA_10; pfam12846 515619007025 Domain of unknown function DUF87; Region: DUF87; pfam01935 515619007026 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619007027 NlpC/P60 family; Region: NLPC_P60; pfam00877 515619007028 Domain of unknown function (DUF4315); Region: DUF4315; pfam14193 515619007029 Domain of unknown function (DUF4366); Region: DUF4366; pfam14283 515619007030 Cysteine-rich VLP; Region: Cys_rich_VLP; pfam14194 515619007031 Domain of unknown function (DUF4316); Region: DUF4316; pfam14195 515619007032 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 515619007033 Protein of unknown function (DUF1559); Region: SBP_bac_10; pfam07596 515619007034 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 515619007035 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619007036 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 515619007037 non-specific DNA binding site [nucleotide binding]; other site 515619007038 salt bridge; other site 515619007039 sequence-specific DNA binding site [nucleotide binding]; other site 515619007040 Helix-turn-helix domain; Region: HTH_17; pfam12728 515619007041 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619007042 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007043 active site 515619007044 phosphorylation site [posttranslational modification] 515619007045 intermolecular recognition site; other site 515619007046 dimerization interface [polypeptide binding]; other site 515619007047 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 515619007048 DNA binding site [nucleotide binding] 515619007049 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619007050 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 515619007051 dimer interface [polypeptide binding]; other site 515619007052 phosphorylation site [posttranslational modification] 515619007053 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 515619007054 ATP binding site [chemical binding]; other site 515619007055 Mg2+ binding site [ion binding]; other site 515619007056 G-X-G motif; other site 515619007057 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619007058 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619007059 Walker A/P-loop; other site 515619007060 ATP binding site [chemical binding]; other site 515619007061 Q-loop/lid; other site 515619007062 ABC transporter signature motif; other site 515619007063 Walker B; other site 515619007064 D-loop; other site 515619007065 H-loop/switch region; other site 515619007066 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 515619007067 FtsX-like permease family; Region: FtsX; pfam02687 515619007068 FtsX-like permease family; Region: FtsX; pfam02687 515619007069 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 515619007070 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 515619007071 putative active site [active] 515619007072 putative metal binding site [ion binding]; other site 515619007073 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 515619007074 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 515619007075 DNA binding residues [nucleotide binding] 515619007076 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619007077 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 515619007078 catalytic residues [active] 515619007079 catalytic nucleophile [active] 515619007080 Presynaptic Site I dimer interface [polypeptide binding]; other site 515619007081 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 515619007082 Synaptic Flat tetramer interface [polypeptide binding]; other site 515619007083 Synaptic Site I dimer interface [polypeptide binding]; other site 515619007084 DNA binding site [nucleotide binding] 515619007085 Recombinase; Region: Recombinase; pfam07508 515619007086 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619007087 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 515619007088 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 515619007089 Acyltransferase family; Region: Acyl_transf_3; pfam01757 515619007090 putative transposase OrfB; Reviewed; Region: PHA02517 515619007091 HTH-like domain; Region: HTH_21; pfam13276 515619007092 Integrase core domain; Region: rve; pfam00665 515619007093 Integrase core domain; Region: rve_2; pfam13333 515619007094 Helix-turn-helix domain; Region: HTH_28; pfam13518 515619007095 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 515619007096 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 515619007097 Radical SAM superfamily; Region: Radical_SAM; pfam04055 515619007098 FeS/SAM binding site; other site 515619007099 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cd02619 515619007100 active site 515619007101 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007102 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007103 Interdomain contacts; other site 515619007104 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007105 Interdomain contacts; other site 515619007106 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007107 Interdomain contacts; other site 515619007108 Cytokine receptor motif; other site 515619007109 CHAP domain; Region: CHAP; cl17642 515619007110 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619007111 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007112 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007113 Interdomain contacts; other site 515619007114 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007115 Interdomain contacts; other site 515619007116 Cytokine receptor motif; other site 515619007117 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007118 Interdomain contacts; other site 515619007119 Cytokine receptor motif; other site 515619007120 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 515619007121 catalytic residues [active] 515619007122 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619007123 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007124 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007125 Interdomain contacts; other site 515619007126 Cytokine receptor motif; other site 515619007127 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007128 Interdomain contacts; other site 515619007129 Cytokine receptor motif; other site 515619007130 Transglutaminase/protease-like homologues; Region: TGc; smart00460 515619007131 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007132 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 515619007133 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007134 Interdomain contacts; other site 515619007135 Cytokine receptor motif; other site 515619007136 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007137 Interdomain contacts; other site 515619007138 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007139 Interdomain contacts; other site 515619007140 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; pfam03816 515619007141 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG5610 515619007142 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 515619007143 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 515619007144 Bacterial sugar transferase; Region: Bac_transf; pfam02397 515619007145 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 515619007146 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 515619007147 active site 515619007148 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 515619007149 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 515619007150 UDP-galactopyranose mutase; Region: GLF; pfam03275 515619007151 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007152 Interdomain contacts; other site 515619007153 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007154 Interdomain contacts; other site 515619007155 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 515619007156 Interdomain contacts; other site 515619007157 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 515619007158 4Fe-4S binding domain; Region: Fer4; pfam00037 515619007159 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 515619007160 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 515619007161 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 515619007162 putative glycosyl transferase; Provisional; Region: PRK10073 515619007163 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 515619007164 active site 515619007165 Domain of unknown function (DUF3543); Region: DUF3543; pfam12063 515619007166 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 515619007167 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 515619007168 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 515619007169 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 515619007170 ABC-2 type transporter; Region: ABC2_membrane; cl17235 515619007171 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 515619007172 ABC-2 type transporter; Region: ABC2_membrane; cl17235 515619007173 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 515619007174 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 515619007175 Walker A/P-loop; other site 515619007176 ATP binding site [chemical binding]; other site 515619007177 Q-loop/lid; other site 515619007178 ABC transporter signature motif; other site 515619007179 Walker B; other site 515619007180 D-loop; other site 515619007181 H-loop/switch region; other site 515619007182 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG5610 515619007183 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 515619007184 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 515619007185 active site 515619007186 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 515619007187 putative ADP-binding pocket [chemical binding]; other site 515619007188 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 515619007189 Bacterial SH3 domain; Region: SH3_3; cl17532 515619007190 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 515619007191 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 515619007192 active site 515619007193 substrate binding site [chemical binding]; other site 515619007194 metal binding site [ion binding]; metal-binding site 515619007195 VanZ like family; Region: VanZ; pfam04892 515619007196 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 515619007197 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 515619007198 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 515619007199 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 515619007200 active site 515619007201 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 515619007202 active site 515619007203 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 515619007204 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 515619007205 active site 515619007206 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 515619007207 dimerization domain swap beta strand [polypeptide binding]; other site 515619007208 regulatory protein interface [polypeptide binding]; other site 515619007209 active site 515619007210 regulatory phosphorylation site [posttranslational modification]; other site 515619007211 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 515619007212 YbbR-like protein; Region: YbbR; pfam07949 515619007213 Uncharacterized conserved protein [Function unknown]; Region: COG1624 515619007214 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 515619007215 flagellar operon protein TIGR03826; Region: YvyF 515619007216 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 515619007217 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 515619007218 active site 515619007219 rod shape-determining protein MreB; Provisional; Region: PRK13930 515619007220 MreB and similar proteins; Region: MreB_like; cd10225 515619007221 nucleotide binding site [chemical binding]; other site 515619007222 Mg binding site [ion binding]; other site 515619007223 putative protofilament interaction site [polypeptide binding]; other site 515619007224 RodZ interaction site [polypeptide binding]; other site 515619007225 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 515619007226 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 515619007227 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 515619007228 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 515619007229 excinuclease ABC subunit B; Provisional; Region: PRK05298 515619007230 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 515619007231 ATP binding site [chemical binding]; other site 515619007232 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 515619007233 nucleotide binding region [chemical binding]; other site 515619007234 ATP-binding site [chemical binding]; other site 515619007235 Ultra-violet resistance protein B; Region: UvrB; pfam12344 515619007236 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 515619007237 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 515619007238 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 515619007239 nucleotide binding region [chemical binding]; other site 515619007240 ATP-binding site [chemical binding]; other site 515619007241 SEC-C motif; Region: SEC-C; pfam02810 515619007242 TSCPD domain; Region: TSCPD; cl14834 515619007243 dipicolinate synthase subunit B; Reviewed; Region: spoVFB; PRK08305 515619007244 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 515619007245 NAD binding site [chemical binding]; other site 515619007246 aspartate kinase; Reviewed; Region: PRK09034 515619007247 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 515619007248 nucleotide binding site [chemical binding]; other site 515619007249 substrate binding site [chemical binding]; other site 515619007250 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-YclM-BS_1; cd04911 515619007251 allosteric regulatory residue; other site 515619007252 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-YclM-BS_2; cd04916 515619007253 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 515619007254 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 515619007255 active site 515619007256 metal binding site [ion binding]; metal-binding site 515619007257 homotetramer interface [polypeptide binding]; other site 515619007258 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 515619007259 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 515619007260 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 515619007261 histidinol-phosphatase; Provisional; Region: PRK07328 515619007262 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Region: PHP_HisPPase_Hisj_like; cd12110 515619007263 active site 515619007264 dimer interface [polypeptide binding]; other site 515619007265 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 515619007266 TrkA-N domain; Region: TrkA_N; pfam02254 515619007267 TrkA-C domain; Region: TrkA_C; pfam02080 515619007268 TrkA-N domain; Region: TrkA_N; pfam02254 515619007269 TrkA-C domain; Region: TrkA_C; pfam02080 515619007270 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 515619007271 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 515619007272 Repair protein; Region: Repair_PSII; pfam04536 515619007273 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 515619007274 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 515619007275 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619007276 Zn2+ binding site [ion binding]; other site 515619007277 Mg2+ binding site [ion binding]; other site 515619007278 Protein of unknown function (DUF1113); Region: DUF1113; pfam06541 515619007279 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 515619007280 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007281 Walker A/P-loop; other site 515619007282 ATP binding site [chemical binding]; other site 515619007283 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619007284 ABC transporter; Region: ABC_tran_2; pfam12848 515619007285 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619007286 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 515619007287 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619007288 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619007289 Helix-turn-helix domain; Region: HTH_18; pfam12833 515619007290 N-terminal-like domain of Paenibacillus sp. YM-1 Laminaribiose Phosphorylase and similar proteins; Region: GH94N_LBP_like; cd11749 515619007291 N-terminal domain of chitobiose phosphorylase (ChBP) and similar proteins; Region: GH94N_ChBP_like; cd11755 515619007292 catalytic domain interface [polypeptide binding]; other site 515619007293 putative homodimer interface [polypeptide binding]; other site 515619007294 Protein of unknown function, DUF608; Region: DUF608; pfam04685 515619007295 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 515619007296 Cupin domain; Region: Cupin_2; pfam07883 515619007297 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619007298 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619007299 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 515619007300 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 515619007301 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 515619007302 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 515619007303 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619007304 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619007305 Domain of unknown function (DUF4173); Region: DUF4173; pfam13777 515619007306 enolase; Provisional; Region: eno; PRK00077 515619007307 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 515619007308 dimer interface [polypeptide binding]; other site 515619007309 metal binding site [ion binding]; metal-binding site 515619007310 substrate binding pocket [chemical binding]; other site 515619007311 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 515619007312 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 515619007313 salt bridge; other site 515619007314 non-specific DNA binding site [nucleotide binding]; other site 515619007315 sequence-specific DNA binding site [nucleotide binding]; other site 515619007316 Protein of unknown function (DUF3036); Region: DUF3036; pfam11234 515619007317 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 515619007318 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619007319 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619007320 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 515619007321 Walker A/P-loop; other site 515619007322 ATP binding site [chemical binding]; other site 515619007323 Q-loop/lid; other site 515619007324 ABC transporter signature motif; other site 515619007325 Walker B; other site 515619007326 D-loop; other site 515619007327 H-loop/switch region; other site 515619007328 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 515619007329 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619007330 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007331 Walker A/P-loop; other site 515619007332 ATP binding site [chemical binding]; other site 515619007333 Q-loop/lid; other site 515619007334 ABC transporter signature motif; other site 515619007335 Walker B; other site 515619007336 D-loop; other site 515619007337 H-loop/switch region; other site 515619007338 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 515619007339 dimer interface [polypeptide binding]; other site 515619007340 ADP-ribose binding site [chemical binding]; other site 515619007341 active site 515619007342 nudix motif; other site 515619007343 metal binding site [ion binding]; metal-binding site 515619007344 A new structural DNA glycosylase; Region: AlkD_like; cd06561 515619007345 active site 515619007346 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 515619007347 Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal...; Region: Ntn_PVA; cd00542 515619007348 active site 515619007349 Chorismate mutase type II; Region: CM_2; cl00693 515619007350 shikimate kinase; Reviewed; Region: aroK; PRK00131 515619007351 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 515619007352 ADP binding site [chemical binding]; other site 515619007353 magnesium binding site [ion binding]; other site 515619007354 putative shikimate binding site; other site 515619007355 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 515619007356 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 515619007357 DctM-like transporters; Region: DctM; pfam06808 515619007358 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 515619007359 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 515619007360 3-dehydroquinate dehydratase [Amino acid transport and metabolism]; Region: AroD; COG0710 515619007361 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 515619007362 active site 515619007363 catalytic residue [active] 515619007364 dimer interface [polypeptide binding]; other site 515619007365 shikimate 5-dehydrogenase; Provisional; Region: PRK12548 515619007366 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 515619007367 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 515619007368 shikimate binding site; other site 515619007369 NAD(P) binding site [chemical binding]; other site 515619007370 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619007371 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619007372 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 515619007373 dimerization interface [polypeptide binding]; other site 515619007374 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619007375 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619007376 The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; Region: PBP2_GltC_like; cd08434 515619007377 putative dimerization interface [polypeptide binding]; other site 515619007378 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 515619007379 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 515619007380 active site 515619007381 FMN binding site [chemical binding]; other site 515619007382 substrate binding site [chemical binding]; other site 515619007383 putative catalytic residue [active] 515619007384 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 515619007385 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 515619007386 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 515619007387 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619007388 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619007389 putative active site [active] 515619007390 putative NTP binding site [chemical binding]; other site 515619007391 putative nucleic acid binding site [nucleotide binding]; other site 515619007392 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619007393 shikimate 5-dehydrogenase; Provisional; Region: PRK12548 515619007394 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 515619007395 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 515619007396 shikimate binding site; other site 515619007397 NAD(P) binding site [chemical binding]; other site 515619007398 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 515619007399 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 515619007400 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_18; cd04677 515619007401 nudix motif; other site 515619007402 chaperone protein DnaJ; Provisional; Region: PRK14291 515619007403 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 515619007404 HSP70 interaction site [polypeptide binding]; other site 515619007405 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 515619007406 substrate binding site [polypeptide binding]; other site 515619007407 dimer interface [polypeptide binding]; other site 515619007408 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 515619007409 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 515619007410 putative dimer interface [polypeptide binding]; other site 515619007411 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619007412 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007413 Walker A/P-loop; other site 515619007414 ATP binding site [chemical binding]; other site 515619007415 Q-loop/lid; other site 515619007416 ABC transporter signature motif; other site 515619007417 Walker B; other site 515619007418 D-loop; other site 515619007419 H-loop/switch region; other site 515619007420 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619007421 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007422 Walker A/P-loop; other site 515619007423 ATP binding site [chemical binding]; other site 515619007424 Q-loop/lid; other site 515619007425 ABC transporter signature motif; other site 515619007426 Walker B; other site 515619007427 D-loop; other site 515619007428 H-loop/switch region; other site 515619007429 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619007430 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619007431 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 515619007432 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007433 Walker A/P-loop; other site 515619007434 ATP binding site [chemical binding]; other site 515619007435 Q-loop/lid; other site 515619007436 ABC transporter signature motif; other site 515619007437 Walker B; other site 515619007438 D-loop; other site 515619007439 H-loop/switch region; other site 515619007440 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619007441 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007442 active site 515619007443 phosphorylation site [posttranslational modification] 515619007444 intermolecular recognition site; other site 515619007445 dimerization interface [polypeptide binding]; other site 515619007446 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619007447 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 515619007448 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619007449 PIN domain; Region: PIN_3; pfam13470 515619007450 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 515619007451 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619007452 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619007453 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 515619007454 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 515619007455 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 515619007456 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 515619007457 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 515619007458 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 515619007459 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 515619007460 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 515619007461 Metal-binding active site; metal-binding site 515619007462 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 515619007463 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 515619007464 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 515619007465 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 515619007466 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 515619007467 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 515619007468 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619007469 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619007470 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619007471 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 515619007472 dimer interface [polypeptide binding]; other site 515619007473 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 515619007474 ABC-ATPase subunit interface; other site 515619007475 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 515619007476 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 515619007477 dimer interface [polypeptide binding]; other site 515619007478 conserved gate region; other site 515619007479 putative PBP binding loops; other site 515619007480 ABC-ATPase subunit interface; other site 515619007481 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 515619007482 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007483 active site 515619007484 phosphorylation site [posttranslational modification] 515619007485 intermolecular recognition site; other site 515619007486 dimerization interface [polypeptide binding]; other site 515619007487 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619007488 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619007489 HAMP domain; Region: HAMP; pfam00672 515619007490 Histidine kinase; Region: His_kinase; pfam06580 515619007491 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 515619007492 ATP binding site [chemical binding]; other site 515619007493 Mg2+ binding site [ion binding]; other site 515619007494 G-X-G motif; other site 515619007495 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 515619007496 LrgB-like family; Region: LrgB; pfam04172 515619007497 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 515619007498 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 515619007499 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619007500 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619007501 metal binding site [ion binding]; metal-binding site 515619007502 active site 515619007503 I-site; other site 515619007504 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619007505 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 515619007506 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 515619007507 gamma subunit interface [polypeptide binding]; other site 515619007508 epsilon subunit interface [polypeptide binding]; other site 515619007509 LBP interface [polypeptide binding]; other site 515619007510 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 515619007511 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 515619007512 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 515619007513 alpha subunit interaction interface [polypeptide binding]; other site 515619007514 Walker A motif; other site 515619007515 ATP binding site [chemical binding]; other site 515619007516 Walker B motif; other site 515619007517 inhibitor binding site; inhibition site 515619007518 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 515619007519 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 515619007520 core domain interface [polypeptide binding]; other site 515619007521 delta subunit interface [polypeptide binding]; other site 515619007522 epsilon subunit interface [polypeptide binding]; other site 515619007523 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 515619007524 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 515619007525 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 515619007526 beta subunit interaction interface [polypeptide binding]; other site 515619007527 Walker A motif; other site 515619007528 ATP binding site [chemical binding]; other site 515619007529 Walker B motif; other site 515619007530 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 515619007531 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 515619007532 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 515619007533 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 515619007534 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 515619007535 F0F1 ATP synthase subunit C; Provisional; Region: PRK13469 515619007536 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 515619007537 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 515619007538 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 515619007539 Uncharacterized protein conserved in bacteria C-term(DUF2220); Region: DUF2220; pfam09983 515619007540 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 515619007541 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 515619007542 active site 515619007543 metal binding site [ion binding]; metal-binding site 515619007544 dihydroorotase; Validated; Region: pyrC; PRK09357 515619007545 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 515619007546 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 515619007547 active site 515619007548 This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases; Region: CHASE; smart01079 515619007549 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 515619007550 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 515619007551 metal binding site [ion binding]; metal-binding site 515619007552 active site 515619007553 I-site; other site 515619007554 PAS domain S-box; Region: sensory_box; TIGR00229 515619007555 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 515619007556 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]; Region: COG3269 515619007557 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 515619007558 S-adenosylmethionine binding site [chemical binding]; other site 515619007559 Predicted HD-superfamily hydrolase [General function prediction only]; Region: COG3481 515619007560 YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is...; Region: YhaM_OBF_like; cd04492 515619007561 generic binding surface II; other site 515619007562 generic binding surface I; other site 515619007563 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619007564 Zn2+ binding site [ion binding]; other site 515619007565 Mg2+ binding site [ion binding]; other site 515619007566 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 515619007567 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 515619007568 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 515619007569 protein binding site [polypeptide binding]; other site 515619007570 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 515619007571 MutS domain III; Region: MutS_III; pfam05192 515619007572 ATP-binding cassette domain of MutS2; Region: ABC_MutS2; cd03280 515619007573 Walker A/P-loop; other site 515619007574 ATP binding site [chemical binding]; other site 515619007575 Q-loop/lid; other site 515619007576 ABC transporter signature motif; other site 515619007577 Walker B; other site 515619007578 D-loop; other site 515619007579 H-loop/switch region; other site 515619007580 Smr domain; Region: Smr; pfam01713 515619007581 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619007582 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007583 active site 515619007584 phosphorylation site [posttranslational modification] 515619007585 intermolecular recognition site; other site 515619007586 dimerization interface [polypeptide binding]; other site 515619007587 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 515619007588 DNA binding site [nucleotide binding] 515619007589 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619007590 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 515619007591 dimerization interface [polypeptide binding]; other site 515619007592 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 515619007593 dimer interface [polypeptide binding]; other site 515619007594 phosphorylation site [posttranslational modification] 515619007595 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 515619007596 ATP binding site [chemical binding]; other site 515619007597 Mg2+ binding site [ion binding]; other site 515619007598 G-X-G motif; other site 515619007599 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 515619007600 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 515619007601 dimer interface [polypeptide binding]; other site 515619007602 anticodon binding site; other site 515619007603 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 515619007604 homodimer interface [polypeptide binding]; other site 515619007605 motif 1; other site 515619007606 active site 515619007607 motif 2; other site 515619007608 GAD domain; Region: GAD; pfam02938 515619007609 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 515619007610 active site 515619007611 motif 3; other site 515619007612 histidyl-tRNA synthetase; Region: hisS; TIGR00442 515619007613 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 515619007614 dimer interface [polypeptide binding]; other site 515619007615 motif 1; other site 515619007616 active site 515619007617 motif 2; other site 515619007618 motif 3; other site 515619007619 DNA/RNA non-specific endonuclease; Region: Endonuclea_NS_2; pfam13930 515619007620 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 515619007621 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 515619007622 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 515619007623 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 515619007624 active site turn [active] 515619007625 phosphorylation site [posttranslational modification] 515619007626 Phosphotransferase system IIA components [Carbohydrate transport and metabolism]; Region: NagE; COG2190 515619007627 HPr interaction site; other site 515619007628 glycerol kinase (GK) interaction site [polypeptide binding]; other site 515619007629 active site 515619007630 phosphorylation site [posttranslational modification] 515619007631 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 515619007632 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 515619007633 active site 515619007634 dimer interface [polypeptide binding]; other site 515619007635 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 515619007636 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 515619007637 active site 515619007638 trimer interface [polypeptide binding]; other site 515619007639 allosteric site; other site 515619007640 active site lid [active] 515619007641 hexamer (dimer of trimers) interface [polypeptide binding]; other site 515619007642 coproporphyrinogen dehydrogenase HemZ; Region: rSAM_HemZ; TIGR03994 515619007643 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 515619007644 FeS/SAM binding site; other site 515619007645 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 515619007646 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 515619007647 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619007648 Zn2+ binding site [ion binding]; other site 515619007649 Mg2+ binding site [ion binding]; other site 515619007650 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 515619007651 synthetase active site [active] 515619007652 NTP binding site [chemical binding]; other site 515619007653 metal binding site [ion binding]; metal-binding site 515619007654 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 515619007655 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 515619007656 ROK family protein (putative glucokinase); Region: ROK_glcA_fam; TIGR00744 515619007657 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 515619007658 nucleotide binding site [chemical binding]; other site 515619007659 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 515619007660 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 515619007661 Probable Catalytic site; other site 515619007662 metal-binding site 515619007663 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619007664 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 515619007665 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 515619007666 active site 515619007667 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 515619007668 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 515619007669 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 515619007670 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 515619007671 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 515619007672 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 515619007673 ATP-grasp domain; Region: ATP-grasp_4; cl17255 515619007674 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 515619007675 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 515619007676 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 515619007677 30S subunit binding site; other site 515619007678 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 515619007679 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619007680 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619007681 ABC transporter; Region: ABC_tran_2; pfam12848 515619007682 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 515619007683 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 515619007684 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 515619007685 Walker A motif; other site 515619007686 ATP binding site [chemical binding]; other site 515619007687 Walker B motif; other site 515619007688 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 515619007689 dimer interface [polypeptide binding]; other site 515619007690 phosphorylation site [posttranslational modification] 515619007691 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 515619007692 ATP binding site [chemical binding]; other site 515619007693 Mg2+ binding site [ion binding]; other site 515619007694 G-X-G motif; other site 515619007695 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619007696 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007697 active site 515619007698 phosphorylation site [posttranslational modification] 515619007699 intermolecular recognition site; other site 515619007700 dimerization interface [polypeptide binding]; other site 515619007701 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 515619007702 DNA binding site [nucleotide binding] 515619007703 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 515619007704 PhoU domain; Region: PhoU; pfam01895 515619007705 PhoU domain; Region: PhoU; pfam01895 515619007706 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 515619007707 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 515619007708 Walker A/P-loop; other site 515619007709 ATP binding site [chemical binding]; other site 515619007710 Q-loop/lid; other site 515619007711 ABC transporter signature motif; other site 515619007712 Walker B; other site 515619007713 D-loop; other site 515619007714 H-loop/switch region; other site 515619007715 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 515619007716 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619007717 DNA-binding site [nucleotide binding]; DNA binding site 515619007718 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 515619007719 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619007720 homodimer interface [polypeptide binding]; other site 515619007721 catalytic residue [active] 515619007722 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1; Region: TIGR00343 515619007723 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 515619007724 active site 515619007725 multimer interface [polypeptide binding]; other site 515619007726 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 515619007727 Glutamine amidotransferase [Amino acid transport and metabolism]; Region: HisH; COG0118 515619007728 predicted active site [active] 515619007729 catalytic triad [active] 515619007730 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619007731 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 515619007732 dimer interface [polypeptide binding]; other site 515619007733 phosphorylation site [posttranslational modification] 515619007734 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 515619007735 ATP binding site [chemical binding]; other site 515619007736 Mg2+ binding site [ion binding]; other site 515619007737 G-X-G motif; other site 515619007738 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619007739 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007740 active site 515619007741 phosphorylation site [posttranslational modification] 515619007742 intermolecular recognition site; other site 515619007743 dimerization interface [polypeptide binding]; other site 515619007744 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 515619007745 DNA binding site [nucleotide binding] 515619007746 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 515619007747 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 515619007748 dimer interface [polypeptide binding]; other site 515619007749 conserved gate region; other site 515619007750 putative PBP binding loops; other site 515619007751 ABC-ATPase subunit interface; other site 515619007752 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 515619007753 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 515619007754 dimer interface [polypeptide binding]; other site 515619007755 conserved gate region; other site 515619007756 putative PBP binding loops; other site 515619007757 ABC-ATPase subunit interface; other site 515619007758 PBP superfamily domain; Region: PBP_like_2; cl17296 515619007759 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 515619007760 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 515619007761 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 515619007762 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 515619007763 NAD(P) binding site [chemical binding]; other site 515619007764 active site 515619007765 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 515619007766 sequence-specific DNA binding site [nucleotide binding]; other site 515619007767 salt bridge; other site 515619007768 Type II secretory pathway, pullulanase PulA and related glycosidases [Carbohydrate transport and metabolism]; Region: PulA; COG1523 515619007769 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme; Region: E_set_GDE_N; cd11234 515619007770 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 515619007771 active site 515619007772 catalytic site [active] 515619007773 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 515619007774 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 515619007775 putative active site [active] 515619007776 putative metal binding site [ion binding]; other site 515619007777 Methyltransferase domain; Region: Methyltransf_31; pfam13847 515619007778 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 515619007779 S-adenosylmethionine binding site [chemical binding]; other site 515619007780 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 515619007781 dimerization interface [polypeptide binding]; other site 515619007782 putative DNA binding site [nucleotide binding]; other site 515619007783 putative Zn2+ binding site [ion binding]; other site 515619007784 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 515619007785 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 515619007786 Soluble P-type ATPase [General function prediction only]; Region: COG4087 515619007787 Heavy-metal-associated domain; Region: HMA; pfam00403 515619007788 metal-binding site [ion binding] 515619007789 phosphoserine phosphatase; Provisional; Region: thrH; PRK13582 515619007790 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 515619007791 HD domain; Region: HD_3; pfam13023 515619007792 RloB-like protein; Region: RloB; pfam13707 515619007793 AAA domain; Region: AAA_21; pfam13304 515619007794 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007795 ABC transporter signature motif; other site 515619007796 Walker B; other site 515619007797 D-loop; other site 515619007798 H-loop/switch region; other site 515619007799 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 515619007800 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 515619007801 substrate binding site [chemical binding]; other site 515619007802 active site 515619007803 catalytic residues [active] 515619007804 heterodimer interface [polypeptide binding]; other site 515619007805 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 515619007806 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 515619007807 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619007808 catalytic residue [active] 515619007809 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 515619007810 active site 515619007811 ribulose/triose binding site [chemical binding]; other site 515619007812 phosphate binding site [ion binding]; other site 515619007813 substrate (anthranilate) binding pocket [chemical binding]; other site 515619007814 product (indole) binding pocket [chemical binding]; other site 515619007815 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 515619007816 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 515619007817 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 515619007818 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 515619007819 Glutamine amidotransferase class-I; Region: GATase; pfam00117 515619007820 glutamine binding [chemical binding]; other site 515619007821 catalytic triad [active] 515619007822 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 515619007823 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 515619007824 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 515619007825 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 515619007826 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619007827 Coenzyme A binding pocket [chemical binding]; other site 515619007828 AAA ATPase domain; Region: AAA_16; pfam13191 515619007829 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 515619007830 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 515619007831 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 515619007832 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007833 Walker A/P-loop; other site 515619007834 ATP binding site [chemical binding]; other site 515619007835 Q-loop/lid; other site 515619007836 ABC transporter signature motif; other site 515619007837 Walker B; other site 515619007838 D-loop; other site 515619007839 H-loop/switch region; other site 515619007840 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619007841 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 515619007842 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 515619007843 Coenzyme A binding pocket [chemical binding]; other site 515619007844 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 515619007845 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 515619007846 catalytic residues [active] 515619007847 proline aminopeptidase P II; Provisional; Region: PRK10879 515619007848 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 515619007849 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 515619007850 active site 515619007851 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 515619007852 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 515619007853 23S rRNA interface [nucleotide binding]; other site 515619007854 L3 interface [polypeptide binding]; other site 515619007855 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 515619007856 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 515619007857 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 515619007858 dimerization interface 3.5A [polypeptide binding]; other site 515619007859 active site 515619007860 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 515619007861 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13637 515619007862 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 515619007863 Walker A/P-loop; other site 515619007864 ATP binding site [chemical binding]; other site 515619007865 Q-loop/lid; other site 515619007866 ABC transporter signature motif; other site 515619007867 Walker B; other site 515619007868 D-loop; other site 515619007869 H-loop/switch region; other site 515619007870 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13633 515619007871 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 515619007872 Walker A/P-loop; other site 515619007873 ATP binding site [chemical binding]; other site 515619007874 Q-loop/lid; other site 515619007875 ABC transporter signature motif; other site 515619007876 Walker B; other site 515619007877 D-loop; other site 515619007878 H-loop/switch region; other site 515619007879 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 515619007880 hypothetical protein; Validated; Region: PRK07682 515619007881 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 515619007882 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619007883 homodimer interface [polypeptide binding]; other site 515619007884 catalytic residue [active] 515619007885 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 515619007886 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 515619007887 AsnC family; Region: AsnC_trans_reg; pfam01037 515619007888 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypE; COG0309 515619007889 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 515619007890 dimerization interface [polypeptide binding]; other site 515619007891 ATP binding site [chemical binding]; other site 515619007892 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 515619007893 VanW like protein; Region: VanW; pfam04294 515619007894 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 515619007895 active site 515619007896 catalytic site [active] 515619007897 substrate binding site [chemical binding]; other site 515619007898 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 515619007899 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 515619007900 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 515619007901 FeS/SAM binding site; other site 515619007902 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 515619007903 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619007904 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 515619007905 salt bridge; other site 515619007906 non-specific DNA binding site [nucleotide binding]; other site 515619007907 sequence-specific DNA binding site [nucleotide binding]; other site 515619007908 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 515619007909 CAAX protease self-immunity; Region: Abi; pfam02517 515619007910 Domain of unknown function (DUF4190); Region: DUF4190; pfam13828 515619007911 Predicted membrane protein [Function unknown]; Region: COG1971 515619007912 X-X-X-Leu-X-X-Gly heptad repeats; Region: xxxLxxG_by_4; TIGR03057 515619007913 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 515619007914 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 515619007915 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 515619007916 nudix motif; other site 515619007917 ORF6N domain; Region: ORF6N; pfam10543 515619007918 Immunoglobulin domain; Region: Ig; cl11960 515619007919 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; cl17315 515619007920 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 515619007921 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 515619007922 S-adenosylmethionine binding site [chemical binding]; other site 515619007923 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 515619007924 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 515619007925 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 515619007926 EamA-like transporter family; Region: EamA; pfam00892 515619007927 EamA-like transporter family; Region: EamA; pfam00892 515619007928 Beta propeller domain; Region: Beta_propel; pfam09826 515619007929 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 515619007930 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619007931 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 515619007932 DNA binding residues [nucleotide binding] 515619007933 Catalytic domain of Protein Kinases; Region: PKc; cd00180 515619007934 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 515619007935 active site 515619007936 ATP binding site [chemical binding]; other site 515619007937 substrate binding site [chemical binding]; other site 515619007938 activation loop (A-loop); other site 515619007939 CAAX protease self-immunity; Region: Abi; pfam02517 515619007940 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 515619007941 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619007942 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007943 Walker A/P-loop; other site 515619007944 ATP binding site [chemical binding]; other site 515619007945 Q-loop/lid; other site 515619007946 ABC transporter signature motif; other site 515619007947 Walker B; other site 515619007948 D-loop; other site 515619007949 H-loop/switch region; other site 515619007950 ATP-binding cassette domain of the bacitracin-resistance transporter; Region: ABC_BcrA_bacitracin_resist; cd03268 515619007951 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619007952 Walker A/P-loop; other site 515619007953 ATP binding site [chemical binding]; other site 515619007954 Q-loop/lid; other site 515619007955 ABC transporter signature motif; other site 515619007956 Walker B; other site 515619007957 D-loop; other site 515619007958 H-loop/switch region; other site 515619007959 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 515619007960 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 515619007961 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 515619007962 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 515619007963 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 515619007964 dimer interface [polypeptide binding]; other site 515619007965 active site 515619007966 metal binding site [ion binding]; metal-binding site 515619007967 Flavodoxin domain; Region: Flavodoxin_3; pfam12641 515619007968 Predicted ATPase [General function prediction only]; Region: COG3910 515619007969 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007970 Walker A/P-loop; other site 515619007971 ATP binding site [chemical binding]; other site 515619007972 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 515619007973 Walker B; other site 515619007974 D-loop; other site 515619007975 H-loop/switch region; other site 515619007976 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 515619007977 dimer interface [polypeptide binding]; other site 515619007978 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 515619007979 CAAX protease self-immunity; Region: Abi; pfam02517 515619007980 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 515619007981 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39B; cd02418 515619007982 putative active site [active] 515619007983 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 515619007984 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619007985 Walker A/P-loop; other site 515619007986 ATP binding site [chemical binding]; other site 515619007987 Q-loop/lid; other site 515619007988 ABC transporter signature motif; other site 515619007989 Walker B; other site 515619007990 D-loop; other site 515619007991 H-loop/switch region; other site 515619007992 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 515619007993 HlyD family secretion protein; Region: HlyD; pfam00529 515619007994 HlyD family secretion protein; Region: HlyD_3; pfam13437 515619007995 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619007996 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619007997 active site 515619007998 phosphorylation site [posttranslational modification] 515619007999 intermolecular recognition site; other site 515619008000 dimerization interface [polypeptide binding]; other site 515619008001 LytTr DNA-binding domain; Region: LytTR; smart00850 515619008002 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 515619008003 ATP binding site [chemical binding]; other site 515619008004 Mg2+ binding site [ion binding]; other site 515619008005 G-X-G motif; other site 515619008006 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 515619008007 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 515619008008 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 515619008009 putative RNA binding site [nucleotide binding]; other site 515619008010 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 515619008011 S-adenosylmethionine binding site [chemical binding]; other site 515619008012 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 515619008013 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 515619008014 putative metal binding site; other site 515619008015 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 515619008016 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 515619008017 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 515619008018 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 515619008019 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 515619008020 DHHA1 domain; Region: DHHA1; pfam02272 515619008021 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 515619008022 FtsX-like permease family; Region: FtsX; pfam02687 515619008023 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619008024 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619008025 Walker A/P-loop; other site 515619008026 ATP binding site [chemical binding]; other site 515619008027 Q-loop/lid; other site 515619008028 ABC transporter signature motif; other site 515619008029 Walker B; other site 515619008030 D-loop; other site 515619008031 H-loop/switch region; other site 515619008032 L(+)-tartrate dehydratase subunit beta; Validated; Region: PRK08228 515619008033 tartrate dehydratase subunit alpha; Validated; Region: PRK08230 515619008034 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 515619008035 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 515619008036 transmembrane helices; other site 515619008037 Transcriptional regulators [Transcription]; Region: GntR; COG1802 515619008038 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619008039 DNA-binding site [nucleotide binding]; DNA binding site 515619008040 FCD domain; Region: FCD; pfam07729 515619008041 Transcriptional regulators [Transcription]; Region: GntR; COG1802 515619008042 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619008043 DNA-binding site [nucleotide binding]; DNA binding site 515619008044 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619008045 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 515619008046 ATP binding site [chemical binding]; other site 515619008047 Mg2+ binding site [ion binding]; other site 515619008048 G-X-G motif; other site 515619008049 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619008050 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008051 active site 515619008052 phosphorylation site [posttranslational modification] 515619008053 intermolecular recognition site; other site 515619008054 dimerization interface [polypeptide binding]; other site 515619008055 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 515619008056 DNA binding site [nucleotide binding] 515619008057 trigger factor; Provisional; Region: tig; PRK01490 515619008058 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 515619008059 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 515619008060 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 515619008061 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 515619008062 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 515619008063 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 515619008064 Walker A/P-loop; other site 515619008065 ATP binding site [chemical binding]; other site 515619008066 Q-loop/lid; other site 515619008067 ABC transporter signature motif; other site 515619008068 Walker B; other site 515619008069 D-loop; other site 515619008070 H-loop/switch region; other site 515619008071 Predicted transcriptional regulators [Transcription]; Region: COG1725 515619008072 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619008073 DNA-binding site [nucleotide binding]; DNA binding site 515619008074 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619008075 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 515619008076 Walker A/P-loop; other site 515619008077 ATP binding site [chemical binding]; other site 515619008078 Q-loop/lid; other site 515619008079 ABC transporter signature motif; other site 515619008080 Walker B; other site 515619008081 D-loop; other site 515619008082 H-loop/switch region; other site 515619008083 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 515619008084 MgtE intracellular N domain; Region: MgtE_N; pfam03448 515619008085 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 515619008086 Divalent cation transporter; Region: MgtE; pfam01769 515619008087 Sulfatase; Region: Sulfatase; cl17466 515619008088 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 515619008089 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 515619008090 Domain of unknown function (DUF4258); Region: DUF4258; pfam14076 515619008091 antitoxin MqsA for MqsR toxin; Region: MqsA; cd12870 515619008092 toxin interface [polypeptide binding]; other site 515619008093 Zn binding site [ion binding]; other site 515619008094 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 515619008095 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 515619008096 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619008097 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619008098 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 515619008099 Walker A/P-loop; other site 515619008100 ATP binding site [chemical binding]; other site 515619008101 Q-loop/lid; other site 515619008102 ABC transporter signature motif; other site 515619008103 Walker B; other site 515619008104 D-loop; other site 515619008105 H-loop/switch region; other site 515619008106 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 515619008107 catalytic site [active] 515619008108 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 515619008109 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619008110 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 515619008111 DNA binding residues [nucleotide binding] 515619008112 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 515619008113 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 515619008114 AAA domain; Region: AAA_14; pfam13173 515619008115 Nuclease-related domain; Region: NERD; pfam08378 515619008116 ATP phosphoribosyltransferase; Region: HisG; cl15266 515619008117 CAAX protease self-immunity; Region: Abi; pfam02517 515619008118 Putative small multi-drug export protein; Region: Sm_multidrug_ex; pfam06695 515619008119 CAAX protease self-immunity; Region: Abi; pfam02517 515619008120 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 515619008121 ATP binding site [chemical binding]; other site 515619008122 Mg2+ binding site [ion binding]; other site 515619008123 G-X-G motif; other site 515619008124 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619008125 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008126 active site 515619008127 phosphorylation site [posttranslational modification] 515619008128 intermolecular recognition site; other site 515619008129 dimerization interface [polypeptide binding]; other site 515619008130 LytTr DNA-binding domain; Region: LytTR; smart00850 515619008131 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 515619008132 Cation efflux family; Region: Cation_efflux; pfam01545 515619008133 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 515619008134 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 515619008135 Catalytic site [active] 515619008136 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 515619008137 ATP binding site [chemical binding]; other site 515619008138 Mg2+ binding site [ion binding]; other site 515619008139 G-X-G motif; other site 515619008140 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 515619008141 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619008142 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3944 515619008143 Chain length determinant protein; Region: Wzz; cl15801 515619008144 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 515619008145 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 515619008146 homopentamer interface [polypeptide binding]; other site 515619008147 active site 515619008148 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 515619008149 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 515619008150 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 515619008151 dimerization interface [polypeptide binding]; other site 515619008152 active site 515619008153 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 515619008154 Lumazine binding domain; Region: Lum_binding; pfam00677 515619008155 Lumazine binding domain; Region: Lum_binding; pfam00677 515619008156 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 515619008157 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 515619008158 catalytic motif [active] 515619008159 Zn binding site [ion binding]; other site 515619008160 RibD C-terminal domain; Region: RibD_C; cl17279 515619008161 RNA polymerase sigma factor SigW; Reviewed; Region: PRK09642 515619008162 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619008163 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 515619008164 DNA binding residues [nucleotide binding] 515619008165 Putative zinc-finger; Region: zf-HC2; pfam13490 515619008166 glutamate dehydrogenase; Provisional; Region: PRK09414 515619008167 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 515619008168 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 515619008169 NAD(P) binding site [chemical binding]; other site 515619008170 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 515619008171 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 515619008172 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 515619008173 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 515619008174 dimer interface [polypeptide binding]; other site 515619008175 active site 515619008176 CoA binding pocket [chemical binding]; other site 515619008177 Acetyl-CoA carboxylase beta subunit [Lipid metabolism]; Region: AccD; COG0777 515619008178 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 515619008179 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 515619008180 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 515619008181 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 515619008182 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 515619008183 dimer interface [polypeptide binding]; other site 515619008184 active site 515619008185 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 515619008186 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 515619008187 NAD(P) binding site [chemical binding]; other site 515619008188 homotetramer interface [polypeptide binding]; other site 515619008189 homodimer interface [polypeptide binding]; other site 515619008190 active site 515619008191 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 515619008192 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 515619008193 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 515619008194 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 515619008195 FMN binding site [chemical binding]; other site 515619008196 substrate binding site [chemical binding]; other site 515619008197 putative catalytic residue [active] 515619008198 acyl carrier protein; Provisional; Region: acpP; PRK00982 515619008199 AAA domain; Region: AAA_14; pfam13173 515619008200 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 515619008201 Thiamine transporter protein (Thia_YuaJ); Region: Thia_YuaJ; cl17491 515619008202 Transglycosylase; Region: Transgly; pfam00912 515619008203 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 515619008204 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 515619008205 stage V sporulation protein T; Region: spore_V_T; TIGR02851 515619008206 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 515619008207 Ligand binding site; other site 515619008208 metal-binding site 515619008209 xanthine dehydrogenase subunit XdhA; Provisional; Region: PRK09970 515619008210 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 515619008211 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 515619008212 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 515619008213 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 515619008214 catalytic loop [active] 515619008215 iron binding site [ion binding]; other site 515619008216 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 515619008217 FAD binding domain in molybdopterin dehydrogenase; Region: FAD_binding_5; pfam00941 515619008218 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 515619008219 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 515619008220 SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response...; Region: SirA_like_N; cd03421 515619008221 selenium metabolism protein YedF; Region: selenium_YedF; TIGR03527 515619008222 CPxP motif; other site 515619008223 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 515619008224 selenophosphate synthetase; Provisional; Region: PRK00943 515619008225 dimerization interface [polypeptide binding]; other site 515619008226 putative ATP binding site [chemical binding]; other site 515619008227 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 515619008228 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 515619008229 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619008230 catalytic residue [active] 515619008231 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 515619008232 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619008233 Walker A/P-loop; other site 515619008234 ATP binding site [chemical binding]; other site 515619008235 Q-loop/lid; other site 515619008236 ABC transporter signature motif; other site 515619008237 Walker B; other site 515619008238 D-loop; other site 515619008239 H-loop/switch region; other site 515619008240 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 515619008241 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 515619008242 dimer interface [polypeptide binding]; other site 515619008243 conserved gate region; other site 515619008244 putative PBP binding loops; other site 515619008245 ABC-ATPase subunit interface; other site 515619008246 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 515619008247 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 515619008248 MOSC domain; Region: MOSC; pfam03473 515619008249 XdhC Rossmann domain; Region: XdhC_C; pfam13478 515619008250 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 515619008251 molybdenum cofactor biosynthesis protein A, bacterial; Region: moaA; TIGR02666 515619008252 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 515619008253 FeS/SAM binding site; other site 515619008254 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 515619008255 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 515619008256 putative MPT binding site; other site 515619008257 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 515619008258 MPT binding site; other site 515619008259 trimer interface [polypeptide binding]; other site 515619008260 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 515619008261 trimer interface [polypeptide binding]; other site 515619008262 dimer interface [polypeptide binding]; other site 515619008263 putative active site [active] 515619008264 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 515619008265 HlyD family secretion protein; Region: HlyD_3; pfam13437 515619008266 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cd01983 515619008267 xanthine permease; Region: pbuX; TIGR03173 515619008268 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 515619008269 catalytic core [active] 515619008270 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 515619008271 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 515619008272 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 515619008273 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 515619008274 domain interfaces; other site 515619008275 active site 515619008276 Uncharacterized metal-binding protein [General function prediction only]; Region: COG3894 515619008277 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 515619008278 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 515619008279 Protein of unknown function (DUF464); Region: DUF464; cl01080 515619008280 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 515619008281 active site 515619008282 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 515619008283 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 515619008284 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 515619008285 DNA binding residues [nucleotide binding] 515619008286 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619008287 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 515619008288 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 515619008289 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619008290 Zn2+ binding site [ion binding]; other site 515619008291 Mg2+ binding site [ion binding]; other site 515619008292 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 515619008293 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 515619008294 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 515619008295 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 515619008296 nudix motif; other site 515619008297 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 515619008298 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 515619008299 active site 515619008300 HIGH motif; other site 515619008301 KMSKS motif; other site 515619008302 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 515619008303 tRNA binding surface [nucleotide binding]; other site 515619008304 anticodon binding site; other site 515619008305 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 515619008306 dimer interface [polypeptide binding]; other site 515619008307 putative tRNA-binding site [nucleotide binding]; other site 515619008308 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619008309 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 515619008310 Walker A/P-loop; other site 515619008311 ATP binding site [chemical binding]; other site 515619008312 Q-loop/lid; other site 515619008313 ABC transporter signature motif; other site 515619008314 Walker B; other site 515619008315 D-loop; other site 515619008316 H-loop/switch region; other site 515619008317 putative lipid kinase; Reviewed; Region: PRK13337 515619008318 cyclic lactone autoinducer peptide; Region: quorum_AgrD; TIGR04223 515619008319 Accessory gene regulator B; Region: AgrB; cl01873 515619008320 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619008321 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008322 active site 515619008323 phosphorylation site [posttranslational modification] 515619008324 intermolecular recognition site; other site 515619008325 dimerization interface [polypeptide binding]; other site 515619008326 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619008327 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619008328 ATP binding site [chemical binding]; other site 515619008329 Mg2+ binding site [ion binding]; other site 515619008330 G-X-G motif; other site 515619008331 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619008332 Zn2+ binding site [ion binding]; other site 515619008333 Mg2+ binding site [ion binding]; other site 515619008334 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 515619008335 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 515619008336 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 515619008337 Predicted membrane protein [Function unknown]; Region: COG1971 515619008338 Domain of unknown function DUF; Region: DUF204; pfam02659 515619008339 Domain of unknown function DUF; Region: DUF204; pfam02659 515619008340 Predicted transcriptional regulators [Transcription]; Region: COG1695 515619008341 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 515619008342 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 515619008343 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 515619008344 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 515619008345 DUF based on E. rectale Gene description (DUF3880); Region: DUF3880; pfam12996 515619008346 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 515619008347 DUF based on E. rectale Gene description (DUF3880); Region: DUF3880; pfam12996 515619008348 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 515619008349 Integrase core domain; Region: rve; pfam00665 515619008350 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 515619008351 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 515619008352 Walker A motif; other site 515619008353 ATP binding site [chemical binding]; other site 515619008354 Walker B motif; other site 515619008355 arginine finger; other site 515619008356 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 515619008357 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 515619008358 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 515619008359 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 515619008360 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 515619008361 Double zinc ribbon; Region: DZR; pfam12773 515619008362 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 515619008363 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 515619008364 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 515619008365 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 515619008366 Helix-turn-helix domain; Region: HTH_28; pfam13518 515619008367 Winged helix-turn helix; Region: HTH_29; pfam13551 515619008368 DDE superfamily endonuclease; Region: DDE_3; pfam13358 515619008369 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 515619008370 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 515619008371 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 515619008372 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 515619008373 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 515619008374 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 515619008375 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 515619008376 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 515619008377 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 515619008378 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 515619008379 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 515619008380 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 515619008381 inhibitor-cofactor binding pocket; inhibition site 515619008382 pyridoxal 5'-phosphate binding site [chemical binding]; other site 515619008383 catalytic residue [active] 515619008384 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 515619008385 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 515619008386 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 515619008387 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 515619008388 NAD(P) binding site [chemical binding]; other site 515619008389 active site 515619008390 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 515619008391 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 515619008392 pseudaminic acid synthase; Region: PseI; TIGR03586 515619008393 NeuB family; Region: NeuB; pfam03102 515619008394 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 515619008395 NeuB binding interface [polypeptide binding]; other site 515619008396 putative substrate binding site [chemical binding]; other site 515619008397 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 515619008398 ligand binding site; other site 515619008399 tetramer interface; other site 515619008400 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 515619008401 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 515619008402 NAD(P) binding site [chemical binding]; other site 515619008403 homodimer interface [polypeptide binding]; other site 515619008404 substrate binding site [chemical binding]; other site 515619008405 active site 515619008406 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 515619008407 flagellin; Provisional; Region: PRK12804 515619008408 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 515619008409 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 515619008410 Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliS; COG1516 515619008411 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 515619008412 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 515619008413 FlaG protein; Region: FlaG; pfam03646 515619008414 replicative DNA helicase; Region: DnaB; TIGR00665 515619008415 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 515619008416 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 515619008417 Walker A motif; other site 515619008418 ATP binding site [chemical binding]; other site 515619008419 Walker B motif; other site 515619008420 DNA binding loops [nucleotide binding] 515619008421 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 515619008422 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 515619008423 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 515619008424 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 515619008425 DHH family; Region: DHH; pfam01368 515619008426 DHHA1 domain; Region: DHHA1; pfam02272 515619008427 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 515619008428 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 515619008429 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 515619008430 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 515619008431 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 515619008432 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 515619008433 dimer interface [polypeptide binding]; other site 515619008434 ssDNA binding site [nucleotide binding]; other site 515619008435 tetramer (dimer of dimers) interface [polypeptide binding]; other site 515619008436 Ribosomal protein S6; Region: Ribosomal_S6; pfam01250 515619008437 Bacterial protein of unknown function (DUF951); Region: DUF951; pfam06107 515619008438 NAD-dependent deacetylase; Provisional; Region: PRK00481 515619008439 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 515619008440 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 515619008441 TrkA-N domain; Region: TrkA_N; pfam02254 515619008442 TrkA-C domain; Region: TrkA_C; pfam02080 515619008443 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 515619008444 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 515619008445 Predicted methyltransferases [General function prediction only]; Region: COG0313 515619008446 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 515619008447 putative SAM binding site [chemical binding]; other site 515619008448 putative homodimer interface [polypeptide binding]; other site 515619008449 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 515619008450 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 515619008451 S-adenosylmethionine binding site [chemical binding]; other site 515619008452 Uncharacterized homolog of PSP1 [Function unknown]; Region: COG1774 515619008453 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 515619008454 DNA polymerase III, delta subunit; Region: DNA_pol3_delta2; pfam13177 515619008455 Walker A motif; other site 515619008456 ATP binding site [chemical binding]; other site 515619008457 Walker B motif; other site 515619008458 ATPase involved in DNA replication [DNA replication, recombination, and repair]; Region: HolB; COG0470 515619008459 Protein of unknown function (DUF327); Region: DUF327; pfam03885 515619008460 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 515619008461 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 515619008462 active site 515619008463 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 515619008464 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 515619008465 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619008466 catalytic residue [active] 515619008467 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 515619008468 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 515619008469 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 515619008470 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 515619008471 active site 515619008472 nucleophile elbow; other site 515619008473 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 515619008474 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 515619008475 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 515619008476 S-adenosylmethionine binding site [chemical binding]; other site 515619008477 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 515619008478 TPR motif; other site 515619008479 Tetratricopeptide repeat; Region: TPR_12; pfam13424 515619008480 binding surface 515619008481 peptidase T; Region: peptidase-T; TIGR01882 515619008482 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 515619008483 metal binding site [ion binding]; metal-binding site 515619008484 dimer interface [polypeptide binding]; other site 515619008485 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 515619008486 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 515619008487 ATP binding site [chemical binding]; other site 515619008488 Mg++ binding site [ion binding]; other site 515619008489 motif III; other site 515619008490 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 515619008491 nucleotide binding region [chemical binding]; other site 515619008492 ATP-binding site [chemical binding]; other site 515619008493 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 515619008494 RNA binding site [nucleotide binding]; other site 515619008495 BioY family; Region: BioY; pfam02632 515619008496 Maf-like protein; Region: Maf; pfam02545 515619008497 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 515619008498 active site 515619008499 dimer interface [polypeptide binding]; other site 515619008500 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 515619008501 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619008502 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 515619008503 dimerization interface [polypeptide binding]; other site 515619008504 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 515619008505 dimer interface [polypeptide binding]; other site 515619008506 phosphorylation site [posttranslational modification] 515619008507 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 515619008508 ATP binding site [chemical binding]; other site 515619008509 Mg2+ binding site [ion binding]; other site 515619008510 G-X-G motif; other site 515619008511 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619008512 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008513 active site 515619008514 phosphorylation site [posttranslational modification] 515619008515 intermolecular recognition site; other site 515619008516 dimerization interface [polypeptide binding]; other site 515619008517 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 515619008518 DNA binding site [nucleotide binding] 515619008519 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 515619008520 PLD-like domain; Region: PLDc_2; pfam13091 515619008521 putative active site [active] 515619008522 catalytic site [active] 515619008523 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 515619008524 PLD-like domain; Region: PLDc_2; pfam13091 515619008525 putative active site [active] 515619008526 catalytic site [active] 515619008527 N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes; Region: E_set_CDase_PDE_N; cd02857 515619008528 homodimer interface [polypeptide binding]; other site 515619008529 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 515619008530 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 515619008531 active site 515619008532 homodimer interface [polypeptide binding]; other site 515619008533 catalytic site [active] 515619008534 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 515619008535 Penicillinase repressor; Region: Pencillinase_R; pfam03965 515619008536 The LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains. LytC is composed of a...; Region: GH25_LytC-like; cd06414 515619008537 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 515619008538 active site 515619008539 Bacterial SH3 domain homologues; Region: SH3b; smart00287 515619008540 Bacterial SH3 domain; Region: SH3_3; pfam08239 515619008541 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 515619008542 SUKH-3 immunity protein; Region: SUKH-3; pfam14433 515619008543 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 515619008544 Transposase; Region: DEDD_Tnp_IS110; pfam01548 515619008545 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 515619008546 LXG domain of WXG superfamily; Region: LXG; pfam04740 515619008547 Domain of unknown function (DUF4176); Region: DUF4176; cl01867 515619008548 membrane protein P6; Region: PHA01399 515619008549 Transposase; Region: DEDD_Tnp_IS110; pfam01548 515619008550 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 515619008551 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 515619008552 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 515619008553 potential frameshift: common BLAST hit: gi|229819374|ref|YP_002880900.1| rhs protein 515619008554 HNH/ENDO VII superfamily nuclease with conserved GHE residues; Region: GH-E; pfam14410 515619008555 LXG domain of WXG superfamily; Region: LXG; pfam04740 515619008556 Domain of unknown function (DUF4176); Region: DUF4176; pfam13780 515619008557 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619008558 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 515619008559 hybrid cluster protein; Provisional; Region: PRK05290 515619008560 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 515619008561 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 515619008562 hybrid metal cluster; other site 515619008563 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 515619008564 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 515619008565 putative active site; other site 515619008566 catalytic triad [active] 515619008567 putative dimer interface [polypeptide binding]; other site 515619008568 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 515619008569 agmatine deiminase; Region: agmatine_aguA; TIGR03380 515619008570 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 515619008571 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 515619008572 dimer interface [polypeptide binding]; other site 515619008573 active site 515619008574 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 515619008575 catalytic residues [active] 515619008576 substrate binding site [chemical binding]; other site 515619008577 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 515619008578 Shikimate / quinate 5-dehydrogenase; Region: Shikimate_DH; pfam01488 515619008579 spermidine synthase; Provisional; Region: PRK00811 515619008580 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 515619008581 S-adenosylmethionine binding site [chemical binding]; other site 515619008582 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 515619008583 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 515619008584 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 515619008585 catalytic residue [active] 515619008586 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 515619008587 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; Region: COG2405 515619008588 Domain of unknown function (DUF3368); Region: DUF3368; pfam11848 515619008589 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619008590 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619008591 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 515619008592 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 515619008593 putative dimer interface [polypeptide binding]; other site 515619008594 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619008595 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 515619008596 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 515619008597 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619008598 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619008599 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619008600 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 515619008601 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 515619008602 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 515619008603 putative dimer interface [polypeptide binding]; other site 515619008604 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619008605 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 515619008606 EDD domain protein, DegV family; Region: DegV; TIGR00762 515619008607 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619008608 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 515619008609 Predicted ATPase [General function prediction only]; Region: COG3910 515619008610 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 515619008611 Walker A/P-loop; other site 515619008612 ATP binding site [chemical binding]; other site 515619008613 Q-loop/lid; other site 515619008614 ABC transporter signature motif; other site 515619008615 Walker B; other site 515619008616 D-loop; other site 515619008617 H-loop/switch region; other site 515619008618 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 515619008619 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 515619008620 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 515619008621 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 515619008622 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 515619008623 active site 515619008624 DNA binding site [nucleotide binding] 515619008625 Int/Topo IB signature motif; other site 515619008626 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 515619008627 Putative transposase; Region: Y2_Tnp; pfam04986 515619008628 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 515619008629 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 515619008630 Int/Topo IB signature motif; other site 515619008631 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619008632 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 515619008633 non-specific DNA binding site [nucleotide binding]; other site 515619008634 salt bridge; other site 515619008635 sequence-specific DNA binding site [nucleotide binding]; other site 515619008636 Helix-turn-helix domain; Region: HTH_17; cl17695 515619008637 Predicted integral membrane protein [Function unknown]; Region: COG5658 515619008638 Protein of unknown function (DUF1648); Region: DUF1648; pfam07853 515619008639 SdpI/YhfL protein family; Region: SdpI; pfam13630 515619008640 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 515619008641 dimerization interface [polypeptide binding]; other site 515619008642 putative DNA binding site [nucleotide binding]; other site 515619008643 putative Zn2+ binding site [ion binding]; other site 515619008644 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 515619008645 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 515619008646 active site 515619008647 DNA binding site [nucleotide binding] 515619008648 Int/Topo IB signature motif; other site 515619008649 Putative transposase; Region: Y2_Tnp; pfam04986 515619008650 potential frameshift: common BLAST hit: gi|89897033|ref|YP_520520.1| sugar fermentation stimulation protein A 515619008651 Sugar fermentation stimulation protein; Region: SfsA; cl00647 515619008652 Sugar fermentation stimulation protein; Region: SfsA; cl00647 515619008653 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 515619008654 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 515619008655 maltose O-acetyltransferase; Provisional; Region: PRK10092 515619008656 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 515619008657 active site 515619008658 substrate binding site [chemical binding]; other site 515619008659 trimer interface [polypeptide binding]; other site 515619008660 CoA binding site [chemical binding]; other site 515619008661 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 515619008662 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 515619008663 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 515619008664 transmembrane helices; other site 515619008665 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 515619008666 Melibiase; Region: Melibiase; pfam02065 515619008667 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 515619008668 Melibiase; Region: Melibiase; pfam02065 515619008669 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 515619008670 Divergent AAA domain; Region: AAA_4; pfam04326 515619008671 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 515619008672 PIN domain; Region: PIN_3; pfam13470 515619008673 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 515619008674 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 515619008675 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619008676 dimer interface [polypeptide binding]; other site 515619008677 putative CheW interface [polypeptide binding]; other site 515619008678 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 515619008679 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 515619008680 putative dimer interface [polypeptide binding]; other site 515619008681 Flagellin and related hook-associated proteins [Cell motility and secretion]; Region: FlgL; COG1344 515619008682 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 515619008683 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 515619008684 Global regulator protein family; Region: CsrA; pfam02599 515619008685 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619008686 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619008687 putative active site [active] 515619008688 putative NTP binding site [chemical binding]; other site 515619008689 putative nucleic acid binding site [nucleotide binding]; other site 515619008690 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619008691 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 515619008692 active site 515619008693 DNA binding site [nucleotide binding] 515619008694 Int/Topo IB signature motif; other site 515619008695 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 515619008696 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 515619008697 flavodoxin; Provisional; Region: PRK06242 515619008698 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 515619008699 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 515619008700 motif II; other site 515619008701 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 515619008702 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 515619008703 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 515619008704 active site 515619008705 metal binding site [ion binding]; metal-binding site 515619008706 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 515619008707 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 515619008708 active site 515619008709 catalytic residues [active] 515619008710 metal binding site [ion binding]; metal-binding site 515619008711 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 515619008712 active site 515619008713 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 515619008714 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619008715 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 515619008716 non-specific DNA binding site [nucleotide binding]; other site 515619008717 salt bridge; other site 515619008718 sequence-specific DNA binding site [nucleotide binding]; other site 515619008719 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 515619008720 Catalytic site [active] 515619008721 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 515619008722 non-specific DNA binding site [nucleotide binding]; other site 515619008723 salt bridge; other site 515619008724 sequence-specific DNA binding site [nucleotide binding]; other site 515619008725 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 515619008726 DDE superfamily endonuclease; Region: DDE_5; cl17874 515619008727 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 515619008728 active site 515619008729 catalytic residues [active] 515619008730 metal binding site [ion binding]; metal-binding site 515619008731 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 515619008732 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 515619008733 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 515619008734 dimerization interface [polypeptide binding]; other site 515619008735 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 515619008736 dimer interface [polypeptide binding]; other site 515619008737 putative CheW interface [polypeptide binding]; other site 515619008738 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 515619008739 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 515619008740 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 515619008741 putative ADP-ribose binding site [chemical binding]; other site 515619008742 putative active site [active] 515619008743 lysine biosynthesis protein LysW; Region: lysW; TIGR01206 515619008744 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 515619008745 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b3; cd09205 515619008746 PLD-like domain; Region: PLDc_2; pfam13091 515619008747 putative homodimer interface [polypeptide binding]; other site 515619008748 putative active site [active] 515619008749 catalytic site [active] 515619008750 DEAD-like helicases superfamily; Region: DEXDc; smart00487 515619008751 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 515619008752 ATP binding site [chemical binding]; other site 515619008753 putative Mg++ binding site [ion binding]; other site 515619008754 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 515619008755 nucleotide binding region [chemical binding]; other site 515619008756 ATP-binding site [chemical binding]; other site 515619008757 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 515619008758 Methyltransferase domain; Region: Methyltransf_23; pfam13489 515619008759 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 515619008760 S-adenosylmethionine binding site [chemical binding]; other site 515619008761 The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p; Region: HIRAN; smart00910 515619008762 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 515619008763 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 515619008764 putative active site [active] 515619008765 putative NTP binding site [chemical binding]; other site 515619008766 putative nucleic acid binding site [nucleotide binding]; other site 515619008767 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 515619008768 Virulence protein [General function prediction only]; Region: COG3943 515619008769 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 515619008770 Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly...; Region: Macro; cl00019 515619008771 ADP-ribose binding site [chemical binding]; other site 515619008772 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 515619008773 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 515619008774 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 515619008775 ParB-like nuclease domain; Region: ParBc; pfam02195 515619008776 ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. 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...; Region: ASCH_Ef3133_like; cd06553 515619008777 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 515619008778 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619008779 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619008780 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 515619008781 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 515619008782 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 515619008783 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 515619008784 active site 515619008785 catalytic tetrad [active] 515619008786 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 515619008787 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 515619008788 flavodoxin; Provisional; Region: PRK07116 515619008789 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619008790 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619008791 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 515619008792 dimerization interface [polypeptide binding]; other site 515619008793 Domain of unknown function, E. rectale Gene description (DUF3879); Region: DUF3879; pfam12995 515619008794 Protein of unknown function (DUF1847); Region: DUF1847; cl02037 515619008795 Predicted membrane protein [Function unknown]; Region: COG2364 515619008796 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 515619008797 AAA domain; Region: AAA_14; pfam13173 515619008798 FtsH Extracellular; Region: FtsH_ext; pfam06480 515619008799 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 515619008800 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 515619008801 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 515619008802 Walker A motif; other site 515619008803 ATP binding site [chemical binding]; other site 515619008804 Walker B motif; other site 515619008805 arginine finger; other site 515619008806 Peptidase family M41; Region: Peptidase_M41; pfam01434 515619008807 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 515619008808 active site 515619008809 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 515619008810 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 515619008811 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 515619008812 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619008813 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 515619008814 dimerization interface [polypeptide binding]; other site 515619008815 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 515619008816 dimer interface [polypeptide binding]; other site 515619008817 phosphorylation site [posttranslational modification] 515619008818 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 515619008819 ATP binding site [chemical binding]; other site 515619008820 Mg2+ binding site [ion binding]; other site 515619008821 G-X-G motif; other site 515619008822 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619008823 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008824 active site 515619008825 phosphorylation site [posttranslational modification] 515619008826 intermolecular recognition site; other site 515619008827 dimerization interface [polypeptide binding]; other site 515619008828 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 515619008829 DNA binding site [nucleotide binding] 515619008830 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 515619008831 putative active site [active] 515619008832 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 515619008833 MarR family; Region: MarR_2; pfam12802 515619008834 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_1_2; cd06113 515619008835 dimer interface [polypeptide binding]; other site 515619008836 Citrate synthase; Region: Citrate_synt; pfam00285 515619008837 active site 515619008838 citrylCoA binding site [chemical binding]; other site 515619008839 oxalacetate/citrate binding site [chemical binding]; other site 515619008840 coenzyme A binding site [chemical binding]; other site 515619008841 catalytic triad [active] 515619008842 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 515619008843 Radical SAM superfamily; Region: Radical_SAM; pfam04055 515619008844 FeS/SAM binding site; other site 515619008845 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 515619008846 MarR family; Region: MarR_2; cl17246 515619008847 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 515619008848 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 515619008849 integrase; Provisional; Region: int; PHA02601 515619008850 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 515619008851 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 515619008852 Int/Topo IB signature motif; other site 515619008853 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619008854 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 515619008855 non-specific DNA binding site [nucleotide binding]; other site 515619008856 salt bridge; other site 515619008857 sequence-specific DNA binding site [nucleotide binding]; other site 515619008858 Helix-turn-helix domain; Region: HTH_17; cl17695 515619008859 MobA/MobL family; Region: MobA_MobL; pfam03389 515619008860 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 515619008861 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 515619008862 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619008863 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008864 active site 515619008865 phosphorylation site [posttranslational modification] 515619008866 intermolecular recognition site; other site 515619008867 dimerization interface [polypeptide binding]; other site 515619008868 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 515619008869 DNA binding site [nucleotide binding] 515619008870 VanZ like family; Region: VanZ; pfam04892 515619008871 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619008872 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 515619008873 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 515619008874 dimer interface [polypeptide binding]; other site 515619008875 phosphorylation site [posttranslational modification] 515619008876 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 515619008877 ATP binding site [chemical binding]; other site 515619008878 Mg2+ binding site [ion binding]; other site 515619008879 G-X-G motif; other site 515619008880 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619008881 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 515619008882 Walker A/P-loop; other site 515619008883 ATP binding site [chemical binding]; other site 515619008884 Q-loop/lid; other site 515619008885 ABC transporter signature motif; other site 515619008886 Walker B; other site 515619008887 D-loop; other site 515619008888 H-loop/switch region; other site 515619008889 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 515619008890 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 515619008891 DNA binding site [nucleotide binding] 515619008892 active site 515619008893 Int/Topo IB signature motif; other site 515619008894 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 515619008895 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 515619008896 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619008897 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 515619008898 sequence-specific DNA binding site [nucleotide binding]; other site 515619008899 salt bridge; other site 515619008900 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619008901 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619008902 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 515619008903 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619008904 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 515619008905 dimer interface [polypeptide binding]; other site 515619008906 conserved gate region; other site 515619008907 putative PBP binding loops; other site 515619008908 ABC-ATPase subunit interface; other site 515619008909 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 515619008910 dimer interface [polypeptide binding]; other site 515619008911 conserved gate region; other site 515619008912 putative PBP binding loops; other site 515619008913 ABC-ATPase subunit interface; other site 515619008914 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619008915 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 515619008916 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 515619008917 Histidine kinase; Region: His_kinase; pfam06580 515619008918 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 515619008919 ATP binding site [chemical binding]; other site 515619008920 Mg2+ binding site [ion binding]; other site 515619008921 G-X-G motif; other site 515619008922 Response regulator receiver domain; Region: Response_reg; pfam00072 515619008923 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619008924 active site 515619008925 phosphorylation site [posttranslational modification] 515619008926 intermolecular recognition site; other site 515619008927 dimerization interface [polypeptide binding]; other site 515619008928 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 515619008929 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619008930 Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]; Region: Fes; COG2382 515619008931 Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]; Region: Fes; COG2382 515619008932 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; Region: CitX; cl01498 515619008933 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 515619008934 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619008935 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 515619008936 catalytic residues [active] 515619008937 catalytic nucleophile [active] 515619008938 Recombinase; Region: Recombinase; pfam07508 515619008939 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619008940 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 515619008941 catalytic residues [active] 515619008942 catalytic nucleophile [active] 515619008943 Recombinase; Region: Recombinase; pfam07508 515619008944 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619008945 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619008946 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 515619008947 catalytic residues [active] 515619008948 catalytic nucleophile [active] 515619008949 Recombinase; Region: Recombinase; pfam07508 515619008950 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619008951 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 515619008952 PemK-like protein; Region: PemK; pfam02452 515619008953 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 515619008954 DNA binding residues [nucleotide binding] 515619008955 Sporulation initiation factor Spo0A C terminal; Region: Spo0A_C; pfam08769 515619008956 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619008957 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 515619008958 non-specific DNA binding site [nucleotide binding]; other site 515619008959 salt bridge; other site 515619008960 sequence-specific DNA binding site [nucleotide binding]; other site 515619008961 phage transcriptional regulator, ArpU family; Region: phage_arpU; TIGR01637 515619008962 DNA polymerase IV; Reviewed; Region: PRK03103 515619008963 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 515619008964 active site 515619008965 DNA binding site [nucleotide binding] 515619008966 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 515619008967 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619008968 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 515619008969 non-specific DNA binding site [nucleotide binding]; other site 515619008970 salt bridge; other site 515619008971 sequence-specific DNA binding site [nucleotide binding]; other site 515619008972 Predicted transcriptional regulator [Transcription]; Region: COG2932 515619008973 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 515619008974 Catalytic site [active] 515619008975 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 515619008976 non-specific DNA binding site [nucleotide binding]; other site 515619008977 salt bridge; other site 515619008978 sequence-specific DNA binding site [nucleotide binding]; other site 515619008979 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 515619008980 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 515619008981 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 515619008982 hypothetical protein; Validated; Region: PRK00124 515619008983 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 515619008984 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619008985 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 515619008986 DNA binding site [nucleotide binding] 515619008987 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 515619008988 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 515619008989 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 515619008990 FtsX-like permease family; Region: FtsX; pfam02687 515619008991 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 515619008992 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 515619008993 Walker A/P-loop; other site 515619008994 ATP binding site [chemical binding]; other site 515619008995 Q-loop/lid; other site 515619008996 ABC transporter signature motif; other site 515619008997 Walker B; other site 515619008998 D-loop; other site 515619008999 H-loop/switch region; other site 515619009000 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 515619009001 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 515619009002 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 515619009003 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 515619009004 dimer interface [polypeptide binding]; other site 515619009005 phosphorylation site [posttranslational modification] 515619009006 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 515619009007 ATP binding site [chemical binding]; other site 515619009008 Mg2+ binding site [ion binding]; other site 515619009009 G-X-G motif; other site 515619009010 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 515619009011 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619009012 active site 515619009013 phosphorylation site [posttranslational modification] 515619009014 intermolecular recognition site; other site 515619009015 dimerization interface [polypeptide binding]; other site 515619009016 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 515619009017 DNA binding site [nucleotide binding] 515619009018 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 515619009019 non-specific DNA binding site [nucleotide binding]; other site 515619009020 salt bridge; other site 515619009021 sequence-specific DNA binding site [nucleotide binding]; other site 515619009022 TIGR02594 family protein; Region: TIGR02594 515619009023 YodL-like; Region: YodL; pfam14191 515619009024 Domain of unknown function (DUF4316); Region: DUF4316; pfam14195 515619009025 Methyltransferase domain; Region: Methyltransf_26; pfam13659 515619009026 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 515619009027 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 515619009028 DEAD-like helicases superfamily; Region: DEXDc; smart00487 515619009029 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 515619009030 ATP binding site [chemical binding]; other site 515619009031 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 515619009032 helicase superfamily c-terminal domain; Region: HELICc; smart00490 515619009033 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009034 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009035 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009036 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009037 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009038 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009039 Cna protein B-type domain; Region: Cna_B; pfam05738 515619009040 LPXTG-motif cell wall anchor domain; Region: LPXTG_anchor; TIGR01167 515619009041 DNA topoisomerase III; Provisional; Region: PRK07726 515619009042 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 515619009043 active site 515619009044 putative interdomain interaction site [polypeptide binding]; other site 515619009045 putative metal-binding site [ion binding]; other site 515619009046 putative nucleotide binding site [chemical binding]; other site 515619009047 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 515619009048 domain I; other site 515619009049 DNA binding groove [nucleotide binding] 515619009050 phosphate binding site [ion binding]; other site 515619009051 domain II; other site 515619009052 domain III; other site 515619009053 nucleotide binding site [chemical binding]; other site 515619009054 catalytic site [active] 515619009055 domain IV; other site 515619009056 Domain of unknown function (DUF4366); Region: DUF4366; pfam14283 515619009057 Domain of unknown function (DUF4315); Region: DUF4315; pfam14193 515619009058 3D domain; Region: 3D; cl01439 515619009059 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 515619009060 Peptidase family M23; Region: Peptidase_M23; pfam01551 515619009061 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 515619009062 NlpC/P60 family; Region: NLPC_P60; pfam00877 515619009063 AAA-like domain; Region: AAA_10; pfam12846 515619009064 Domain of unknown function DUF87; Region: DUF87; pfam01935 515619009065 PrgI family protein; Region: PrgI; pfam12666 515619009066 Maff2 family; Region: Maff2; pfam12750 515619009067 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619009068 Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a...; Region: SR_TndX_transposase; cd03770 515619009069 putative catalytic residues [active] 515619009070 catalytic nucleophile [active] 515619009071 Recombinase; Region: Recombinase; pfam07508 515619009072 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619009073 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 515619009074 Transposon-encoded protein TnpW; Region: TnpW; pfam14202 515619009075 hypothetical protein; Validated; Region: PRK08116 515619009076 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 515619009077 Walker A motif; other site 515619009078 ATP binding site [chemical binding]; other site 515619009079 Walker B motif; other site 515619009080 arginine finger; other site 515619009081 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 515619009082 Cysteine-rich VLP; Region: Cys_rich_VLP; pfam14194 515619009083 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 515619009084 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 515619009085 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 515619009086 ABC-2 family transporter protein; Region: ABC2_membrane_5; pfam13346 515619009087 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 515619009088 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 515619009089 Walker A/P-loop; other site 515619009090 ATP binding site [chemical binding]; other site 515619009091 Q-loop/lid; other site 515619009092 ABC transporter signature motif; other site 515619009093 Walker B; other site 515619009094 D-loop; other site 515619009095 H-loop/switch region; other site 515619009096 Predicted transcriptional regulators [Transcription]; Region: COG1725 515619009097 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 515619009098 DNA-binding site [nucleotide binding]; DNA binding site 515619009099 Maff2 family; Region: Maff2; pfam12750 515619009100 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 515619009101 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 515619009102 Transposon-encoded protein TnpW; Region: TnpW; pfam14202 515619009103 Virulence-associated protein E; Region: VirE; pfam05272 515619009104 CHC2 zinc finger; Region: zf-CHC2; cl17510 515619009105 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 515619009106 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 515619009107 catalytic residues [active] 515619009108 catalytic nucleophile [active] 515619009109 Recombinase; Region: Recombinase; pfam07508 515619009110 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 515619009111 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3416 515619009112 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 515619009113 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 515619009114 Walker A motif; other site 515619009115 ATP binding site [chemical binding]; other site 515619009116 Protein of unknown function (DUF3801); Region: DUF3801; pfam12687 515619009117 hypothetical protein; Validated; Region: PRK08116 515619009118 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 515619009119 Walker A motif; other site 515619009120 ATP binding site [chemical binding]; other site 515619009121 Walker B motif; other site 515619009122 arginine finger; other site 515619009123 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 515619009124 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 515619009125 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 515619009126 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 515619009127 dimer interface [polypeptide binding]; other site 515619009128 ssDNA binding site [nucleotide binding]; other site 515619009129 tetramer (dimer of dimers) interface [polypeptide binding]; other site 515619009130 ParB-like nuclease domain; Region: ParB; smart00470 515619009131 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 515619009132 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 515619009133 P-loop; other site 515619009134 Magnesium ion binding site [ion binding]; other site 515619009135 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 515619009136 Magnesium ion binding site [ion binding]; other site 515619009137 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N2; pfam13495 515619009138 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 515619009139 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 515619009140 DNA binding site [nucleotide binding] 515619009141 Int/Topo IB signature motif; other site 515619009142 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 515619009143 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 515619009144 non-specific DNA binding site [nucleotide binding]; other site 515619009145 salt bridge; other site 515619009146 sequence-specific DNA binding site [nucleotide binding]; other site 515619009147 Cupin domain; Region: Cupin_2; cl17218 515619009148 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 515619009149 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 515619009150 ATP11 protein; Region: ATP11; pfam06644 515619009151 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 515619009152 Zn2+ binding site [ion binding]; other site 515619009153 Mg2+ binding site [ion binding]; other site 515619009154 Maltose acetyltransferase; Region: Mac; pfam12464 515619009155 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 515619009156 putative CoA binding site [chemical binding]; other site 515619009157 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 515619009158 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 515619009159 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 515619009160 motif II; other site 515619009161 Chromate transporter; Region: Chromate_transp; pfam02417 515619009162 Chromate transporter; Region: Chromate_transp; pfam02417 515619009163 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 515619009164 Chromate transporter; Region: Chromate_transp; pfam02417 515619009165 Chromate transporter; Region: Chromate_transp; pfam02417 515619009166 Transcriptional regulator [Transcription]; Region: LysR; COG0583 515619009167 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 515619009168 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 515619009169 putative dimerization interface [polypeptide binding]; other site 515619009170 Membrane-associated tegument protein; Region: UL11; cl17374 515619009171 flavodoxin; Provisional; Region: PRK06242 515619009172 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 515619009173 Isochorismatase family; Region: Isochorismatase; pfam00857 515619009174 catalytic triad [active] 515619009175 conserved cis-peptide bond; other site 515619009176 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 515619009177 putative active site [active] 515619009178 putative ADP-ribose binding site [chemical binding]; other site 515619009179 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 515619009180 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 515619009181 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 515619009182 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 515619009183 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 515619009184 Domain of unknown function, E. rectale Gene description (DUF3879); Region: DUF3879; pfam12995 515619009185 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619009186 ATP binding site [chemical binding]; other site 515619009187 Mg2+ binding site [ion binding]; other site 515619009188 G-X-G motif; other site 515619009189 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619009190 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619009191 active site 515619009192 phosphorylation site [posttranslational modification] 515619009193 intermolecular recognition site; other site 515619009194 dimerization interface [polypeptide binding]; other site 515619009195 LytTr DNA-binding domain; Region: LytTR; pfam04397 515619009196 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 515619009197 Domain of unknown function, E. rectale Gene description (DUF3879); Region: DUF3879; pfam12995 515619009198 Predicted integral membrane protein [Function unknown]; Region: COG5658 515619009199 Protein of unknown function (DUF1648); Region: DUF1648; pfam07853 515619009200 SdpI/YhfL protein family; Region: SdpI; pfam13630 515619009201 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 515619009202 dimerization interface [polypeptide binding]; other site 515619009203 putative DNA binding site [nucleotide binding]; other site 515619009204 putative Zn2+ binding site [ion binding]; other site 515619009205 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 515619009206 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619009207 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 515619009208 active site 515619009209 phosphorylation site [posttranslational modification] 515619009210 intermolecular recognition site; other site 515619009211 LytTr DNA-binding domain; Region: LytTR; smart00850 515619009212 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 515619009213 active site 515619009214 metal binding site [ion binding]; metal-binding site 515619009215 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 515619009216 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 515619009217 salt bridge; other site 515619009218 non-specific DNA binding site [nucleotide binding]; other site 515619009219 sequence-specific DNA binding site [nucleotide binding]; other site 515619009220 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 515619009221 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 515619009222 Ca binding site [ion binding]; other site 515619009223 active site 515619009224 catalytic site [active] 515619009225 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 515619009226 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 515619009227 dimer interface [polypeptide binding]; other site 515619009228 conserved gate region; other site 515619009229 putative PBP binding loops; other site 515619009230 ABC-ATPase subunit interface; other site 515619009231 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 515619009232 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 515619009233 dimer interface [polypeptide binding]; other site 515619009234 conserved gate region; other site 515619009235 putative PBP binding loops; other site 515619009236 ABC-ATPase subunit interface; other site 515619009237 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 515619009238 Transcriptional regulators [Transcription]; Region: PurR; COG1609 515619009239 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 515619009240 DNA binding site [nucleotide binding] 515619009241 domain linker motif; other site 515619009242 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 515619009243 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 515619009244 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 515619009245 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 515619009246 beta-galactosidase; Region: BGL; TIGR03356 515619009247 PTS_IIA, PTS system, lactose/cellobiose 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_lac; cd00215 515619009248 active site 515619009249 methionine cluster; other site 515619009250 phosphorylation site [posttranslational modification] 515619009251 metal binding site [ion binding]; metal-binding site 515619009252 Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]; Region: CelB; COG1455 515619009253 cellobiose phosphotransferase system IIC component; Reviewed; Region: celD; PRK09592 515619009254 PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N; Region: PTS_IIB_chitobiose_lichenan; cd05564 515619009255 active site 515619009256 P-loop; other site 515619009257 phosphorylation site [posttranslational modification] 515619009258 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 515619009259 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 515619009260 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 515619009261 putative active site [active] 515619009262 Domain of unknown function, E. rectale Gene description (DUF3881); Region: DUF3881; pfam12997 515619009263 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 515619009264 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 515619009265 Zn2+ binding site [ion binding]; other site 515619009266 Mg2+ binding site [ion binding]; other site 515619009267 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 515619009268 ParB-like nuclease domain; Region: ParB; smart00470 515619009269 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 515619009270 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 515619009271 P-loop; other site 515619009272 Magnesium ion binding site [ion binding]; other site 515619009273 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 515619009274 Magnesium ion binding site [ion binding]; other site 515619009275 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 515619009276 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 515619009277 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 515619009278 active site 515619009279 phosphorylation site [posttranslational modification] 515619009280 intermolecular recognition site; other site 515619009281 dimerization interface [polypeptide binding]; other site 515619009282 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 515619009283 DNA binding residues [nucleotide binding] 515619009284 dimerization interface [polypeptide binding]; other site 515619009285 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 515619009286 Histidine kinase; Region: HisKA_3; pfam07730 515619009287 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 515619009288 ATP binding site [chemical binding]; other site 515619009289 Mg2+ binding site [ion binding]; other site 515619009290 G-X-G motif; other site 515619009291 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 515619009292 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 515619009293 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 515619009294 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 515619009295 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 515619009296 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 515619009297 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 515619009298 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 515619009299 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 515619009300 trmE is a tRNA modification GTPase; Region: trmE; cd04164 515619009301 G1 box; other site 515619009302 GTP/Mg2+ binding site [chemical binding]; other site 515619009303 Switch I region; other site 515619009304 G2 box; other site 515619009305 Switch II region; other site 515619009306 G3 box; other site 515619009307 G4 box; other site 515619009308 G5 box; other site 515619009309 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 515619009310 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 515619009311 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 515619009312 G-X-X-G motif; other site 515619009313 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 515619009314 RxxxH motif; other site 515619009315 60Kd inner membrane protein; Region: 60KD_IMP; pfam02096 515619009316 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 515619009317 Haemolytic domain; Region: Haemolytic; pfam01809 515619009318 ribonuclease P; Reviewed; Region: rnpA; PRK00499 515619009319 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399